dataesr/scientific-paragraphs-categorization huggingface dataset:
All these adaptations required numerous and substantial code-source changes of the original e-commerce software. A second group of modifications concerns the relational associations between tags and questions, and between related questions to facilitate the user's navigation interface to explore questions. To do so, the following PrestaShop modules were implemented: REPOSITION MODULE to allow a drop-down presentation of question categories and subcategories; FILTER SEARCH COMMUNITY EDITION to filter questions according to our desired criteria; PRODUCT BOUGHT BY OTHER PEOPLE to enable users to examine which questions were associated in questionnaires in previous questionnaires built by EpiBasket users; and CY-RELATED PRODUCTS which provides a list of those questions sharing keyword similarities with the question currently displayed.
A third group of specific developments concerned the EpiBasket questionnaire outputs. The open-source QUEXML tool  (12)  was implemented in the Eclipse EpiBasket project and was used to generate a questionnaire according to the encoding XML 1. 0 standard scheme. The XML questionnaire template was in turn used to generate pdf or csv versions. A questionnaire written in XML can easily be converted to paper (pdf format), enabling rapid deployment of paper-and-pencil surveys, whereas the converted csv file can be directly imported into the LimeSurvey freeware, enabling rapid deployment of an online survey. LimeSurvey (  13 ) is an open-source online-survey application written in PHP, based on a MySQL, PostgreSQL or MSSQL database, and distributed under the GNU General Public License. It is particularly user friendly, as it enables users to develop and publish surveys, and collect responses, without doing any coding  (14).
Discussion Herein, we described a prototype that, by adapting WEB tools and e-commerce concepts to epidemiology, should accelerate the creation of an epidemiological questionnaire at the time of a public health emergency. The strength of our approach is that it relies on and takes full advantage of past knowledge and experiences in similar events. The goal is not only avoiding that epidemiologists 'reinvent the wheel' when they are faced with situations similar, or partly similar, to those the past. It also strives to indirectly encourage more standardised and better quality questionnaires. Another indirect attribute of the proposed approach is to promote interactions among epidemiologists. Indeed, despite informatics advances, which make it easy, at least in theory, to devise databases easily sharable and accessible from any place, the fact is that, in practice, this is not yet reality  (15).
Thus, the EpiBasket prototype described herein is far from what a full-size 'EpiBasket' could be. The design and computer implementation of that ideal project would require a workforce (i. e. , epidemiologists and software engineers) that exceeds the resources of a single research group. We think the software aspect is likely the easiest, as it was shown here that the efforts already made in the profitable field of e-commence can be relatively easily adapted to epidemiology. The future editorial and organisational aspects are much more difficult to foresee. The editorial work covers the definitions of the means applied to 'value' the questions. For the prototype, we chose the best journal IF among published papers on similar events that used the question. It is also possible, for example, that an Editorial Committee would prefer a mechanism according high values to questions submitted by experts in the field.
In that scenario, coding recommendations should certainly be made by subcommittees. One of the organisational issues concerns copyrighted questionnaires, particularly those that are available only for a fee. The current EpiBasket version does not address such issues. Finally, because a major objective of EpiBasket is to support collaborative epidemiology, additional tools could be added to the users' community at very little informatics cost: for example, a registry of epidemiological investigations on outbreaks or public health disasters, where epidemiologists could register their new studies before publication with a brief description, authors' names, affiliations and addresses. The difference with the current database on clinical trials  (16)  would be that epidemiologists would be free to register or not.
vivax  (Mu et al. 2005  The time to the most recent common ancestor (TMRCA) of the global P. vivax sample was estimated using four approaches. The *BEAST analysis of the multispecies data set produced the smallest estimate of the posterior mean of the TMRCA, which was 230 thousand of years ago (95% HPD: 78-446 ka), while the largest estimate was obtained from the skyline analyses and was 283 ka (95% HPD: 81-542 ka). Intermediate values were obtained from the two phylogeographical analyses (see below), these being 235 ka (95% HPD: 85-431 ka) for the 9 region subdivision and 259 ka (95% HPD: 97-480 ka) for the 18 region subdivision. As the models implemented in these analyses make different assumptions about the demography of P. vivax, it is unsurprising that they yield somewhat different estimates of the TMRCA.
Likewise, it should be noted that phylogenetic analysis of the multispecies dataset did not clearly identify the root of the mitochondrial tree of P. vivax. Unfortunately, the loss of the putative source populations makes it difficult to rigorously test this model, although the recovery of ancient DNA from a European sample of P. vivax could be used to this end. However, while ancient DNA has been recovered from P. falciparum samples  (Taylor et al. 1997; Sallares and Gomzi 2001; Frı ´as et al. 2013) , we are unaware of any similar successes involving P. vivax. Two scenarios that our data clearly rule out are 1) a single recent (post-European-contact) introduction of P. vivax into the Americas either accompanied or followed by a severe bottleneck  (Grynberg et al. 2008)  and 2) recurrent immigration of parasites into the Americas from other extant populations of P.
To detect mixed infections, samples were both cloned and sequenced directly. In all cases, at least two independent 5,800 bp PCR products were cloned using the pGEM Õ -T Easy Vector System (Promega, USA), and four clones were sequenced from each individual from the two independent PCR reactions. Both strands of the cloned inserts were sequenced using internal primers with at least 100 bp overlap. Mixed infections yield overlapping peaks in the sequence electropherogram when they are sequenced directly. In order to reduce further the risk of PCR errors, additional PCR amplifications and clones were sequenced until the haplotype was confirmed. All of the confirmed haplotypes were included in this study. The sequences reported in this investigation were deposited in Genbank under the accession numbers KC330370-KC330678.
Plasmodium mtDNA Genomes Data In addition to the new 309 mtDNA genomes that were sequenced as part of this study, we retrieved all publicly available complete P. vivax mitochondrial genome sequences from GenBank, giving a total of 731 P. vivax mitochondrial genomes  (Miao et al. 2012; Culleton et al. 2011). Two sequences were of unknown origin and were excluded from further analysis. Analyses requiring an outgroup were performed on an expanded data set that also included 33 mitochondrial genomes from the following ten Plasmodium species: P. cynomolgi, P. inui, P. hylobati, P. simiovale, P. fieldi, P. coatneyi, P. knowlesi, P. fragile, P. gonderi, and Plasmodium sp. from mandrills  (Coatney et al. 1971; Mu. et al. 2005; Pacheco et al. 2012). This expanded set of sequences was aligned using ClustalX v2.
0. 12 and then edited by hand. Subsequent gapstripping left 5,712 sites in the alignment containing all 11 Plasmodium species, whereas the P. vivax alignment (731 sequences) comprises 5,837 sites. A list of all the P. vivax sequences used in this study, along with their countries of origin and accession numbers, is provided in supplementary table  S2 , Supplementary Material online.
Haplotype Networks Network v4. 6. 1. 0 (Fluxus Technologies 2011) was used to infer a median joining network for the complete set of P. vivax mtDNA haplotypes, with transversions weighted twice as much as transitions, with the epsilon parameter set equal to 0, and with up to three rounds of star contraction, 2061 Evolutionary History of Plasmodium vivax. doi:10. 1093/molbev/mst104 MBE which collapses star-like structures in the network into single nodes. However, because the resulting networks were obscured by numerous intersecting edges, we repeated this analysis using a smaller data set containing the 70 haplotypes that were represented by at least two sequences in the global sample as well as an additional 14 singleton haplotypes that appeared unusually divergent in the complete network (India10, Pak_K21, Thai1, Thai39, Indo11, Camb13, Camb14, Turkey9, Turkey10, Turkey13, Ven4, Brz_Bel17, Brz_Bel18, Brz_Ma1; see supplementary table  S2 , Supplementary Material online, for haplotype definitions.
We first ran two independent chains lasting 100 and 200 million generations, respectively, and then used the combined results of these two chains to estimate the posterior distribution of the genealogy of our P. vivax samples. Clades with strong support in this distribution were identified in two ways: first by using TreeAnnotator v1. 7. 1 to construct the MCC tree and second by using the SumTrees script in the DendroPy v3. 9. 0 library  (Sukumaran and Holder 2010)  to construct the majority rules consensus tree from the sampled genealogies. We then ran two additional chains lasting 100 million generations apiece to estimate the ages and posterior probabilities of the major clades identified in the first stage. The first 20 million generations of each run were discarded as burn-in and all four runs were combined to obtain improved estimates of the consensus tree and demography of the global P.
Acknowledgments The authors thank the  DNA laboratory at the School of Life Sciences  for their technical support. This work was supported by the  US National Institutes of Health  ( R01 GM080586  to A. A. E. , the  Latin American Center for Malaria Research and Control U19AI089702 , and the  Intramural Research Program  of the  National Institute of Allergy and Infectious Diseases  to R. M. F. ). The content of this article is solely the responsibility of the authors and does not represent the views of the  US National Institutes of Health.
This paper is concerned with a physical model of an interdigitated sensor working in a frequency range from 100 Hz to 10 MHz. A theoretical approach is proposed to optimize the use of the sensor for bioimpedance spectroscopy. The correlation between design parameters and frequency behavior in coplanar impedance sensors are described. CoventorWare  software was used to model the biological medium loaded interdigital sensor in three dimensions to measure its electrical impedance. Complete system simulation by a finite element method (FEM) was used for sensor sensitivity optimization. The influence of geometrical parameters (number of fingers, width of the electrodes) on the impedance spectroscopy of the biological medium was studied. The simulation results are in agreement with the theoretical equations of optimization.
This paper presents a new approach of physical modeling system of a microelectrodes biological sensor. The correlation between design parameters and frequency behavior in a coplanar impedance sensor is presented. The theoretical optimization of the geometrical parameters of the sensor is conducted by developing impedance equations and modeling equivalent circuits. One objective was to get the optimal ratio between the width of the electrodes and the gap between the electrodes to expand the useful frequency band, and the optimal number of electrodes. A sensor model including a priori the human blood medium was described with the finite element method FEM using CoventorWare® software for simulation. The influence of the medium's physical properties on the frequency sensor response was investigated.
3D Modeling system In this section, the design of the physical model of the sensor loaded by the blood is described. This model was developed for simulation with a finite element method (FEM) using the CoventorWare ® software. We used the microelectromechanical systems (MEMS) module for electro quasi-static harmonic response provided by the library of the software and according to this approach. This approach is valid only when the frequency used is less than 10 7 Hz.
Modeling the blood medium From Figures  1  and 3 , the components C Cell and R Sol models the dielectric properties of the medium under testing, and the component C DL models the properties of the double layer interface phenomena. Therefore the total medium is composed of two sub-media. In physical modeling these two sub-media are translated into two layers, one over the other, horizontally on top of the electrodes. On the other hand, in general the type of the equivalent circuit of Figure  1  exempted of the resistances R lead must be physically modeled in two layers one on top the other in the modeling of CoventorWare according to the references provided by the software package itself  [20]. This again verifies our choice of two layers one over the other. The two layers that describe the interface phenomena occurring at the electrode-electrolyte interface are simplified to a single equivalent layer.
Conclusion This paper presents a comparative approach for simulation of an interdigitated sensor in a biological medium using CoventorWare® software. Three dimensional interdigital sensor simulation techniques were done to analyze the influence of the physical properties of the medium and the impedance response by optimizing the geometry of sensor was used. This optimization method used for bioimpedance spectroscopy sensor was obtained from theoretical equations, by developing total impedance equations and modeling equivalent circuits. Sensitivity related to the number of electrodes has been studied and a geometrical structure of the sensor was optimized. The simulation results are in agreement with the theoretical equations of optimization. We found that the optimized geometry of an interdigital sensor is to choose a ratio between the gap and the width of electrodes equal 0.
Fundamental problem Even if some architectural software companies (such as Autodesk Revit) are proposing new tools for exporting point clouds, in architecture there is no software ensuring a direct shift from point clouds to complete CAD models. The specificity of architectural components makes this task more difficult than in the field of mechanics. In fact, any dedicated software can handle heavy point clouds issued from laser scanning and structure or segment them. However, this task is not sufficient to build an efficient digital representation of buildings. For that, it is essential to analyze and understand the entire chain that goes from the point cloud to the structured enriched 3D model. This process should take into account three main steps: the acquisition, the segmentation, and the enriched 3D modeling (BIM).
 Approaches based on ontologies A last modeling approach is the approach based on ontologies. This method introduced by  (Hmida et al. , 2012) , and which is based on knowledge anthology inspired by the model of the semantic web, uses a priori knowledge of objects and environment. This knowledge is extracted from databases, CAD drawings, GIS, technical reports or expert knowledge belonging to particular fields. Therefore, this knowledge constitutes the basis of a knowledge-based selective detection and recognition of objects in point clouds. In such a scenario, the knowledge of these objects must include detailed information on the geometry of the object structure, 3D algorithms, etc. All approaches mentioned previously identify some or all of the characteristic elements of a scene. Their performance and efficiencies are probably related to the complexity of the scene.
Introduction and Motivation In Model-Driven Engineering (MDE), various activities require the modification of several areas of a model that satisfy specific properties. Such activities may take the shape of refactoring tasks or search-and-replace tasks similar to those supported in textual editors of Integrated Development Environments  (IDEs). Others appear as model-completion transformations or aspect-oriented model weaving. These activities are composed of atomic add, change, and remove operations similar to Create, Read, Update, Delete (CRUD) operations of databases. Although these operations are problem-independent, generic solutions that can be easily reused and customized for arbitrary domains are rare. Existing solutions are restricted to certain types of models, do not support conditional application of changes, ignore domain-specific properties, or introduce accidental complexity.
Nevertheless, industrial domain-specific applications of model weaving, e. g. for communication infrastructure  [4]  or robustness modelling  [1] , suggest that these shortcomings can be overcome. This paper presents a generic, extensible, and practical model weaver, called GeKo  [5] , together with a demonstration of its use in different domains. Our approach is generic because it is defined on top of a metamodelling language. It can be applied to all instances of arbitrary metamodels that were defined using this metamodelling language. Our approach is extensible because domain-specific solutions can be used without modifications of the generic core weaving logic. Finally, it is practical because it can be used together with existing MDE tools. It is not necessary to learn new notations or to understand new frameworks in order to apply the weaver.
In our approach, users declaratively define which elements of the pointcut correspond to which elements of the advice. This indirect weaving specification relieves the user from the need to explicitly specify weaving steps as they are inferred from the mapping. In most cases the mapping can even be determined automatically. In contrast to declarative transformation languages like QVT-R, this mapping is metamodelindependent. The foundations of such declarative weaving instructions have been presented previously  [22] , and continue to be a unique feature of GeKo. Metamodel-independent Operations. Our generic model weaver is able to process instances of arbitrary metamodels. This is possible because weaving operations are based on the properties of the metamodel to which the model conforms. These metamodel properties are automatically retrieved for every metamodel and not hard-coded for a specific metamodel.
They can be attributes, which store primitive types, or references to complex types. Attributes and references are part of various metamodelling languages, such as the standard EMOF 2. 0 or KM3  [12]. Therefore, our approach can even be used for different metamodelling languages. Metamodel-independent operations have already been proposed  [22] , but have never been realised in a completely generic way. Our current implementation  [5]  is based on the metamodelling language Ecore, which is a variant of EMOF 2. 0.
Customizing GeKo to Support BIM Weaving To give the reader a better idea of the extension capabilities of our generic approach we present a set of weaver extensions for IFC models of buildings. The first two extensions to our model weaver are necessary because we cannot use default XMI serialisation for IFC models. We load IFC models serialised in ASCII text files as instances of an Ecore metamodel using a technological bridge  [27]. In our first extension (EP 1) we propagate the IFC-specific changes in the bridge's code generator into the code generator for the relaxed pointcut and advice metamodels. The second extension (EP 2) customizes the resource loader to retrieve content model elements from wrapping elements that model the serialisation format. Because the serialisation and the domain metamodel are defined using Ecore, we do not have to provide all loading and storing infrastructure but can reuse most of the generic facilities of GeKo and EMF.
Although JPDDs provide specialised constructs for behavioural weaving, the authors state that Almazara can be used with any modelling language. We are, however, not aware of such non-UML applications. The Atlas Model Weaver (AMW) was developed to establish links between models that can be stored as so called weaving models. The links are created semi-automatically and can be used for comparing, tracing, or matching related elements. Published applications of AMW  [6]  use the links for heterogeneous model transformations and model comparison, but they can also be used to weave elements into a model instance. An unpublished example  [2] , in which attributes are woven into metaclasses, shows that join points have to be specified manually as no means are provided for pointcut definition or join point detection.
Conclusions and Future Work In this paper we have presented GeKo, a generic model weaver working purely on metamodelling language constructs. We have shown that GeKo is both practical and generic because it uses declarative aspects formulated in existing notations and because it can be applied on instances of any kind of well-defined metamodel. With a selection of extension points for the refinement of weaving behaviour we have also shown that GeKo is easily extensible. This feature is crucial for a generic approach, in that it allows for customizations for domain-specific needs while reusing generic core operations. Finally, we have shown how the formalisation of GeKo allows the management of challenging weaving scenarios such as duplication, merge, and removal. With examples based on BIM and LTS we have illustrated that the operations induced by related pointcut and advice snippets can solve the problems of these scenarios in a generic way.
Results Table  1  contains the results of the experimental evaluation, where each line represents a trace of a program. The columns #Sym. and #Cycles represent respectively the number of symbol occurrences and the number of cycles in a trace. For each generated grammar, Table  1  contains its size Size() and its compression ratio Comp(). Figure  8  displays the arithmetic average of the compression ratios over the five collected traces of the program. Note that the use of other average measures give different values, but the same result: a clear difference of compression ratios between Sequitur and Cyclitur. The compression ratio varies between 0 and 1, where 0 represents the best compression, and 1 the worst. For example, for program P1, we observe that our approach produces better compression than Sequitur.
Third, they reason about method calls. In optimized microcontroller code, function calls alone are inadequate to understand the program, since the core logic of a program is sometimes coded in a single function. Generic data compression methods have been used for execution traces, e. g. , Gzip [?]. However, almost no analysis can be performed on the compressed form of the execution trace. Larus [?] proposes to compress control flow paths using Sequitur. As Sequitur finds regularities in the path (e. g. , repeated code), the output grammar can be used to detect hot subpaths, i. e. , short acyclic paths that are costly. Our work consists in compressing traces by detecting and exploiting cycles. It allows us to reach better compression ratios than Sequitur. Burtscher et al. [?] also propose a value predictor-based compression algorithm for execution trace that obtain better compression ratios than Gzip or Sequitur.