dataesr/scientific-paragraphs-categorization huggingface dataset:
9b  shows the difference between the updated a posteriori fluxes after 10 minimisation iterations, x out , and x tr. The true fluxes have been almost completely retrieved in all grid cells, with only two grid cells still having errors larger than 0. 25 kg SF 6 s -1. The RMSE of a flux vector x, RMSE x , is defined as RMSE x = (x -x tr ) 2. ( 15 ) The RMSE of the a priori emissions, RMSE x b , is equal to 0. 1 kg s -1 , while RMSE x out is equal to 0. 02 kg s -1 , meaning that approximately 80 % of the total error in the a priori  emissions have been corrected by INVICAT. It should be noted that the test described here does not include any random error term being ascribed to the observations, which would be a significant issue for future inversions using real data. This test should therefore not been seen to be representative of the performance of INVICAT in a real application, but as an assessment of the capability of ATOMCAT and the minimisation program to retrieve a known set of emissions.
Summary We have presented thorough details of the development and testing of an adjoint version of the transport section of the TOMCAT CTM and a variational inverse model for the purpose of updating surface fluxes through data assimilation. These models are named ATOMCAT and INVICAT, respectively, and are initially intended to analyse the carbon and methane cycles using observed atmospheric concentration data from in situ measurements and remote sensing. The adjoint model was coded by hand, without the use of automatic differentiation tools, for transport subroutines representing advection in three separate directions, convection and boundary layer mixing. In each case, the discrete adjoint of each subroutine was created directly from the original TOM-CAT code, rather than developing a continuous adjoint from the equations governing the transport in the forward model.
Meanwhile, since the adjoint model depends upon the state of the forward model at each time step, the forward TOMCAT model was updated in order to save the necessary information so that they may be read by ATOMCAT. We investigated the accuracy of the transport scheme included in the TOMCAT model using the atmospheric trace gas SF 6. TOMCAT had previously been included in the TransCom CH 4 model intercomparison, where it had performed accurately in comparison both with observations and with other transport models for SF 6. Further tests showed that TOMCAT captures the seasonality of atmospheric transport well at surface stations, and that reducing the resolution of the model grid by approximately 50 % did not significantly impact the model transport representation. Initially, it is therefore likely that INVICAT will initially be run using the lower model grid resolution in order to maximise running speed and minimise data storage.
, 2014). This takes advantage of the property of time symmetry held by the Prather advection scheme by using an Eulerian backtracking method to find adjoint sensitivities. Due to the differing philosophies behind RETRO-TOM and ATOMCAT, each adjoint model has its own distinct advantages. RETRO-TOM does not require output from a forward model simulation, and so is currently likely to be better suited as an alternative to Lagrangian backtracking (e. g. Haines and Esler, 2014). This also means that RETRO-TOM can easily be run using different model grid resolutions. However, ATOMCAT has the advantage that it is not reliant upon its component transport routines being time symmetric, which allows greater freedom of choice than for RETRO-TOM. RETRO-TOM is not currently coupled to a data assimilation of inverse modelling framework, but it would be an interesting avenue of further study to explore the possibility of including RETRO-TOM as an option for adjoint transport within INVICAT.
Code availability TOMCAT/SLIMCAT (www. see. leeds. ac. uk/tomcat) is a UK community model. It is available to UK (or NERC-funded) researchers who normally access the model on common facilities or who are helped to install it on their local machines. As it is a complex research tool, new users will need help to use the model optimally. We do not have the resources to release and support the model in an open way. Any potential user interested in the model should contact Martyn Chipperfield. The model updates described in this paper (INVICAT and ATOMCAT) will be included in the standard model library in the future and therefore will be similarly available only to those who are able to support TOMCAT. The minimisation code M1QN3, meanwhile, is protected by copyright and cannot be distributed except with the permission of its authors.
Acknowledgements. This work was supported by funding from  NERC  and  NCEO. The TOMCAT model is also supported by  NCAS. Manuel Gloor  was financially supported by the  NERC  Consortium grant AMAZONICA ( NE/F005806/1 ) and the  EU 7th Framework GEOCARBON  project (grant no. agreement 283080),  Chris Wilson  by a  NERC   DARC studentship  and the  NERC  consortium grant GAUGE. The authors are grateful for data obtained from the  World Data Centre of Greenhouse Gases , provided by  NOAA/ESRL. The minimisation program M1QN3 is part of the MODULOPT library at  INRIA  (https://who. rocq. inria. fr/Jean-Charles. Gilbert/modulopt/), and the authors thank the company for its permission to use the minimiser. We also thank  Wuhu Feng  (NCAS). Edited by:  A. Sandu.
In the course of our VLTI young stellar object PIONIER imaging program, we have identified a strong visibility chromatic dependency that appeared in certain sources. This effect, rising value of visibilities with decreasing wavelengths over one base, is also present in previous published and archival AMBER data. For Herbig AeBe stars, the H band is generally located at the transition between the star and the disk predominance in flux for Herbig AeBe stars. We believe that this phenomenon is responsible for the visibility rise effect. We present a method to correct the visibilities from this effect in order to allow "gray" image reconstruction software, like Mira, to be used. In parallel we probe the interest of carrying an image reconstruction in each spectral channel and then combine them to obtain the final broadband one.
The hint then, is to measure a quantity that is the sum of the phases over a baseline triangle. In that case, the atmospheric influence vanishes and we obtain only an astrophysical quantity called the closure phase. So, in practice, there are two interferometric measurements: the squared amplitude of the visibilities V 2 and the closure phases. We noticed in several datasets that the visibility is higher at short wavelengths. If B is a baseline length projected on the sky plan and λ the wavelength, we can plot the squared visibilities V 2 in function of B/λ (which is the spatial frequency). For a monochromatic object, we expect the points to follow a general trend in the visibility curve, since B/λ represents only the spatial frequency. But, this is not the case. Indeed, we can see (Fig. 1 ) that the rising curve of visibilities per base is not fitting the general trend of the data for different baselines.
Its distance is poorly constrained (d = 500 pc ± 150 pc, van Leeuwen 2007). In Section 2 we will describe the chromatic effects in the visibilities and the Section 3 will show the different methods to deal with them. Finally we will apply them to the astrophysical case of MWC 158 in the Section 4. Right: PIONIER closure phases. For PIONIER data the gray scale varies in function of the wavelength. We can see on the visibility graphs than a "coma" trend appear for visibilities belonging to the same baseline.
Chromatism Since interferometric instruments with spectral dispersion exist, we need to take into account the flux variations with the wavelength in order to correctly analyze the data and have access to the spectral super synthesis. In the case of Young Stellar Objects (YSOs), we noticed that the visibilities have a strong spectral dependence such as the geometrical shape of the object could not explain it. For Herbig AeBe star, the chromatic effect explained in the Section 1 exists typically for the Near Infrared interferometry. In the following, we explore the possibility that this effect is caused by a different spectral index between the central star and its surrounding media. In order to confirm that, we made a simple model with a central star and its dusty disk.
Conclusions The chromatic effect due to the flux predominances of two objects of different sizes is well understood and can be used in order to find astrophysical information of the object. In the case of Herbig AeBe stars we are able to have an approximation of the temperature of the components. If the chromatic information is given, we can perform gray disk image reconstructions. They are contributing to the astrophysical analysis of the object because they show the P. A. and the inclinations of the disk. Moreover, in the case of MWC 158 it brought us the idea of the second extended component, even if it is poorly constrain (we can have the information on the flux ratio). By the fit we were able to find a value for the inner rim radius and its temperature and to compare what we found with the data from photometry.
Since the regularization will tend to smooth the Fourier plan, the algorithm will favor the added parameters to fit the fixture. Indeed, the parameters will not be constrained by the regularization and the gradient will be stronger on it than on the pixels values. For these objects, there is a need to include parametric models in the image reconstruction algorithms and to develop a global chromatic image reconstruction algorithm. This work is supported by the French ANR POLCA project (Processing of pOLychromatic interferometriC data for Astrophysics, ANR-10-BLAN-0511).
Collaborative writing applications (CWAs)  [18, 19]  are a category of social media that has surged in popularity in recent years, including within the health care sector  [2, 6, 18, 20]. CWAs consist of software that allows users to create online content that anyone who has access can edit or supplement  [21]. With these contributions, CWAs can become rich multimodal communication tools enriched with hyperlinks, images, videos, and audio. For example, Internet users have turned to wikis  [22, 23]  to produce a Wikipedia entry on the Global Plan to Stop Tuberculosis  [4] ; to Google Knol  [24, 25]  to exchange research on influenza at the Public Library of Science  [26] ; and to Google Docs  [19, 27]  to review the literature on emergency medicine  [28, 29]. Although now defunct, Google Knol was a Google project that aimed to include user-written articles on a range of topics that could be edited only if the original authors gave access to editing the text.
Stage 2: Identifying Studies and Grey Literature Seven scientific databases (Cochrane Library, PubMed, EMBASE, CINAHL, PsycINFO, ERIC, ProQuest Dissertations and Theses) were searched systematically for the period covering January 1, 2001 (Wikipedia's inaugural year), to September 16, 2011. Our search strategy was peer-reviewed using the PRESS criteria  [89]. The following keywords were used and adapted to each database: "wiki", "wikis", "Web 2. 0", "social media", "Google Knol", "Google Docs", and "collaborative writing applications" (see Table  1 ). We did not exclude any citations based on language. In addition, study reference lists; the 2010 and 2011 editions of the Medicine 2. 0, WikiSym, and American Medical Informatics Association conference proceedings; clinicaltrials. gov and Open Medicine's websites; expert consultation (eg, the authors of WikiProject Medicine  [4] ), OpenSIGLE (before 2005), and the Health Technology Assessment international Vortal were searched.
Furthermore, environmental scans of the grey literature indexed by Google, Bing, Yahoo, and Mednar were performed. Finally, via email, Twitter, Mendeley, Google Docs, and a health librarianship page (HLWIKI), we called for the crowdsourcing of studies that could potentially fall within the scope of this review. Table  1. Full search strategy for each database. Wiki*[All Fields] OR "Web 2. 0"[TIAB] OR "Web2. 0"[TIAB] OR (google* AND knol) OR (google* AND docs) OR "Social media" [TIAB] OR (Collaborative [tiab] AND writing  [tiab] ) OR (collaborative technolog*) OR (collaborative software*) Pubmed wiki* OR "collaborative technology" OR "collaborative technologies" OR "collaborative writing" OR "collaborative writings" OR "collaborative software" OR "collaborative softwares" OR "google docs" OR "google knol" OR "ehealth 2.
Stage 3: Selecting Studies Three teams of 2 reviewers (SR/MF, TB/AB, PA/CK) independently screened titles, abstracts, and grey literature and retained articles that presented empirical data about any CWA applied to the field of health care. In case of disagreements, a third reviewer was consulted (PA, TB, or SR). To reach a high level of agreement, we conducted 4 series of assignments (400 abstracts in total) whereby the screening of a number of studies was followed by a teleconference to reach agreement about which studies to include and to discuss uncertainties. Once consensus was reached for all cases, the remaining studies were coded by the same 3 pairs of screeners (SR/MF, TB/AB, PA/CK). Subsequently, 2 reviewers (TB and PA) conducted another round of screening based on full text studies.
Stage 4: Charting the Data A data-charting form was developed and built into EPPI-Reviewer for the extraction of quantitative and qualitative variables and to facilitate data coding. It was tested and refined by 4 reviewers (PA, CN, ME, CF) using the first 50 studies. Three pairs of 2 reviewers (CN/CF, CN/ME, ME/CF) then independently extracted data from the remaining studies. Disagreements were resolved through discussion with a third reviewer (PA or TB). Using EPPI-Reviewer's inductive coding function, we extracted all the pre-planned variables described in our published protocol  [86].
Barriers/Facilitators A second thematic content analysis was performed on the data regarding barriers and facilitators to the use of CWAs in health care with the initial coding scheme reflecting an existing framework concerning the determinants of ICT adoption  [78]. Many new determinants of social media were inductively added to this framework. Our 3 reviewers created new codes for units of text that could not otherwise be coded using the original framework, thus refining and expanding the list. We also systematically searched each article to determine if a theoretical framework was used to report barriers and facilitators. If so, relevant elements were also added to the existing framework.
Study Characteristics We found 4 experimental studies, 5 quasi-experimental, 5 observational analytic, 52 case studies, 22 describing the quality of wikis, and 23 surveys on wiki use (Multimedia Appendix 1;  [27, [29] [30] [31] [32] 38, 42, 53, 54, 58, 61, 63, 72, 74, 76, ). Wikis (n=106) and Google Docs (n=6) are the main types of CWAs used in health care. One grey literature report compared Google Knol to Wikipedia  [96]. Wikipedia was the focus of a large number of studies (n=36). The most frequently used wiki software were MediaWiki (n=44), PBworks (n=8), Wikispaces (n=6), Wetpaint (n=6), Microsoft SharePoint (n=3), and Google Sites (n=3). One paper described two wikis using Semantic MediaWiki (WikiEcho  [97]  and WikiDoc  [98, 99] ). There were studies describing custom-built hybrid wikis (Wikibreathe (n=2)  [100, 101] , Orthochina (n=1)  [102] , and FreyaWIKI (n=1)  [103] ; the use of virtual learning environments (eg, Blackboard) to host wikis as aids for supporting educational activities (n=8); and the use of more sophisticated social media platforms (eg, Drupal  [104] , MijnZorgNet  [105] , Atlassian  [76] , and MinJournal  [106] ) that offer wikis and other social media such as blogs and social networking services.
Strengths of This Study This is the first study that has conducted a scoping review to examine the depth and breadth of evidence about the use of CWAs in health care. We rigorously followed scoping review methodology and conducted a systematic and broad search of CWA use in multiple scientific databases and grey literature sources. A scoping review was the ideal methodology to employ for a number of reasons. First, it is an explorative method used when the relevant literature is considered to be broad and diverse  [312]. Moreover, the study of these applications is an emerging field that is being examined with diverse methods  [28, 32, 61] , with different theoretical frameworks  [29]  and in different contexts  [46, 313]. We used a high-quality collaborative Web-based software to manage our review, to import studies, to extract data and to create reports.
Acknowledgments Funding for this project was provided by a  Canadian Institutes for Health Research Knowledge Synthesis Grant  ( FRN 116632 ); a  Fonds de recherche du Québec - Santé career scientist award  ( 24856 ); a  Fonds de Recherche du Québec-Santé , Establishment of young researchers-Juniors 1 Grant (24856); and a research grant from the  Centre de santé et services sociaux Alphonse-Desjardins  ( CHAU de Lévis ). The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript. We gratefully thank the following people for helping us with importing and reviewing the astonishing number of 7461 abstracts:  Michèle Dugas ,  Cynthia Fournier ,  Mathieu Édmond ,  Azadeh Bojmehrani ,  Catherine Nadeau , and  Hugo-Pierre Racine. We gratefully thank  Elmie Peters  and  Monique Clar  for their advice on search strategies in scientific databases.
THE DoPill ® DoPill ® is an electronic dispenser with 28 compartments covered by a dynamic membrane which allows events detection (Figure  1 ). Each compartment can contain multiple pills. The patient's pharmacist is responsible for programming the device, doing the usual safety checks, and dispending the medication as prescribed. Visual and sound alarms alert the user when it's time to take medication and the compartment from which it must be taken. Finally, sensors record the time of opening and upload the data to a secure server on Internet which calculates an adherence ratio (pill taken/pills given), and where clinicians can consult the adherence in real time. Ten prototypes were provided free of charge by the manufacturer.
Cost of non-adherence was estimated by the cost of wasted pills. Descriptive statistics were used for baseline sociodemographic and clinical characteristics of patients, for cost analysis, and for proportion of patients with <70 and <90% AAR. The results in the BARS did not follow a normal distribution since most scores fell toward 100% adherence. However, a Brown-Forsythe test allowed us to verify homogeneity of variance. Repeated measures ANOVA, with adherence rate, BARS, group and visit number as variables, were preformed with the non-parametric Scheirer-Ray-Hare test extension of the Kruskal-Wallis test. The level of significance for two-sided hypothesis tests was set at a P-value less than 0. 05. The SPSS 17. 0 (Chicago, IL, USA) statistical software was used for all analyses.
Potential heterogeneity In the data set, extracted for each patient, we noticed that some patients did not take all the medication prescribed by the psychiatrist and choose or selected only some of the pills from the dispenser. As illustrated in Table  3 , we can see that for instance in subject EET-20 venlafaxine was 38% taken versus 43% for procyclidine. This can also be explained if the patient forgot most often morning drugs but not evening ones because of environmental or time factors.
However, MEMS ® excluded, there are no other device that integrates the pharmacist in the process, and no other device that were studied in a clinical trial. This professional is the most important to ensure that drug regimens are safe and effective, and it's critical that he validates the final disposition and identification of drugs before administration. This is a significant strength of the DoPill ® , because it's the patient's pharmacist who prepares and identifies the 7 days medication card, and who sends the data in the patient's device by Internet. All this is integrated seamlessly in the pharmacy software, with the usual security checks. MEMS ® remains the most studied device to monitor adherence, but it does not include reminders, and every dosage of a drug needs a separate device.
Therefore, simplifying user interfaces should be a designer's and software engineer's main focus, but this limits clinical trial duration to give the opportunity to developers to test new improved versions. Universal design is a term which refers to accessible, comprehensible, and intuitive design solutions for all, regardless of age, ability, or status, but also solutions that avoid stigmatization and digital exclusion. In schizophrenia it is crucial. Today more than ever, designers are sensitive to the need for simple and meaningful products, especially considering the complexity and continuously changing nature of digital products and devices. In our trial, the findings and patient feedback were continuously shared with the manufacturer to improve our patient's safety and satisfaction with the DoPill ®.
ACKNOWLEDGMENTS Emmanuel Stip is holder of the Eli Lilly Chair of Schizophrenia from the  Université de Montréal. We wish to thank all clinicians who collaborated to this project:  Millie Lum ,  Dr. Marie Villeneuve ,  Dr. Lahcen Ait Bentaleb ,  Dr. Pierre Lalonde ,  Dr. Anne Décary ,  Dr. Nathalie Shamlian , and  Judith Babin. We also wish to thank  Pierre Bourassa ,  Camille Lapierre , and  Benoit Demers from Domedic  for providing ten DoPills ® and improving the device for our patients. Simon Zhornitsky is recipient of a postdoctoral fellowship from the  MS Society of Canada.
Discussion A new algorithm to extract significant places and derive a timetable of visits from raw GPS data based on kernel density computation is assessed in comparison to a more  'classical' distance threshold algorithm. Artificial tracks with known characteristics are processed and allow precise performance evaluation. Motivations driving the development of this algorithm were both practicalthat is, to provide an efficient solution to derive activity locations from GPS datasets in order to improve the characterization of activity spaces and related environmental exposures in epidemiological modellingand technical, by trying to offer a solution for which the sensitivity of the algorithm parameter choice was low, i. e. where a broad range of parameter values would perform well under various conditions.
The Python code for automatic generation of artificial tracks as presented here is made available on the authors' lab website at www. spherelab. org/tools. Second, the proposed set of performance indicators is useful for algorithm evaluation. Looking at one performance criteria only (such as the number of detected stops for example) may be misleading, as trade-off sometimes occurs, for example between spatial and temporal accuracy. Third, the proposed kernel-based algorithm has outperformed the more 'traditional' fixed-threshold method along all measured performance indicators. Because of its ease of implementation, we recommend its use for activity location detection in health research. To facilitate usage, an ArcToolbox version of the algorithm for ArcGIS 10 is made available on the authors' website.