dataesr/scientific-paragraphs-categorization huggingface dataset:
In particular, the detailed evaluation provides a clear evidence that the proposed approach for optimal neighborhood size selection is beneficial in comparison to the other neighborhood definitions, since it often yields a significant improvement with respect to performance and behaves close to the best performance otherwise. A strong indicator for the quality of the derived results has been defined by the mean class recall, as only a high overall accuracy may not be sufficient for analyzing the derived results. For the Oakland 3D Point Cloud Dataset, for instance, we have an unbalanced test set and an overall accuracy of 70. 5% can be obtained if only the instances of the class ground are correctly classified. This clear trend to overfitting becomes visible when considering the respective mean class recall of only 20.
4 Paris-rue-Madame database: MINES ParisTech 3D mobile laser scanner dataset from Madame street in Paris. c 2014 MINES Paris-Tech. MINES ParisTech created this special set of 3D MLS data for the purpose of detection-segmentation-classification research activities, but does not endorse the way they are used in this project or the conclusions put forward. The database is publicly available at http://cmm. ensmp. fr/∼serna/rueMadameDataset. html (last access: 30 March 2014).
© 2014 Zhang et al. ; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/2. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
SELENITE As mentioned above, control of NK cell activation is either achieved by KIR/HLA interactions but also NKG2A/HLA-E interaction. In healthy individuals, at steady state, the two systems compensate for each other to ensure a total control of NK cell reactivity. Regarding NKG2A-mediated inhibition of NK cells by HLA-E expressing tumor cells, very few data are available. Interestingly, an FDA-approved reagent, selenium, may be a promising tool. Supplementation with selenium has been associated with reduced risk of solid cancer  (117). The mechanism of action of selenium is not entirely known, but it induces apoptosis of tumor cells by generating an oxidative stress, which may be more effective on tumor cells compared to healthy cells  (118, 119). Alternatively, selenium blocks the synthesis of HLA-E and consequently increases cytotoxicity mediated by NKG2A-positive NK cells  (120).
Introduction We have conducted experiments on three different annotation tasks in order to guarantee an appreciable generality of our findings. The first two experiments correspond to an ordinal annotation. They concern the affective dimension of language (emotion and opinion annotation). They have been conducted with naïve coders to preserve the spontaneity of judgment which is searched for in affective computing. The third experiment concerns coreference annotation. It is a nominal annotation that has been designed to be used as a comparison with the previous ordinal annotations tasks. The corresponding annotated corpora are available (TestAccord database) on the french Parole_Publique 1  corpus repository under a CC-BY-SA Creative Commons licence.
This experiment has been carried out on a corpus of film reviews. The reviews were relatively short texts written by ordinary people on dedicated French websites (www. senscritique. com and www. allocine. fr). They concerned the same French movie. The corpus contains 183 sentences. Its annotation was conducted by the 25 previous subjects. The methodology is identical to the emotion annotation task. The subjects were asked to qualify the opinion that was conveyed by every sentence of the reviews by means of the same scale of values (Table  1 ). This scale encompasses this time the polarity and sentiment strength dimensions. Once again, the sentences were given in a random order and contextual order respectively. The criterion of data significance is satisfied here too. On both annotations, experiments with the random or the contextual order give similar results.
Corpus Emotion (fairy tales) In the coreference corpus, two classes are highly dominant, but they are not prevalent alone. There is no indication in the literature that the prevalence of two balanced categories has a bias on data reliability measure. For all these reasons, we didn't investigate the influence of prevalence. Besides, relevant works are questioning the importance of the influence of prevalence on inter-coders agreement measures  (Vach, 2005). 5-classes -2 -2 -2 -2 -1 -1 -1 -1 0 0 0 0 1.
Influence of coders set permutation "a coefficient for assessing the reliability of data must treat coders as interchangeable  (Krippendorff, 2004b). We have studied the stability of reliability measures computed on any combination of 10 coders (among 25) on the affective corpora, and 4 coders (among 9) on the corefer-ence corpus. The influence of permutation is quantified by a measure of relative standard deviation (e. g. related to the average value) among the sets of coders (Table  5 ). Binary metrics do not differ on this criterion: multi-κ, multi-π and α b present very similar results. On the opposite, the benefit of a Euclidian distance of agreement is clear: α is significantly less influenced by coders set permutation.
A literature survey and analysis was conducted to describe the epidemiology of dengue disease in Malaysia between 2000 and 2012. Published literature was searched for epidemiological studies of dengue disease, using specific search strategies for each electronic database; 237 relevant data sources were identified, 28 of which fulfilled the inclusion criteria. The epidemiology of dengue disease in Malaysia was characterized by a non-linear increase in the number of reported cases from 7,103 in 2000 to 46,171 in 2010, and a shift in the age range predominance from children toward adults. The overall increase in dengue disease was accompanied by a rise in the number, but not the proportion, of severe cases. The dominant circulating dengue virus serotypes changed continually over the decade and differed between states.
Methods The overall methodology, search strategy, and inclusion and exclusion criteria for this literature analysis and review are included in a protocol that was developed by a Literature Review Group (LRG). The protocol was based on the preferred reporting items of systematic reviews and meta-analyses (PRISMA) guidelines  [15]  and was registered on PROSPERO, an international database of prospectively registered systematic reviews in health and social care managed by the Centre for Reviews and Dissemination, University of York, on 16 July 2012 (http:// www. crd. york. ac. uk/prospero/display_record. asp?ID=CRD4201 2002293).
Search strategy and selection criteria The LRG guided the literature analysis process, defined the search strategy, and prepared the protocol and review documents. Search strings for each database were designed with reference to the expanded Medical Subject Headings thesaurus, encompassing the terms 'dengue', 'epidemiology', and 'Malaysia. Different search string combinations were used for each electronic database with the aim of increasing the query's sensitivity and specificity. The protocol directed that only studies published in English during the survey period (1 January 2000 to 23 February 2012) were to be included in the analysis. For databases that did not allow language and/or date limitations, references not meeting these criteria were deleted manually at the first review stage. No limits were imposed by sex, age, and race of study participants or by study type, although single-case reports were excluded, as were studies that only reported data for the period before 1 January 2000.
To avoid duplicate publication of data, literature reviews and editorials utilising previously published peer-reviewed data were excluded. Unpublished reports were included if they were identified in one of the sources listed above. Finally, publications not identified by the approved search strategy and unpublished data sources that met the inclusion criteria were included if recommended by members of the LRG. Searches of published literature were conducted for epidemiological studies of dengue disease between 9 February 2012 and 23 February 2012, in the following databases: PubMed, Excerpta Medica Database (EMBASE), MedLine, WHO Library database (WHOLIS), WPRO, Index Medicus for South-East Asia Region (IMSEAR), and the Malaysian Ministry of Health (MoH) official bulletins. Literature relating to key congresses, grey literature such as lay publications, Dengue Bulletins, and theses, and general internet searches were conducted to complement data gathered in the published literature.
Sources were reviewed by the Literature Review Group to ensure they complied with the search inclusion and exclusion criteria. In particular, single-case reports and studies conducted before or after the defined search period were excluded, as were publications of duplicate data sets, unless the articles were reporting different outcome measures. We chose not to exclude articles and other data sources nor formally rank them on the basis of the quality of evidence. Whilst we recognize that assessing study quality can potentially add value to a literature review, the consensus of the Literature Review Group was that given the expected high proportion of surveillance data among the available data sources and the nature of surveillance data (passive reporting of clinically-suspected dengue), such quality assessment would not add value to our review.
Author summary Dengue disease is a tropical and subtropical mosquitoborne viral illness, and is a major health concern in Malaysia. We conducted this literature analysis and review to describe the epidemiology of dengue disease in Malaysia between 2000 and 2012, to determine the impact of dengue disease on the Malaysian population, and to identify future research priorities. We used well-defined methods to search and identify relevant research, and data were selected according to predetermined inclusion criteria. This long-term review highlights the changing epidemiology of dengue fever in Malaysia. Although the overall incidence has stabilized in recent years, dengue disease remains a public health burden. Our review demonstrates an increased incidence of all forms of dengue disease and a predominantly adult age distribution.
Overall, approximately 50% of dengue disease cases in Malaysia were confirmed by laboratory analysis. This percentage varied from 39?6% to 53?0% in the period 2000-2007, the last year for which data were available  [9]. The majority of dengue disease cases were reported as DF, rising from 6692 in 2000 to 42,140 in 2010, the numbers closely matching those of the total cases. The total number of annual DHF cases also increased, from 411 in 2000 to 4031 in 2010 (Figure  3A ). The ratio of DF to DHF cases remained fairly constant, being 16?3:1 in 2000 and 10?5:1 in 2010  [3, 9, 12, 13, [16] [17] [18] [19] [20] [21] [22] [23]. Again, there were fewer cases of DF and DHF in 2011 compared with previous years (DF 18,466 cases; DHF 1418 cases). The annual number of deaths from dengue disease increased from 45 in 2000 to 134 in 2010, although the case fatality rate (CFR) remained constant at 0?2-0?3%, with 0?63% reported for the year 2000 (Figure  3B , 3C)  [3, 9, 12, 21].
Age, sex, and racial distribution The data we collected indicate that number of reported cases of dengue disease declined in children but was more stable in adults during the review period. Similar age distributions were reported for both males and females and in the Malay and Indian racial groups, with the highest proportion of dengue disease cases occurred in people aged 10-29 years  [12, 16]. The number of deaths due to dengue disease in children (0-14 years) declined markedly up to 2007 as did the CFR (from 1?3% to 0?17%), while the number in adults (aged $15 years) increased slightly and the CFR changed little  [3, 9]. National data published by the WHO for the period 2000-2008 demonstrated that there was a predominance of males with dengue disease (55-62%). This relationship was confirmed by the proportion of males with dengue disease in all years being significantly greater (p,0?001) than the proportion of males in the population (50?8% in 2000)  [16].
Regional epidemiology For 2007, dengue disease incidence data were available for all 14 Malaysian states. Regionally, the west peninsular states of Malaysia were most affected by dengue disease. Incidence rates in Kuala Lumpur, Selangor, Kelantan, and Penang areas were 455?7, 320?3, 224?5, and 204?5 per 100,000 population, respectively; with the exception of Pahang (179?1 per 100,000 population) the remaining states were less affected (,140 per Figure  2. Results of literature search and evaluation of identified studies according to PRISMA. All references identified in the on-line database searches were assigned a unique identification number. Following the removal of duplicates and articles that did not satisfy the inclusion criteria from review of the titles and abstracts, the full papers of the first selection of references were retrieved either electronically or in paper form.
A further selection was made based on review of the full text of the articles. EMBASE, Excerpta Medica Database; PRISMA, preferred reporting items of systematic reviews and meta-analyses; WHO IMSEAR, World Health Organization Index Medicus for South-East Asia Region; WHO WHOLIS, World Health Organization Library Database; WHO SEAR MALAYSIA, World Health Organization Regional Office for Southeast Asia Malaysia; WHO WPRO, World Health Organization Western Pacific Region. doi:10. 1371/journal. pntd. 0003159. g002 100,000 population) and incidence rates in south peninsular area (Malacca and Johor) and the Borneo states were ,105 per 100,000 population  [3]. In 2008, 63% of the national total of reported dengue disease cases occurred in the Klang Valley, which includes the state of Selangor and the Federal Territory of Kuala Lumpur  [31].
Furthermore, we have incorporated 2011 data that reveal a sharp decline in incidence compared with previous years. As dengue disease is known to be unpredictable with respect to its incidence in any one year  [3] , it is difficult to draw any firm conclusions from the decline in incidence reported in 2011  [12]. Whilst annual changes in the level of under-reporting in any passive surveillance system may account for a reduction in the number of reported cases, the recent implementation of new action measures against dengue disease by the Malaysian MoH in 2009 may also be a factor. The measures include a strategic plan covering the years 2009-2013  [31] , introducing clear treatment guidelines in 2010  [9]. In future, a new Sentinel Surveillance System in 2012 in which samples were collected from 40 sentinel sites (hospitals and health clinics) representing all states in Malaysia and sent to the nearest Public Health Laboratory for testing, and a protocol for sampling for virological confirmation and serotype assessment will ensure that the data collected are regionally representative and will contribute to future improvements in the knowledge of regional serotype circulation across Malaysia.
Acknowledgments The authors take full responsibility for the content of this contribution and thank  Peter Blakeborough  and  Graham Joint  ( Communigen Ltd ) for assisting with the preparation of manuscript drafts (supported by  Sanofi Pasteur). The authors would like to thank  Gee Marsh  ( Sanofi Pasteur ) for provision of critical comments and suggestions on the drafts, as well as  Shunitra Chandrasegran  for critical comments.
Currently this consortium consist of 16 partners, covering Europe and the Mediterranean region and including some north African countries. The code of the ALADIN model  (Bubnová et al. , 1995)  is mostly shared with the code of the French global ARPEGE (Action de Recherche Petite Echelle Grande Echelle) model and the IFS (Integrated Forecast System) of ECMWF (European Centre for Medium-Range Weather Forecasts). The lateralboundary conditions (LBCs) of the operational ALADIN model configurations are imposed by the Davies scheme  (Davies, 1976; Radnóti, 1995; Termonia et al. , 2012)  at regular time intervals of 3 h  (Termonia et al. , 2009)  with LBC data provided by either ARPEGE, IFS or a larger ALADIN domain. For the present study the version of  Radnóti (1995)  is used. ALADIN has been further developed with a physics parameterization package called ALARO, which has been designed specifically to be run at convection-permitting resolutions.
, 2008). The ALARO physics package is coupled to the dynamics of the ALADIN model via a physics-dynamics interface based on a flux-conservative formulation of the equations proposed by  Catry et al. (2007). The configuration of the model with these physics runs operationally in a number of countries of the ALADIN and HIRLAM consortia 1 for the national NWP applications since 2008. Historically ARPEGE, ALADIN and ALARO models relied on the ISBA scheme developed by  Noilhan and Planton (1989)  and  Noilhan and Mahfouf (1996)  for 1 At,  Be, Cz, Hr, Hu, No, Pt, Ro, Se, Si, Sk and Tr. the parameterization of the surface processes. It is also used within the ARPEGE climate model of Météo-France  (Mahfouf et al. , 1995). The ISBA scheme has also been implemented in the meso-NH model of Météo-France  (Lafore et al.
The rationale for this externalization was twofold. First, once this externalization is done, and if the scheme is plugged into any applications, it becomes available within all the applications. Secondly, SURFEX contains the ISBA scheme for its soil and vegetation interactions, so there is a priori no need to maintain the ISBA scheme separately in the different model versions ARPEGE, ALADIN, AROME, ALARO, ARPEGE climate and ALADIN climate. In operational contexts it is important that the scheme is sufficiently numerically stable to run with the long time steps imposed by the operational applications. Hence the implicit coupling proposed by  Best et al. (2004)  has been used. The physiographic characteristics of the surface in SURFEX are specified by the ECOCLIMAP database (see  Masson et al.
An attempt to find reproducibility of the model behaviour by replacing the old ISBA scheme within the ALADIN configuration by the SURFEX-ISBA did not succeed. Nevertheless, the question of the first rationale still stands: why should one maintain different ISBA schemes to serve a large community of users? The obviously preferable version of the two ISBA is the one within SUR-FEX due to its higher potential for rapidly scientific evolution. For instance, new surface data assimilation schemes are being developed for SURFEX, as will be briefly discussed in the last section of the present paper, and it will be necessary to switch to SURFEX in order to benefit from these developments. The aim of the present study is to address the following question: can one, by exhibiting the novel features developed in SURFEX over the past decade plus the additional options in the configuration of the atmospheric part of ARPEGE/ALADIN/ALARO models, reproduce forecast performance that is equivalent or better in terms of the set of verification scores that are put forth in the operational context of each of the participating ALADIN partners? Apart from the user-oriented goal of allowing a science-based decision for the configuration of the NWP system by each partner within the consortium, this provides a very extensive validation of the SURFEX scheme rather than a specific validation such as in  Hamdi et al.
(1995). The ECUME (Exchange Coefficients from Unified Multi-campaign Estimates) parameterization of sea surface fluxes is used over seas  (Belamari and Pirani, 2007). It is a bulk iterative scheme developed in order to obtain an optimized parameterization covering a wide range of atmospheric and oceanic conditions, while ALARO used the classical Charnock formula  (Charnock, 1955). Physiographic data have also been improved compared to the one used by ALARO (GTOPO30, ECOCLIMAP  (Masson et al. , 2003) , and FAO maps  (FAO, 2006)  for soil texture). For two months (January 2010 and July 2010), a series of simulations is performed, with (OPER + SFX) and without SURFEX (OPER), with one simulation of 36 h (60 h for the 7 km domain) each day, starting at 00:00 UTC (from the operational ALADIN French forecast model analysis).
Surface fluxes: test with data from Cabauw tower The Cabauw tower is situated in the central river delta in the south-western part of the Netherlands, 0. 7 m below mean sea level. The surroundings are flat and consist of meadows and ditches with scattered villages, orchards and lines of trees. The immediate surroundings of the tower are free of obstacles up to a few hundred metres in all directions, with the local surface consisting mainly of short grass. For the predominant wind direction (south-west), the flow is unperturbed over an upstream distance of about 2 km. The routine observations include profiles of wind speed, wind direction, air temperature and dew point temperature at 10, 20, 40, 80, 140 and 200 m above ground level. The temperature is also measured at 2 m, and fluxes of momentum and heat at 5 m.
Daytime During daytime, the use of SURFEX has a neutral impact on the 2 m temperature at the Cabauw site. However, as it can be seen from Table  5 , there is a significant improvement of the upward shortwave radiation. In fact, the average mean bias and rmse of the upward shortwave radiation flux is significantly reduced (up to 10 W m -2 , not shown) during the summer when using SURFEX. There is also a significant improvement of the surface heat flux, especially during the summer, with a reduction (not shown) up to 20 W m -2 in the rmse of sensible and latent heat flux. These improvements in the upward radiative flux and surface heat flux when using SURFEX are probably due to (i) the use of improved physiographic data within the ECOCLIMAP database compared to the one used by ALARO, and due to (ii) the tiling approach used in SURFEX since TEB was also activated for the 4 km domain.
Surface data assimilation In order to compare OI and the EKF for surface assimilation, several experiments were run. All experiments have the same setup. The experiments are run with ALARO in combination with the external land surface model SURFEX. All runs were performed on the 4 km domain with 46 vertical levels. Surface assimilation is performed every 6 h. There is no atmospheric assimilation as in  Mahfouf et al. (2009). The screen-level relative humidity and temperature observations are taken from SYNOP and TEMP reports in the Meteorological Archival and Retrieval System (MARS). The screenlevel observations are interpolated on the model grid using an optimum interpolation technique with high background error covariances to minimize the influence of the analysis background. The gridded observations are then used for the pointwise EKF or OI assimilation.
cDNA library construction and high-throughput sequencing Four cDNA libraries, corresponding to the control and treatment groups, were sequenced using Illumina GAIIx technology. One lane per library was used to generate an RNA-seq dataset of four 80-nucleotide paired-end short sequence reads. The samples for this analysis were collected at day 12, which was the last sampling occasion prior to the appearance of symptoms of bleaching or bacterial infection in the thermal stress and virulent treatments, respectively. The total RNA from the 3 coral nubbins of each of the control and treatment groups was extracted using TRIzol reagent (Invitrogen), as previously described  [40]. The cDNA libraries were then constructed following an established protocol  [41]. Briefly, to obtain high quality mRNA, two cycles of oligo (dT) purification were performed using the Ambion Poly(A) Purification kit (Ambion).