dataesr/scientific-paragraphs-categorization huggingface dataset:
The second step consists in a hidden Markov chain (HMC) segmentation using a specific volume transformation within a Bayesian framework. Our method does not introduce any prior on the expected shape of the vertebra within the bounding box and thus deals with the most frequent pathological cases encountered in daily practice. We experiment this method on a set of standard lumbar, thoracic, and cervical vertebrae and on a public dataset, on pathological cases, and in a simple integration example. Quantitative and qualitative results show that our method is robust to changes in shapes and luminance and provides correct segmentation with respect to pathological cases.
Quantitative results When considering vertebral segmentation in CT images, there are few available complete dataset allowing a quantitative evaluation of a method. We use the dataset presented at the CSI 2014 challenge  [26] , available on the public SpineWeb platform  [27]. This dataset contains 10 spine scans from a trauma center, acquired during daily clinical routine work. Patients were aged 16 to 35, and the scans covered thoracic and lumbar vertebrae in most cases. A total of 175 segmented volumes were extracted from the dataset. The performances are measured as the rate of correctly classified voxels (true positives and true negatives). Figure  9  summarizes the results with respect to the provided vertebra segmentation. On average, the proposed method yields 89. 39 ± 5. 54 % of correct segmentation.
On the same dataset, the K-means segmentation provides 81. 65± 12. 23 % correct segmentation. These results imply that our method provide both good results and a small variability on the output. Note that these results concern only the vertebra of interest: a correctly labeled neighboring vertebra is ignored in the measurements. An illustration of the ground truth compared to a segmentation result is provided in Fig. 10. Errors are either false positive (type I error) or false negative (type II). False positive are most encountered in the presence of high-intensity elements, such as calcifications or ribs near thoracic vertebrae. On the other hand, false negatives are either missing voxels at the vertebrae boundary or missing voxels within the vertebral body. These results are satisfying, given that most error sources are known and that specific post-processing could easily remove them.
0001). However, there was no correlation with the decrease in tumor perfusion parameters  [24]. and high level of circulating PlGF at week 12 were associated with several pazopanib-specific toxicities and poorer efficacy  [27]. The role of pro-angiogenic factors in conjunctive tissue tumor treated with anti-angiogenic tyrosine kinase inhibitor warrant further clinical investigations. Our present study displays four limitations. In theory, the present findings required formal validation with an independent prospective chordoma patients. However, this validation is hardly feasible because (i) chordoma is an exceptional cancer (1 case per million of inhabitants), and (ii) sorafenib is not approved for chordoma treatment. However, we think that our findings are of importance since to our knowledge there is no established predictive factor in chordoma patients treated with antiangiogenic agents and because a phase II trial assessing regorafenib is ongoing (NCT02389244).
In the next years the cohort of patients treated with regorafenib might become the validation cohort of our study. The second major limitations of our study is the fact that we are not able to separate the prognostic and the predictive value of our findings. Natural history of chordoma is very slow and the gain of PFS described with molecular targeted therapy like sorafenib might be due to the indolent course of disease. Randomization is required to clearly identify the drug activity (predictive factor) and the natural history of the disease (prognostic)  [5, 28]. The current phase II trial assessing regorafenib and conducted by the French Sarcoma Group is a randomized phase II trial placebo versus regorafenib (NCT02389244). The internal comparator, the patients exposed to regorafenib, will be of major importance to identify prognostic factors and analysis the interaction between drug activity and natural course of the disease.
Statistical analysis Patient's characteristics were described using percentages and frequencies in case of categorical data and median and extreme values or means and standard deviation in case of continuous data. Biomarkers values at D1 and D7 were compared using paired Student t test or Wilcoxon rank test. Our clinical endpoint was the PFS defined as the time between inclusion and the date of progression according to RECIST 1. 1. The response to treatment was assessed according to the RECIST 1. 1 guidelines by comparing unidimensional tumor measurements (computed tomography scans) in pre-and per-treatment imaging studies at 2, 4, 6 and 9 months. An independent third party radiologist reviewed selected imaging studies carried out during the treatment period with the study drug to ensure the consistent and unbiased application of RECIST.
16, 2009)and after declaration to the French Health Products Safety Agency ("Agence Française de Sécurité Sanitaire et des Produits de Santé", date of approval: 1 June 2009). Informed consent was obtained from each patient. This study was registered in the European Clinical Trials Registry (EudraCT N° 2007-004651-10) and ClinicalTrial. gov site (Number: NCT 00874874). The study was conducted in agreement with the Declaration of Helsinki and the International Conference on Harmonization of Good Clinical Practice guidelines. http://www. cancer. gov/clinicaltrials/search/vi ew?cdrid=633547&version=healthprofessional).
Based on the observed pathological, morphological, and life-history criteria, the two most likely diagnoses are osteoid osteoma and osteoblastoma. Taking the demographic data for these two tumour types into account, both options seem possible: both are primary boneforming tumours, osteoblastic in nature; benign; have a predilection for males; and show the highest prevalence in juveniles and adolescents. Osteoid osteoma resembles the observed lesion in terms of size, as these tumours are usually less than 20 mm in diameter, with wellcircumscribed margins and being round or oval in form  23. McCall  22  notes that computed tomography is the most valuable method to investigate this type of lesion. Under CT imaging of osteoid osteoma a small lucency is often recorded, which may have a central high attenuation as a result of mineralisation, and surrounding sclerotic bone is noted with some thickening of the lamina or pedicle.
Statistical Analyses Data were analysed by means of IBM SPSS version 23. 0 (Statistical Package for the Social Sciences) (IBM Corp, Armonk, NY, USA). The analyses included descriptive statistics giving percentages, means and standard deviation. Differences between the non-overweight and overweight young adult groups were evaluated by chi-square and Mann-Whitney tests. All of the four point scale responses were dichotomized, so that often, occasionally, rarely and never were combined. In the binary logistic regression analysis, overweight was used as the dependent variable, and the other parameters were entered individually as independent variables (adjusted for age and gender). p < 0. 05 was considered to indicate a significant difference.
Papers involving FE analysis are now very common in dental research, and young researchers may wonder if specialised journals are not overwhelmed by FE studies. Unfortunately to our knowledge, a study providing a longitudinal overview of dental FE-related (DFE) literature does not exist. The aforementioned question prompted us to investigate whether authors and publishers in dental research are still interested by FE papers. This bibliometric study sought to quantify the evolution of the DFE literature during the last decade (from 1999 to 2010) using the SCI-expanded database of Web of Science ® (WoS, Thomson Reuters).
MATERIAL AND METHODS The data for this study was obtained in November 2011 from the SCI-expanded database of Thomson Scientific Web of Science TM (WoS). To retrieve a comprehensive set of DFE literature, all primary articles or reviews published in journals with at least "finite element" and one of the following keywords in the titles/abstracts were included: endodont*, dentist*, dental, periodont*, temporomandibul*, gingiv*, molar, incisor, "alveolar bone", orthodont*, dentin*, enamel, maxillar*, mandibul*, oral, caries, lingual, jaw, "root canal", prosthodont*, denture, premolar, where the asterisk replaces any subsequent string of characters. Data sets were selected, analyzed, and ranked in decreasing order of productivity by country and journal, using Microsoft Excel. Multi-authored publications were assigned equally to each country appearing in the author address field.
Publications The Number of Publishing Countries Doubled in One Decade (Table  1 ) The number of DFE publications retrieved and analyzed was 80 in 1999-2000 and 473 in 2009-2010. The percentage of DFE publications that was review articles remained stable between the two time periods (5% each). The percentage of DFE papers written in English grew from 97. 5% to 99% in the WoS database over the decade (data not shown). The number of countries publishing DFE literature doubled in one decade, from 24 to 54. The USA published the most at both time points, but its share declined by 10. 5% between 1999-2000 and 2009-2010. Over the same period, the European Union (EU)'s share declined a little bit less (by 8. 7%. ) A country could belong to the top 10 with only three publications in 1999-2000, whereas 16 publications were needed in 2009-2010.
First, the Science Citation Index (SCI) Expanded ® has coverage only since 1991 for 70% of the articles of full-length, English-language, author, abstracts, (http://images. webofknowledge. com/WOK45/help/WOS/h_database. html). The 1991 improvement of the coverage was associated with a sudden 2. 7 fold increase for dental literature in the WoS database between 1990 and 1991 (data not shown). However, the SCI-Expanded provides complete bibliographical information over 8,500 major international journals across 150 disciplines, dating back to 1900. Second, some journals are referenced later than others, and IF are released six months after the year of publication. As a consequence, we could not analyse accurately publications retrieved from the last couple of years. Third, in order to have bigger numbers of publication, we studied publications retrieved from periods of a couple years.
Nine fragments were placed in each petri dish and a 2-cm 2 piece of material was deposited on each of those fragments. Each dish was used for only 1 material, and 4 dishes were prepared for each material. The cultures were incubated at 37°C with 5% CO 2 for 7 days, after which the materials were https://doi. org/10. 5051/jpis. 2016. 46. 6. 362 Biocompatibility study on ceramics for dental abutment removed and stained with neutral red. Next, the total surface area covered by tissue was measured using a stereomicroscope equipped with a camera and Image J software (National Institutes of Health, Bethesda, MD, USA)  [16]. This area corresponded to the total surface of the cell layer minus the initial explant surface. Additionally, the cells were detached from the materials using 0. 025% trypsin-EDTA (Gibco™, Invitrogen) in Isoton ® II electrolyte solution (Beckman Coulter, Villepinte, France).
Allez. Par ici. Viens là" (UK version "On this side, pig. Come on. Over here. Come here". Animals were accustomed mainly to male voices in the facilities therefore we chose an average female voice to minimise the influence of a previous voice experience. The voice was recorded with a microphone (MKH 50 P 48 Sennheiser, Germany) with a microphone module and an acoustic foam windscreen (K6/ME66 Sennheiser, Germany). The microphone was connected to an audio digital portable recorder (Portable Solid State recorder, PMD661 Marantz Professional, The Netherlands; amplitude resolution: 16 bits; sampling rate: 44. 1 kHz) in WAV format. Recordings were prepared and fundamental frequency analysed with the Praat software (5. 2. 01, www. praat. org). Playbacks were broadcasted using a loudspeaker (MA-100su Mipro Electronics, Taiwan) at 80 ± 2 dB max sound pressure level (at 1 m from the source, determined using a sound level meter, SL-100 Voltcraft, Germany).
Data analysis The R software  [47]  was used for the statistical analysis of data. The "previous signals exposure test" (test A). Individual success rates were considered as significantly deviating from chance level for each signal when the number of successful trials was strictly above 13/19 trials (one-tailed binomial test, p = 0. 03). Mixed linear models were used to analyse fixed factor effects and their interactions on the success rates and on the individual latencies to visit the first bowl. "Signal" was used as a fixed factor and "piglet" as random effect in the nlme package  [48]. As conditions for parametric analyses were not met, even after transformation of the data, we used non parametric methods-Friedman and Mann and Whitney tests-to compare the individual latencies to visit the first bowl between signals for each trial outcome.
We used the nlme package  [48]  with "piglet" as random effect. Least square means were compared as post-hoc analyses using the lsmeans package  [49]. We ran a first set of analyses to compare data between the test B, C and D. We included in the model concerning the individual success rates the following factors as fixed effects: "test", "previous signals exposition" (signals+ and signals-groups) and their interaction. We added in the models concerning the individual latencies to visit the first bowl a "trial outcome" (successful or failed) factor and its interaction with the "test" factor. We ran the same analysis for the individual proportions of looks and the individual proportions of stares at the experimenter. A second set of analyses compared data between the sessions of each test, repeating the same models for each test with a "session" factor instead of the "test" factor.
However, in practice, since the demand of this product is high all year round (and not only in winter during the slaughter period of the local breeders), Corsican livers do not suffice to produce enough the volume of ficatelli required by the market. This deficit is covered by large numbers of livers from pigs produced under intensive systems in continental Europe being imported into Corsica to manufacture ficatelli, with a higher risk of being infected with HEV. Indeed, during a previous study on HEV contamination of ficatelli from Corsica  [13] , high sequence identities, as high as 97 to 99%, were observed between HEV from ficatelli (Genbank accession numbers KJ558437, KJ558440, KJ558441, KJ558442, KJ558445, KJ558448, KJ558478, KJ558481, KJ558494) and swine liver from continental France (Genbank accession numbers JF718820, JF718798, JF718817 JF718828, JF718797).
Conclusions In conclusion, this study shows that wild and domestic pig reservoirs of HEV in Corsica are highly exposed to HEV. The phylogenetic analysis of the sequences amplified in both reservoirs was performed in parallel to this study and has shown that the two sequences of pure wild boar and domestic pig (Genbank accession number KT334196 and KT334197) shared 97. 5% identity with a wild boar sequence (KT334191), suggesting that transmission between pure and hybrid forms of wild boar and domestic pigs occur in Corsica  [42]. Hybrid wild boars seem to play an intermediate role in this dissemination of HEV and perhaps other pathogens between populations of domestic pigs and wild boars that requires further investigation. The high levels of prevalence detected in all varieties of Sus scrofa are particularly relevant in terms of public health risk, considering the frequent contacts of local stakeholders with domestic pigs, wild boars and their derived products, the local tradition of processing and consuming pork products with raw pig liver, and the popularity of hunting and extensive pig farming activities in Corsica.
Quantitative information about equine mortality is relatively scarce, yet it could be of great value for epidemiology purposes. Several European projects based on the exploitation of data from rendering plants have been developed to improve livestock surveillance. Similar data are available for equines in France but have never been studied to date. The objective of this research was to evaluate the potential of the French Ministry of Agriculture's Fallen Stock Data Interchange (FSDI) database to provide quantitative mortality information on the French equine population. The quality of FSDI equine data from 2011 to 2014 was assessed using complementary data registered in the French equine census database, SIRE. Despite a perfectible quality, the FSDI database proved to be a valuable source for studying the basal patterns of mortality over time in the French equine population as illustrated by the spatial representation of the number of deaths.
This kind of data is also available in France for the equine population, but their usefulness for surveillance purposes has never been evaluated. Indeed, the equine data collected by fallen stock companies have never been studied nor a quality assessment carried out, although this is a prerequisite to their analysis and interpretation of results  (Boden et al. , 2012; Bronner et al. , 2015). The overall objective of this study was therefore to assess the quality of the French Ministry of Agriculture's Fallen Stock Data Interchange (FSDI) database and to evaluate its potential for providing quantitative mortality information on the French equine population. In France, the main source of equine mortality data is the FSDI database, as all equine cadavers have to be collected by one of the fallen stock companies working in mainland France (law 75-1334 of 31  December 1975).
The FSDI database is composed of removal visits, each visit corresponding to the removal of one or more animals from the same location. The main data collected for each visit are the date and time of the removal request, the date of removal, the zip code of the removal location, the number of animals collected and their age/breed category, the individual identification number and an estimation of global cadaver weight. Additional individual equine data (date of birth and exact breed) are available in the France's centralized SIRE database, which collates the identification data for all equines born in or imported into France, managed by the IFCE (French horse and riding institute). These SIRE data can be considered as a gold standard to determine the age and the breed category of equines. All the data management and analyses were performed with R software (R core team, 2015, Accessed April 5).
To explore equine mortality data, we used the 139,821 visits registered in the FSDI database from January 1st 2011 to December 31st 2014 since records before 2011 were not comprehensive. Ninety-five visits were considered erroneous and were eliminated from the dataset. From the 139,726 selected visits we extracted a subset of 19,192 animals for which the identification number registered in the FSDI database was traceable in the SIRE database (Table  1 ). Data quality was assessed in two steps. Firstly we evaluated the completeness and accuracy of the important fields on the 139,726 visits included in the study. Secondly we quantified the accuracy of age/breed categorization on the data subset of 19,192 individuals using the SIRE database information and indicators designed to evaluate the performance of a biological test: sensitivity, specificity and both positive and negative predictive values for each category.
1 ). The completeness and accuracy of temporal parameters were satisfactory and provided an approximation of the date of death based on the date of the removal request (available in 98. 5% of cases) or the date of removal (1. 5%). The age/breed category was always available. Nevertheless, the subset (19,192 individuals) used for assessing the quality of age/breed category data was not representative of the FSDI database regarding the distribution of age/breed categories (Chi-square test, p b 0. 05), in particular because of an under-representation of young animals (Table  1 ). The accuracy of the age categorization in the FSDI subset varied greatly according to the age group, with very low sensitivity and high specificity for "stillbirth and foal" and, in contrast, high sensitivity but low specificity for "adult" (Table  1 ).
The classification errors mainly concerned "stillbirth and foal" categorized by mistake as "yearling". The accuracy of the breed categorization for adults in the FSDI subset (18,197 individuals) depended on the group with the best sensitivity and specificity values for "donkey" (Table  1 ). The categorization was correct for 16,590 (91. 2%) animals and the classification errors mainly concerned "saddle horse" categorized by mistake as "pony" and conversely "pony" categorized by mistake as "saddle horse". Despite a perfectible quality, the FSDI database appears to be a valuable source of quantitative equine mortality data. The completeness and accuracy of temporal parameters (dates of removal requests and visits) were excellent and we estimated that they were a good proxy for the date of death.
The location of mortality was also assumed to be correct as zip codes for the removal location were always complete and corresponded to actual 'communes' (the smallest administrative units in France). The FSDI database also proved useful in correctly quantifying equine mortality since the completeness of the number of animals removed per visit was also very satisfactory. Finally, the completeness of the categorization by age/breed groups was excellent, probably due to the use of this field for billing purposes. Nevertheless, it was found that the quality of categorization varied greatly with equine type, even though the non-representativeness of the data subset used for the evaluation did not allow us to extrapolate the results to the FSDI database. The main shortcoming of the age categorization appeared to be an unclear delineation of the age categories for young animals, with an overlap between the current two categories ("stillbirth and foal" and "yearling").
The issue of age categories in young animals is a major challenge, but could be overcome. Indeed, if the animal is already identified, registration of its identification number would provide access to its exact age in the SIRE records. Moreover, for foals under 6 months that are often non-identified, the systematical registration of their dam's identification number would give access to the mating or insemination date of the mare recorded in the SIRE database, and thus indirectly to an estimation of the foal's age. For adult equines, the categorization by breed group appeared reasonably satisfactory, but the "saddle horse" category seemed too broad to allow a detailed description of equine mortality by breed. Thus, the systematic registration of identification numbers is the most crucial improvement required of the FSDI database, as this is the link to individual data recorded in the SIRE database.
It would therefore allow very detailed and representative descriptions of equine mortality by sex, age and breed subpopulations (including estimation of death rates and survival analysis) for epidemiology purposes, although some other FSDI database limitations must be mentioned such as its possible incompleteness (due to the possible illegal burial of some small cadavers), the inability to distinguish natural deaths from euthanasia and the lack of information on the cause of death. Moreover, the systematic registration of identification numbers would make possible the combined use of both FSDI and SIRE databases that in the future could provide a better knowledge of the size and location of the equine population, which is fundamental for epidemiologic surveillance  (Boden et al. , 2012; Robin et al.