dataesr/scientific-paragraphs-categorization huggingface dataset:
Hunting statistics The national and cantonal hunting bags and the number of foxes found dead from 1958 to 2017 were obtained from the free-access website of the national hunting statistics: https ://www. uzh. ch/wild/stati c/jagds tatis tik/. Normalized hunting bags in relation to the preferred habitat of foxes (HIPD: hunting indicator of fox population density, i. e. number of foxes shot/terrestrial surface (km 2 ) below 2000 meters of altitude  [55] ) were used as an index of fox density in the respective areas  [56]. The cantonal HIPDs during four 4-year periods  (before, 1946-1950; during, 1980-1984 ; and after the rabies epidemics, 1993-1997 and 2013-2017), the respective factor of increase Fig. 3  Spatiotemporal distribution of red foxes with sarcoptic mange in Switzerland. Municipalities from where red foxes (Vulpes vulpes) were submitted in the framework of the general health surveillance programme for wildlife (1958-2018; source: FIWI) and during the initial part of the rabies eradication campaign ; data on mange not available for 1974 and 1977; source: SRC) are illustrated with different colours depending on whether foxes had sarcoptic mange or not and whether they were tested positive or negative for rabies.
All five data sources converged towards similar trends, complementing and overlapping each other, both geographically and in time. Improvement of wildlife disease surveillance has progressively delivered better information, demonstrating the relevance of wildlife health surveillance programmes to produce reliable information on wildlife disease epidemiology, which allows informed management decisions  [105, 106]. Although the strength of this study lies in the combination of multiple data sources, each single method had limitations. The main limitation of the review of the historical literature included the difficulty to detect all existing documents due to lacking databases  [107]. The use of HIPD is controversial but can be useful to evaluate longterm population trends in large areas  [108, 109].
Acknowledgements We thank the hunting offices of all Swiss cantons and their respective hunters and professional game-wardens for participating in the questionnaire survey and for submitting carcasses for post-mortem examination. We acknowledge the numerous KORA collaborators for the assessment of the camera-trap pictures. We thank  Reto Zanoni  for providing access to the database of the  SRC  and for the permission to use these data and,  Andreas Kappeler  and  Alexander Wandeler  for the collection of data about mangy foxes. Many thanks also go to  Manuela Weber  and  Rebecca Hari  (deceased) for their support with the data management of the questionnaire survey, to  Nadia Robert  and former pathologists for necropsy and histopathology supervision, to the numerous FIWI assistants who performed fox necropsies, to  Urs Breitenmoser  for his contribution to the interpretation of fox population dynamics and to  Iris Marti  for critical reading of the manuscript and support with statistical analyses.
This paper focuses on the syntactic annotation of the corpus and the constitution of a 150,000 words gold standard treebank. The current state of the treebank is accessible at SurfaceSyntacticUD. github. io and can be queried directly at http://match. grew. fr/?corpus=SUD_Naija-NSC@dev. The treebank is currently still undergoing manual and automatic validation. An automatically converted UD version of our treebank will extend the current UD Naija-NSC (available since UD 2. 2  (Nivre et al. , 2018) ) with the upcoming release. Once the 150k words gold section will be completed, the rest of the corpus will be parsed automatically, together with the 250k words of spoken (historic) Nigerian Pidgin data from  Deuber (2005) , resulting in a treebank of about 750k words. Our workflow is explained in section 2, especially the choice of Surface-Syntactic UD, rather than UD.
Corpus Metadata. The variationist analysis we have chosen implies collecting samples representing different types of speakers, and different types of functions. A questionnaire was administered and recorded to provide the relevant metadata about the speakers: time, place and conditions of recording; sex, age, education, professional activity, geographic origin, linguistic background and history. The information was entered into an IMDI 1 database produced using the metadata editor Arbil 2  (Withers, 2012). Transcription. Naija is commonly written, in particular on the internet, in forums, but also for example on the BBC website. Although an official orthography or normalization has not taken place, the speakers of Naija have strong opinions on how most words have to be spelled, and we decided to follow these evolving conventions.
This type of experiment is also important to set a baseline for the development of a Naija parser, to be used for parsing the rest of the NSC corpus (which is transcribed and macrosyntactically annotated) as well as for parsing other spoken and written data without markup. We used a sample of 52k words, with 90% training and 10% test data on the Mate parser. While the POS tagging scores are as expected very similar whether macrosyntactic annotation is present or not, we obtain an LAS error reduction of 11% and a UAS error reduction of 18% through macrosyntactic annotation, see Unsurprisingly, the syntactic functions which most benefit from this type of markup are those that are targeted by the annotation, such as piles (paradigmatic relations like conj:coord, conj:dicto, compound:redup) and coordinators (cc).
Conclusion We have described the workflow for the development of the gold section of the NSC treebank in the SUD annotation scheme, and we have shown the SUD analysis of some interesting syntactic constructions of Naija. In parallel with the treebank construction we develop various interfaces to access the audio corpus, the transcription, and the different annotations. For example the most recent version of the SUD syntactic annotation is accessible at match. grew. fr/?corpus=SUD_Naija-NSC@dev. In order to be part of the UD treebank family, an automatically converted UD version of the treebank will also be distributed, although the current UD platform does not foresee the joint distribution of the audio data. The increasing interest in spoken data will surely bring the UD community to discuss the format that will best allow for phonosyntactic studies.
Acknowledgments This research is financed by the  French National Research Agency  via the project  ANR NaijaSynCor. We would like to express our gratitude to the Nigerian annotators:  Onwueqbuzia Emeka Felix ,  Ajede Chika Kennedy , and  Tella Sansom Adekunle. The quality of the treebank has been largely enhanced by the constant interaction with  Bruno Guillaume , the developer of the Grew platform. Thanks also to the anonymous reviewers of the SyntaxFest 2019 that helped us to clarify this paper.
, 2018; Elder and Hokamp, 2018; King and White, 2018; Madsack et al. , 2018; Puzikov and Gurevych, 2018; Singh et al. , 2018; Sobrevilla Cabezudo and Pardo, 2018). In this paper, we present a brief overview of the LORIA / Lorraine University system. We participated in the shallow track, and delivered solutions for all the languages proposed by the organisers. We also participated in generating output for all the types of corpora: in-domain, outof-domain, and predicted by syntax parsers. Re-sults on the development set are presented, and the system performance for each step of surface realisation is evaluated and discussed. All the code and experiments are available at https: //gitlab. com/shimorina/msr-2019.
Morphological Realisation (MR) Morphological paradigms were learned from pairs of (lemma, POS+features) extracted from the training data (the upos and features fields from CoNLL) using Aharoni and Goldberg (2017)'s model. Lemmas with no morphological features were not used. Since features are not provided for Chinese, Japanese, and Korean treebanks, the morphological realisation module was not trained for those languages. Instead, during the inflection phase (a) for Chinese, analytic language, lemmas were copied verbatim to the ouput; (b) for Korean, agglutinative language, morphemes in a lemma were glued together, and then the lemma was copied; (c) for Japanese, synthetic language, a dictionary of the form (lemma+POS: wordform) was constructed from the training data and looked up. If a key 'lemma+POS' was not present in the dictionary, the lemma was copied to the output verbatim.
The example of the latter is an adjective in Russian, which can have different forms in the accusative case depending on animacy of the noun it modifies (animacy in that case is an underspecified feature). To measure the effect on scores, when converting a sequence of lemmas into a sentence, we applied MR+CG to gold sequences of lemmas (they have the same word order as the reference). Results are shown in Table  2. In general, high accuracies of MR alone (word level, Table  1 ) do not guarantee good performance while evaluating on the sentence level. That type of evaluation enabled us to have more insight into the data used. Some of our findings are listed below. • English: a discrepancy in performance across datasets. The sources of the en ewt ud corpus are blogs, social networks, reviews, emails, where the use of contractions (isn't, ain't, etc) is dominant comparing to formal style.
Since the contraction generation was not applied for English, scores for this particular dataset are lower than for others. • Arabic. We conjecture low scores for the high variability of forms (cf. Table  1 ) and contractions (We did not develop a module for handling contractions in Arabic. ). For instance, some diacritics are optional (e. g. , hamza with alif), so a word form can be written with or without them, being a valid word form in both cases. • Japanese. MR module was not developed for Japanese, so a look-up dictionary based on training data was not sufficient to handle the morphology. The high number of ambiguous forms also impacted the scores, as in the case of Arabic. • Portuguese. The pt gsd ud corpus is not annotated with morphological features, hence 57. 04 score in BLEU compared to 94.
Patient #19 presented with bruises and frequent epistaxis, patient #90 had post-traumatic oral bleeding, spontaneous hematuria and rectal bleeding, and patient #214 suffered from provoked hematoma and severe menorrhagia resolved by replacement therapy. Next-generation sequencing, besides confirming the presence of the causative variants identified by the Sanger approach, also revealed several deep intronic substitutions. Among them, only those with a coverage of 30x and observed in databases with a minor allele frequency (MAF) <0. 05 were analyzed further. Six deep intronic substitutions matched these criteria (Table  2 ). The c. 571+78G>A change, whose pathogenic effect is supported by its co-segregation with the disease phenotype in the family pedigree of patient #28 (Figure  1 ), was the most frequent in our series, being present in ten alleles from unrelated patients living in various areas, including France, North Africa and Lebanon (Table  1 ).
Discussion Uncharacterized F7 pathogenic alleles are mentioned in all patient databases, and NGS would represent a powerful tool to tackle this; however, so far, this has not been fully explored. Here, we applied this approach in 13 FVII deficient patients who were only partially characterized through conventional sequencing, and identified a panel of deep intronic substitutions as candidates to explain the reduced FVII:C levels in patients. However, as for the numerous deep intronic nucleotide changes identified by NGS and associated with inherited diseases, their pathogenic role requires experimental support. The evidence for the pathogenicity of deep intronic variations relies on several clinical and molecular observations. The first aspect to consider is their virtual absence in databases.
This led us to exclude from our selection the c. 64+305G>A and c. 291+846C>T variants, with a minor allelic frequency of 0. 005 and 0. 004, respectively. The same applies to the c. 681+132G>T change, reported in dbSnp databases as rs752129277 but with an estimated frequency of <0. 0004. Another aspect that could suggest the pathogenicity of the nucleotide changes is their distribution among affected relatives or non-related individu-als. This was the case of the c. 571+78G>A, c. 572-392C>G and c. 806-329G>A changes that occurred in eight, two and two unrelated FVII-deficient patients, respectively. Altogether these elements prompted us to explore the impact of these three variants on the splicing process through the expression of minigenes in eukaryotic cells, a well-proven approach used to dissect splicing abnormalities.
4, 13, 14, 42, 45 egarding the c. 571+78G>A variant, the in vitro characterization demonstrated an aberrant splicing profile that was consistent with the FVII:C levels reported in patients. Interestingly, the amount of correctly spliced transcripts (approx. 3%) reflects the FVII:C levels (3% and <1%) in the two c. 571+78A homozygotes (patients #15 and #90) (Table  1 ), which explains the asymptomatic or moderate clinical phenotypes. This finding is also consistent with the observation that the mutation co-segregated with the disease phenotype through the pedigree of patient #28, and the 50% FVII:C levels detected in the heterozygous mother. It is interesting to note that the c. 571+78G>A mutation, albeit absent from databases, occurred in eight apparently unrelated patients in our cohort. The polymorphic analysis in the homozygous patients led us to identify two different haplotypes that suggested two distinct mutational haematologica | 2020; 105(3)  Concerning the c.
Acknowledgments The authors would like to thank  Dr D. Schümperli  for sharing the U7-SmOPT construct. This research was supported by grants from  Bayer  (  2017-INT. A-BD_001  to  D. Balestra ), the  University of Ferrara  and the  University of Montpellier. The authors gratefully acknowledge  H. Chambost ,  K. Pouymayou  ( Marseille) ,  S. Clayssens  (Toulouse),  R. D'Oiron ,  I. Martin-Toutain  (Paris),  V. Gay  (Chambery),  Y. Chevalier ,  S Le-Quellec ,  S. Meunier ,  L. Rugeri  (Lyon),  C. Montaud  (Pau) and  R. Navarro  ( Montpellier, France ) for sending samples and  L. Bison  for technical assistance.
Proband Origins FVII:C (%) FVII:Ag(%) Conventional sequencing Polymorphic pattern NGS sequencing c. 325_324ins/ Mutation Zygosity p. Arg413Gln Additional Zygosity nucleotide change : SEQUENCE Pilot ® module SeqNext, version 4. 3. 1 (JSI medical systems GmbH, Ettenhein, Germany) and SeqOne® (https://app. seq. one). The dataset had a mean coverage of over 300x. For each nucleotide of interest, the sequence depth was at least of 30x and the Phred-based quality score above Q30. #17 Maghreb countries 3 uk p. Met358Ile 10 het A1A1/M1M1 c. 571+78G>A het #19 France 2 <5 p. Met1Val 10 het A1A2/M1M2 c. 571+78G>A het #31 France <1 19 p. Cys162Tyr 10 het A1A1/M1M1 c. 64+305G>A and het c. 806-329G>A #113 France 1 66 p. Arg364Trp 30 het A1A1/M1M1 c. 571+78G>A and het c. 291+846C>T #262 France 3 uk p. Gln160Arg 31 het A1A1/M1M1 c.
Position of the point mutation is referred to the 5' splice site (5'ss) or 3'ss. RS: reference SNP ID number; MAF: minor allele frequency, based on 1000Genome project (http://www. internationalgenome. org). F7 gene reference sequence is NG_009262. 1. NNSPLICE 0. 9 software (www. fruitfly. org/seq_tools/splice. html) was used to predict and calculate the 5'ss or 3'ss of the score. Introns are indicated by legacy nomenclature. wt: wild-type.
To investigate whether CFI had any explanatory value above and beyond current FI, for outcomes where we had found significant effects involving current FI, we then compared the basic model to models in which CFI had also been added, in the five possible ways (namely: only main effect of CFI, main effect plus interaction with gender; main effect plus interaction with AFI, main effect plus both 2-way interactions; main effect plus both 2-way and 3-way interactions). We retained as our final model that with the lowest AICc value. These models are summarised in table  3. For the general linear models, FI predictors were standardized and centred to facilitate interpretation of interactions. All analyses were run in R 3. 3. 3. software (R Core Team, 2016). R scripts and raw data from the study are freely available via the Zenodo repository at: https://doi.
However, the correlations in the dataset between liking of the foods, calorie consumption and BMI are very close to zero. Liking for a food is certainly not the only determinant of consumption  (Brunstrom & Rogers, 2009; Drewnowski, 1997; Finlayson et al. , 2007) , so the low correlation between liking and consumption is not in itself surprising. The mono-factorial hypothesis that variation in liking for foods (or energy-dense foods in particular) explains most of the individual variation in obesity is not well supported by evidence  (Drewnowski, 1997). However, there is a case for a more subtle role of individual differences in hedonic response to particular foods in the pathway to weight gain in at least some individuals  (Finlayson et al. , 2007; Salbe, Delparigi, Pratley, Drewnowski, & Tataranni, 2004).
For example, variation in liking may inhibit flavour-specific satiety for particular types of food, or drive consumption in the absence of homeostatic need (see  Nasser, 2001  for review). Thus, it would be possible for liking of energy-dense foods to be on the causal pathway liking FI to weight gain, without needing to claim that liking for energy-dense foods is the only or main determinant of body weight. However, our data to not directly demonstrate such a role: since liking for chocolate was not significantly related to calories consumed or body weight, it cannot formally be considered a mediator in this dataset. An innovation of our study was the development of new questionnaires for adult FI (AFI) and FI in childhood (CFI). The adult scale broadened the focus of the USDA scale on financial constraints to obtaining food, and instead encompass the experience of irregularity in the food supply, regardless of the reasons for it.
With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort we designed a competition to extensively characterise and rank the performance of 2D and 3D single molecule localization microscopy software packages. We generated realistic simulated datasets for popular imaging modalities -2D, astigmatic 3D, biplane 3D, and double helix 3D -and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software and provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions. This resource allows researchers to identify optimal analytical software for their experiments, allows 3D SMLM software developers to benchmark new software against current state of the art, and provides insight into the current limits of the field.
(PSF). Despite the widespread use of 3D localization microscopy, and challenging nature of 3D SMLM image processing, the performance of software for 3D single molecule localization microscopy has previously only been assessed for 2-3 software packages at a time, and without standard test data or metrics  [11] [12] [13] [14]. In the absence of common reference datasets and reliable assessment, it is not possible to objectively assess how different software affect final image quality, or which algorithmic approaches are most successful. Crucially, end-users cannot determine which 3D SMLM software package and imaging modality is optimal for their application. We therefore ran the first 3D localization microscopy software challenge, to assess the performance of 3D SMLM software. We assessed software performance on simulated datasets designed for maximum realism, incorporating experimentally derived point spread functions, using biologically inspired structures, using signal to noise levels based closely on common experimental conditions, and modelling fluorophore photophysics.
Competition design We established a broad committee from the SMLM community, including experimentalists and software developers, to define the scope of the challenge, ensure realism of the datasets and define analysis metrics. We opened this discussion to all interested parties in an online discussion forum  17. In 2016, we ran a first round of the 3D SMLM competition with explicit submission deadlines, culminating in a special session at the 6th annual Single Molecule Localization Microscopy Symposium (SMLMS 2016). Since then, the challenge has been opened to continuously accept new entries. Thirty-six software packages have been entered in the competition thus far, including four packages used in commercial software (Table  S1 , Supplementary Note 1). Participation in the competition actually led at least eight teams to modify their software to support additional 3D SMLM modalities, showing how competition can foster microscopy software development.
Realistic 3D simulations Testing super-resolution software on experimental data lacks the ground truth information required for rigorous quantification of software performance. Therefore, realistic simulated datasets are required. A critical challenge to in simulating 3D SMLM data was accurate modeling of the experimental microscope PSF for each 3D modality. 3D SMLM inherently involves addition of aberrations to the microscope PSF to encode the Z-position of the molecule. For the PSF models included in the competition: astigmatic (AS), double helix (DH), and biplane (BP), we observed that the PSFs showed complex aberrations not well described by simple analytical models (Fig. S1 ). Even experimental 2D PSFs showed significant aberrations away from the focal plane (Fig. S1 ). We thus combined experimental 3D PSFs with simulated ground truth by performing simulations using PSFs directly derived from experimental calibration data (Fig.
Clearly, the quality of the image reconstruction depends strongly on choice of 3D software. To investigate the reasons for software variation, we inspected plots of software performance as a function of axial position in the low density, high SNR dataset for best-in-class and representative middle-range software (Fig. S4A ). We observed that a key cause of the spread in software performance is variation in software performance away from the focal plane. Near the focal plane, most software packages perform well. However, the axial and lateral RMSE away from the plane of focus is significantly higher for the best in class software, and the Jaccard index is also slightly improved (Fig. S4A ). This is also visibly apparent in the super-resolved images (Fig. 4A ). We observed that best-in-class software had a Z-range (the FWHM range of axially resolved software recall, Methods) of 1170 nm, greater than twothirds of the simulated range.
Outside this range, the recall and Jaccard index dropped sharply, probably due the large increase in PSF size and decrease in effective SNR at large defocus (Fig. S1 ). When we examined results for the low SNR, low density dataset (Fig. 2A , 3F), we found an expected two-fold degradation in best-in-class RMSE (lateral RMSE 39 nm, axial RMSE 60 nm), due to the decrease in image SNR. However, the best-in-class software (SMolPhot 20 ) Jaccard index was effectively constant between the low and high SNR datasets (86 % vs 85 %), although the Z-range did drop at lower SNR (930 nm vs 1120 nm). The best astigmatism software packages were thus remarkably good at finding spots at low SNR, even away from the focal plane. We compared best-in-class software performance to Cramer-Rao lower bound (CRLB) theoretical limits (Fig.