dataesr/scientific-paragraphs-categorization huggingface dataset:
We used Latin hypercube sampling to select 100 combinations of parameter distributions, corresponding to 100 sets of simulations, with the function randomLHS in the R package lhs (Table  S3 ). For each set of simulations, we performed 500 replicated simulations of community dynamics in each food web scenario and 100 replicated simulations for each value of s in the complex community scenario (Fig. S7 ). All model simulations were performed using the function lsoda from the R package deSolve  (38).
ACKNOWLEDGMENTS. We thank  Dave Cruse ,  Sam McNeil ,  Meike Simms ,  Ollie Thomas , and  Calvert Mason  for help with the fieldwork. We thank  Angus Buckling ,  Enric Frago ,  Colin Fontaine , and  Georgianne Griffiths  for comments and discussion. The data reported in the paper are presented in Datasets  S1-S3. The research leading to this paper was funded by  Natural Environment Research Council  Grant  NE/K005650/1  (to F. J. F. v. V. ).
Recent studies revealed that the call of the common cuckoo Cuculus canorus has more inter-individual than intra-individual variation and that the number of syllables depends on environmental conditions, but also the presence of male and female conspecifics. However, still very little is known about how song varies at a global scale, especially considering the wide distribution of this species across most of Europe and Asia. Xeno-canto. org is a vocalization repository for birdsong. We used xeno-canto. org as a data source for investigating the variables that affect the number of syllables in cuckoo calls at a large spatial scale. At a very broad geographical scale, the number of syllables in cuckoo calls predicted bird species richness. Additionally, female calls were associated with shorter males calls, and there was a positive correlation between the interaction between female calls and the number of host races parasitized by the cuckoo.
Collection of data at continental and global scales produces hundreds of millions of observations of thousands of species every year  20. From websites and social media to smartphones, apps, low-cost sensors and search engines data capture become easier and faster  21, 22. The recent availability of 'big data' associated with predictive analytics have profound implications for biological recording activities. An example of globally disseminated resources is www. xeno-canto. org (Xeno-canto, XC), a non-profit website set up to share recordings of bird sounds worldwide  23, 24. Its main goal is to improve knowledge of bird sounds by increasing accessibility and diffusion of bird sound recordings from across the globe  25. Thereby, Xeno-canto data can help improve our knowledge of the complexity of cuckoo calls, and more specifically, the factors that cause such variation on a broader global scale.
Results From the Xeno-canto database source, we identified and analysed 484 call recordings of the common cuckoo from 29 different countries in Europe, Asia and Africa (Fig. 1 ). Most records were from Germany (21. 0%), Bulgaria (12. 4%) and France (9. 1%). Call recordings were registered in 22 different years during 1982-2016. More than 60% of call recordings were registered from 2014 to 2016. Cuckoo call activity patterns. Cuckoo calls were recorded practically throughout the day (ESM, Fig. 1 ). The time of the day with more recordings was between 04:00 to 08:00 (27. 5% of recordings). Conversely, from 12:00 to 16:00 cuckoo calls reached a minimum at 8. 9%. Cuckoo calls were also registered during the night between 20:00 and 04:00 (12. 8%) (ESM, Fig. 1 ). The number of syllables of cuckoo calls was not significantly associated with the date, time of day and duration of records.
Discussion The opportunity for access to a huge amount of data from social media and citizen science projects is changing the way in which scientific studies and analyses of biological records are performed. Such studies allow for analyses at broad spatial and temporal scales, as well as promising to connect the efforts of experts and non-experts in science  20. We explored the characteristics of the calls of male cuckoos based on long-term recordings and calls from across a wide geographical range from the online website Xeno-canto. org. Although the calls of the common cuckoo from the Xeno-canto database derive across Europe, Asia and Africa, most recordings were uploaded from Germany, Bulgaria and France. A similar heterogeneous source of data was observed in a project studying the song dialects of the yellowhammer Emberiza citronella  26.
However, the range in the number of syllables per call reported here was much more variable than in long-term studies in Ukraine and Denmark  27, 28. It is often assumed that the timing of bird calls is related to weather and the function of calls. Therefore, passerines with calls having a function in the context of sexual selection sing mainly in early morning and at dusk  14. The calls of the common cuckoo have not only a function in sexual selection, but may also affect potential hosts  29, 30. We hypothesize that the timing of calls fits the activity of hosts. The Xeno-canto database consisted of cuckoo calls recorded throughout the day. However, most calls were from early morning to midday, while cuckoo calls reached a minimum in the afternoon similar to the diurnal pattern of singing in other bird species  14.
Moreover, Møller et al. (2017) suggested that cuckoo calls are reliable signals of habitat quality expressed as the number of breeding bird species. Here we extended this pattern to a broad geographical scale, across the entire geographical range of the cuckoo. In conclusion, a citizen science project using data from Xeno-canto. org allowed collection of a large number of cuckoo calls from Europe, Asia and Africa. When we analyzed Xeno-canto data we found that cuckoo call characteristics were related to the number of syllables of cuckoo calls and species richness (i. e. a positive correlation with bird species richness). There was also an intra-specific positive relationship between the interaction between female calls and the number of hosts races. Previous ecological studies used big data from citizen science and social media projects  39, 40  , and these studies suggest that social media are changing the approach used in ecological and conservation research.
Methods Data collection. We used Xeno-canto (http://www. xeno-canto. org/) as a data source for common cuckoo call recordings. Even if Xeno-canto mainly focuses on male cuckoos, females are occasionally recorded. Each recording was analysed and the following data were extracted from the dataset: sex (male; female if any; however we have to emphasize that normally recordings were dedicated to males, and that only sometimes were female calls recorded, confirming that the female was present close to the male); number of syllables; time of day (min:sec); date (year-month-day); geographical location (country, GIS coordinates: latitude, longitude); bird species in background; observer/recorder name and catalogue number.
Statistical analysis. We tested for spatial auto-correlation (SAC) of the data by using Mantel tests  48  , based on Monte Carlo permutations (999 randomizations) to test for statistical significance  49. In this study, the Mantel statistic r M evaluates the similarity between the number of syllables among sample sites and the geographical distance among these sites  50. Study sites were treated as statistically independent observations because the spatial autocorrelation in the data was not significant (r M = -0. 033, p = 0. 843, n randomizations = 999). We performed a principal components analysis (PCA) in order to avoid redundancy among variables, as a potential cause of multicollinearity, thereby removing strongly correlated predictors  51. From PCA analysis we selected the following eight descriptors: female recording, date, hour of day, duration of record, number of host races, cuckoo population density, species richness and latitude, adequate to describe the effects of the number of syllables of cuckoo calls.
We used Generalized Linear Mixed Models (GLMM), using the package 'lme4'  52, 53  to explore variation in cuckoo calls in relation to environmental variables and inter-and intraspecific characteristics. The number of syllables was log 10 -transformed and models were fitted supposing a log-normal distribution after exploration of the distribution of this variable, as suggested by Box and Cox 54 using the package 'MASS'  55. The number of syllables in cuckoo calls was used as the response variable, while female call, date, hour of day, number of host races, cuckoo population density, bird species richness and latitude and longitude were used as predictors. The interaction between year and country were added as a random factor in the statistical model. The 'best' model explaining greater variation in data was assessed using Akaike's Information Criterion (AIC)  56.
Viruses and Reagents TRI, an in-house clinical isolate (no sequence data available yet), 3 low passage HCMV laboratory strains (Toledo, TB40/E-GFP and VHL/E; a gift from Dr. Christian Sinzger)  [24, 25] , and BAC4-based HCMV gB-mutated viruses were propagated on MRC-5 cells and used as clarified viral supernatants for trans-infection experiments at a multiplicity of infection (MOI) ranging from 2 to 10. Cytomegalovirus (CMV) supernatants were also tittered by quantitative polymerase chain reaction (qPCR) as described elsewhere  [26]. Chinese hamster ovary (CHO)-derived recombinant HCMV gB and human immunodeficiency virus (HIV)-1 IIIB gp120 were purchased from Sanofi Pasteur (Marcy l'Etoile, France) and ImmunoDx (Woburn, MA), respectively. Glycoproteins were used either as purified or fluorescence-conjugated reagents (Molecular Probes, Thermo Fisher Scientific, Waltham, MA).
There is active development of parallel corpora in this domain (see the recent survey in  (Névéol et al. , 2018) ). In this year alone, three new corpora have been published in a single conference: a compilation of full texts from the Scielo database for English, Portuguese, and Spanish  (Soares et al. , 2018) , medical documents and glossaries for Spanish/English  (Villegas et al. , 2018)  and a biomedical corpus for Romanian  (Mitrofan and Tufis, 2018). However, in spite of the growing number of parallel corpora and the many open source tools for MT (e. g. , Moses  (Koehn et al. , 2007) , OpenNMT  (Klein et al. , 2017)  and  Marian (Junczys-Dowmunt et al. , 2018) ), there is still no ready-to-use tool for automatic translation of biomedical publications for any language pair. With the aim of fostering advances in this field, we organized the third edition of the Biomedical Translation Task in the Conference for Machine Translation (WMT).
The number 120 accounts for possible errors in the preprocessing of the abstract in order to have a final test set of 100 abstracts to be split into the two translation directions. The documents were automatically split using the Stanford CoreNLP tool and the respective available models for each languages, i. e. , Chinese, French, German and Spanish  (Manning et al. , 2014). 2 Since for Portuguese and Romanian no models are available in the Stanford CoreNLP tools, we used models for other similar Roman languages (Spanish for Portuguese and French for Romanian). The sentences were then automatically aligned using the GMA tool for which we provided a list of stopwords for each language. 3 After a short analysis of the alignment of the Chinese/English abstracts, and given the bad alignments that we obtained, we carried out a new automatic alignment using the Champollion tool  (Ma, 2006).
The authors highlight that the word segmentation used on the German language for both translation directions were responsible for the good performance of the system in the human evaluation. TFG TALP UPC (Technical University of Catalunya, Spain). For their system that provides translations into English, the TGF TALP UPC team participated with a Transformer architecture  (Kaiser et al. , 2017; Vaswani et al. , 2017)  using both single-language and multi-source systems  (Tubay and Costa-Jussà, 2018). The systems were trained on the Scielo and Medline titles made available by the shared task in the last years. The multi-source systems utilized a concatenation of training data from es/en, fr/en and pt/en. UFRGS (Universidade Federal do Rio Grande do Sul, Brazil). The UFRGS team participated with two runs based either on Moses  (Koehn et al.
,   2007) or OpenNMT  (Klein et al. , 2017)  systems  (Soares and Becker, 2018). Training data was prepared by concatenating several in-domain and outof-domain resources. The in-domain corpora included scientific articles (full texts) from Scielo, the UFAL medical corpus, the EMEA corpus and Brazilian theses and dissertations. Due to possible overlap with the test sets from Medline, the team applied some procedures to automatically exclude some publications from the Scielo training data. Terminological resources such as the Unified Medical Language System (UMLS)  (Bodenreider, 2004)  were used as well.
The only submission for de/en was a Transformer without ensemble. TFG TALP UPC. Each two submissions for language pairs es/en, fr/en and pt/en utilized either multi-source (run1, primary run) or the singlesource (run2) training. UFRGS. The two submissions from the UFRGS teams seem to have differed only on the MT tool that they used, i. e. , either OpenNMT (run1, primary run) or Moses (run2). UHH-DS. The three submissions for each of the language pairs (en/es, en/pt, en/ro, es/en and pt/en) differed on whether the under-sampling algorithm was applied only on the English side (run1), on the non-English side (run2) or on both sides (run3, primary run).
The reason are misaligned sentences in the German reference. Automatic German translations on the other hand are most often correct in translation and alignment of content. Indeed, the quality of the German dataset was one of the lowest (cf. Section 2. 1). We present the results for the manual evaluation of the EDP test sets in Table  10. Based on the number of times that the submission was validated as being better than the reference translation, we ranked the two translations as follow: • en/fr: Hunter < reference.
21 to UFRGS, 58 vs. 24 to UHH-DS). While no difference in ranking was observed between teams UHH-DS and UFRGS, in comparison to the automatic evaluation, team TGF TAP UPC moved from being the last ranked in the automatic evaluation to the best ranked one on the manual evaluation. We can only hypothesize that the better BLEU scores that the UFRGS team obtained were probably due to better translation of particular concepts or due to using the same terms as in the reference translations. However, the TGF TAP UPC team could obtain higher quality of the manual translations using their Transformer architecture. The better performance of the TGF TAP UPC team could also have been due to the test set being included in the their training corpus, i. e. overlaps between Medline and the Scielo databases.
However, more parallel corpora are certainly necessary not only for those languages that scored worst in this challenge, but also for the many other languages that we did not evaluate here. Unfortunately, open-access databases such as Scielo are not available for most languages. Nevertheless, the number of parallel abstracts in Medline are increasing and corpora derived from these are starting to being published, e. g. MeSpEn  (Villegas et al. , 2018).
, 2016; Jimeno Yepes et al. , 2017). From values below the 20 points in 2016, results from en/pt jumped to almost 40 in 2017 and over the latter (up to 43. 14) this year. A similar increase was observed for en/es that increased more slowly from up to 33 points in 2016, up to 36 points in 2017 and up to 44 this year. On the other hand, not much improvement can be noticed from en/fr in 2016 (up to 22. 75) to this year's best score  (23. 24). These values are also similar to the scores reported on another MEDLINE dataset in 2013  (Jimeno-Yepes and Névéol, 2013). Regarding translations into English, for es/en, BLEU scores experienced an improvement from 37 to 43 points in the last year. However, the same could not be noticed for pt/en that remained rather constant around 41-43 points. Finally, during our manual validation, we observed for the first time that the quality of some automatic translations was either equal or better than the reference translation.
German: Interestingly, for 80% of the sentences automatic translation was evaluated equally good or even better than the German reference. This observed result has different reasons. Often the German reference translation is correct but either contains additional information or misses information present in the English source sentence while the automatic translation does not have this error. As previously mentioned this is strongly related to the frequent alignment errors present in the German dataset. In some cases validation was very difficult as both translations were very good but we still tried to differentiate between them. For instance, "thromboembolic complications" was translated to "thromboembolische Ereignisse" (events) in the reference and to "thromboembolische Komplikationen" (complications) in the automatic translation.
Some translation were exactly like the reference translations, which makes us suspect that those abstracts could be included in the Scielo corpus used for training data by the systems. However, there were just a couple of such cases and these should not compromise overall evaluation. In spite of the above, we also found very good translations even for complex and long sentences and for biomedical terms with multiple modifiers, such as in "esclerose múltipla secundária progressiva". Spanish: Considering previous years of the challenge, the translations seem to improve and there are fewer issues compared to previous years. On the other hand, the issues we identified are similar to the ones identified in the Portuguese sets. As with the translations from Spanish into English, there were some cases of source words not being translated into Spanish, as in "el estado fsico motor 20 Meter Shuttle Run Test" and "Substance-induced fueron".
Both types of methods seem to suffer from gender and number agreement for determiners as in "La pulsos mejor en las" and sometimes for verbs in terms of number as in "Legendre describen el primer modelo", which might be misleading. We also found that some systems displayed a preference for starting sentences with lower case letters; however, different from the case in Portuguese, for the manually evaluated cases there no issues with acronyms or spaces between hyphenated words. Romanian: This year there fewer participants than in the previous year. Especially regrettable is the absence of the top performers from the University of Edinburgh. The only team which participated last year as well is that of the University of Hamburg, which improved this year by using a training dataset subsampling heuristic in their SMT translator, but trailed again the NMT system in this task.
Recent publications include parallel corpora from the database that were previously used for obtaining our test sets. These new corpora include Medline parallel abstracts  (Villegas et al. , 2018)  and full texts from Scielo  (Soares et al. , 2018). Therefore, manual translation for building the future test could be considered in the following editions of the challenge. Finally, future improvements should also address problems reported by the participants regarding the current format of the test sets. In the three years of the challenge, we have used BioC as the format for data exchange, which seemed to cause some difficulties for sentence alignment. We will evaluate available formats for data exchange with the participants or inspired in other shared task in WMT.
Statistical methods Randomization and blinding. From the 17 patients enrolled, 15 were randomized at T0 (7 of whom were assigned to the diacerein group and 8 of whom were assigned to the control group). For randomization, random numbers computergenerated on the basis of the random sorting method were used. 16 Blinding based on the 4-eyes principle was done after randomization. Two patients were recruited in a second recruitment round to replace dropouts. Data collection, sample size planning, and evaluation. Sample size planning was based on the results from a pilot study, in which a significant difference of means of 9. 3 (standard deviation, 3. 4) was calculated. The empirical correlation was r = 0. 96. A maximum 10% dropout rate was expected. On the basis of a 2-sided dependent Student t test, a type I error of 5%, and a sample size of 15, a power of at least 80% was achieved to detect an effect of 9.
Nevertheless, the 17 patients enrolled were recruited from 4 countries. For data acquisition, we believed that counting the blisters was the most reliable and patient-relevant way of monitoring the effect of a diacerein treatment. This method would also compensate for a lack of photographic technology that could ensure absolutely representative pictures for calculating blister areas. Finally, the counted blister numbers represented a consensus among the 3 independent raters who based their counts on the photographs taken at each visit and provided the basis for outcome evaluation. The results demonstrated that diacerein significantly reduced blister numbers in patients with EBSgen/sev. A more than 40% reduction of blister numbers, which is regarded to be a clinically meaningful outcome, was reached in 60% of patients in the diacerein group.
SUPPLEMENTAL METHOD 2: DATA EVALUATION Data were checked for consistency in terms of typing errors, and ranges were inspected for validity. Because the data did not follow a normal distribution, specific distributions were used to model the underlying distributions in the generalized estimating equation (GEE) models: the Poisson distribution was used for the number of blisters, and the Tweedie distribution was used to model blisters expressed as a percentage, whereby the number of blisters of each patient was normalized to 100% at times T0 and T8. The patient identification number was the subject factor. Group, time, and treatment period were treated as fixed factors, with group and time treated as main and interaction factors. Treatment period was treated as main factor only. The robust estimator for the covariance matrix was used.
Evaluation of reduction of blister numbers For calculating the average reduction of blister numbers, only those patients who had complete data for both treatment periods were included in the evaluation. In this manner, the strength of the crossover trial design, which is that there are diacerein and placebo data available for all patients and thus every patient serves as his own control, is reflected. Here, only the 13 patients who had complete data for both diacerein and placebo treatment phases were included in the analyses (Supplemental Fig 3, D and Supplemental Fig 4). Table  showing  the number of patients is included in the respective evaluations. Supplemental Fig 1. Assessment of pruritus and pain. Pain (A) and pruritus (B) were assessed by the study nurse at each visit by using a visual analogue scale with continuous numbers from 0 to 10, where 0 indicated no pain/pruritus and 10 indicated significant pain/ pruritus.
Quality of life data were analyzed by using 2 different testing approaches based on relative effects (a nonparametric Behrens-Fisher situation S2 ): score distribution before and after the treatment and score change distributions. Interestingly, the impact of pain and pruritus in this disease rated the highest scores in the patients' quality of life assessment, but these scores did not correspond to the nurse-recorded scores on the analogue scale. We assume that this difference may be accounted for by the low percentage of body surface area treated, individual differences in pain sensation (which resulted in widely differing scores at the beginning of the treatment), and difficulty in separating the perception of pain and pruritus in the treated body surface area from that in the rest of the body.