dataesr/scientific-paragraphs-categorization huggingface dataset:
2-month-old A30P mice are pre-symptomatic (psA30P mice) Gait analysis has been used to show onset of obvious PD manifestations in mice  [34]. We analyzed ten gait parameters of A30P and wild type (WT) mice using the CatWalk XT system. Animal footprints were automatically captured by the video camera of the system and were further categorized into individual paws like right forepaw (RF), right hindpaw (RH), left forepaw (LF), and left hindpaw (LH) via the software (Fig. 1a ). To characterize pre-symptomatic PD or phenotypemanifested PD in mice, we assessed the gait in two age groups: 2 months old and 12-13 months old. Body mass was not different between 2-month-old A30P and WT mice, but 12-13-month-old A30P mice were significantly heavier than age-matched WT mice (Supplementary Fig. 1 ). As expected, the older A30P mice showed significant motor impairments in all tested parameters compared to age-matched controls: maximum contact area, terminal dual stance, body speed, body speed variation, run maximum variation (p ≤ 0.
4e ). Categorization into groups by the STRING database yielded i. a. six different functional clusters: actin and microtubule organization, vesicle transport, calcium binding, ubiquitination, and response to oxidative stress (Fig. 4f ). Proteins in these groups are known to be involved in PD pathogenesis in mice and humans, mainly affecting the CNS. This functional classification emphasized that more proteins are dysregulated in the LI than in the SI. Therefore,   c-f ) and large intestine (LI) motility (j-m). Less SI and LI motility was shown in psA30P mice compared with WT. The gut diameter in the heatmaps (pixel color) is indicated on the y-axis, the time on the x-axis. Contraction numbers were significantly lower in the SI (g) and the LI (n) of psA30P mice compared with WT controls. Mean intervals were slightly higher with more variation in the SI of psA30P mice compared with WT (i), while in the LI of psA30P mice mean intervals were significantly prolonged compared with WT (p).
Velocity was significantly decreased in the SI and LI of psA30P mice compared with WT (h, o). WT mice are shown in blue, psA30P mice in red. Calculations were performed with LabView and GraphPad Prism 8. Quantitative data are expressed as means ± SD from segments of n = 7 psA30P mice and n = 6 age-matched WT controls for mean interval and contraction numbers. For velocity determination, n = 5 psA30P mice and n = 5 WT mice were examined. * p ≤ 0. 05, and ** p ≤ 0. 01 using Student's t test and Cohen's d (Supplementary Table  7b ), ns = not significant we focused all further investigations on the LI. We selected three proteins with altered expression for detailed examinations: neurofilament light chain (Nefl), vesicle-associated membrane protein 2 (Vamp2) and calbindin 2 (Calb2). We chose these proteins because they have already been implicated in PD pathology.
Acknowledgements The authors thank  Tobias Fritz  for technical support with the  CatWalk XT System , which was performed at the  Saarland University, Homburg. We thank  Salam Warda  for analyzing the motility videos,  David Grundmann  and  Alexandra Conrad  for the help with the myenteric plexus isolation used for the proteomics. We thank  Liz Spycher  for technical assistance.
The class 'Carici caryophylleae-Genistetea lobelii Klein 1972' corresponds to Cyrno-Sardian oromediterranean cushion-scrubs and related grasslands. In France, this class is only present in Corsica and the syntaxonomic scheme is debated among phytosociologists. This paper aims to highlight the main plant associations of the Carici caryophylleae-Genistetea lobelii Klein 1972 and to define the diagnostic species for each phytosociological unit. Diagnostic species are defined as species with a distinct concentration of occurrence or abundance in a particular vegetation unit. We compiled 519 vegetation plots and we applied the EuroVegChecklist expert system for the classes of European vegetation to only retain vegetation plots belonging to the Carici caryophylleae-Genistetea lobelii. We obtained a dataset with 189 vegetation plots, and we classified them using the Modified TWINSPAN classification.
Dataset The data used were provided by the bibliography (Table  1 , Appendix S1 for the list of data sources) and vegetation plots that were carried out under the CarHAB Program between 2012 and 2014 according to sigmatist phytosociology  (Dengler, 2017). We have taken into account all the vegetation plots found in the literature that were assigned to the Carici caryophylleae-Genistetea lobelii communities by the authors. We also considered plant communities for which the syntaxonomic inclusion within the Carici caryophylleae-Genistetea lobelii was uncertain. This is the case for the Paronychio polygonifoliae-Armerietum multicepitis, which has a very similar floristic composition to the Berberido aetnensis-Genistetum lobelioidis but which was included in the Caricetea curvulae  (Reymann et al.
, 2016). Therefore, we have integrated all the vegetation plots assigned to the Paronychio polygonifoliae-Armerietum multicepitis in our database, to compare the floristic composition with that of other plant communities and to verify its syntaxonomic inclusion in the synsystem. We also retained the vegetation plots which were characterized as = 'scrubs' or 'grasslands' by these authors. In total, 519 vegetation plots sharing 651 taxa were stored in Turboveg 2  (Hennekens & Schaminée, 2001). The vegetation data are phytosociological vegetation plots with specific reference to the cover-abundance for each species, recorded between 1926 and 2014. The dataset was filtered using the species list for the Carici caryophylleae-Genistetea lobelii class as listed in an appendix to the EuroVegChecklist  (Mucina et al.
, 2016). To obtain a selection of the vegetation plots corresponding to this class, we classified the initial dataset using the EuroVegChecklist expert system for the classes of European vegetation in the JUICE program  (Tichý, 2002). For our study, we selected only those vegetation plots that have been recognized as the Carici caryophylleae-Genistetea lobelii (code 'GEN' in the EuroVegChecklist). Vegetation plots that contained a total of more than 20% trees or scrubs were excluded. Vegetation plots with fewer than five species (representing < 1% of the selected plots) were excluded because they were considered to be poorly representative of these typically species-rich scrubs and related grasslands. We chose to analyze all the plots except those with an area smaller than 1 m 2 or larger than > 100 m 2.
We did not exclude plots that did not indicate their surface area because we assumed that most of them were sampled on plots ranging in size from 5 to 100 m 2 and that their exclusion would result in the loss of data. The dataset contains 189 vegetation plots and 399 species. Vegetation plots without geographical coordinates were georeferenced, using the QGIS software, according to the descriptions of their localities reported in the original publications. The uncertainty of the georeferencing was less than 1 km in most cases.
Species list and nomenclature We checked and homogenized the species lists using the taxonomic nomenclature in the book Flora Corsica  (Jeanmonod & Gamisans, 2013)  because numerous origins have been listed in the vegetation plots. Once the typing errors and synonymy problems were resolved, we deleted the rare species (less than 0. 1% of occurrence) to avoid a biased analysis for this rare species. As we used plots sampled by numerous different authors over several decades, in some cases it was not possible to determine the original description of the taxon, particularly when subspecies belonging to the same species have an overlapping geographic distribution. The selected dataset counted 189 vegetation plots which contain a total of 262 plant species. The nomenclature of the syntaxa follows the EuroVegChecklist  (Mucina et al.
Pooling analysis We classified our dataset using the modified TWINSPAN classification  (Roleček et al. , 2009)  in version 7. 0. 208 of the JUICE program  (Tichý, 2002)  to obtain a hierarchical pool. We used the default settings (cut levels = 0%, 5%, 25%; minimum group size = 5) and the Bray-Curtis index as a dissimilarity measure producing 15 terminal pools. To obtain this number of pools, we did several iterations to highlight the most coherent number of pools with the literature and our field knowledge. The number of pools greater than 15 led to the identification of a syntaxonomic level lower than the sub-association (facies in particular). In contrast, a number lower than 15 pools led to the identification of a higher level (alliance level). However, we are aware that the definition of the number of pools and the dissimilarity measures are the main limitations of this method because it mainly depends on the choice of the authors  (Chuman & Romportl, 2010).
Expert system An Expert System (ES) is a tool that is used to identify vegetation based on the floristic and geographical boundaries of the syntaxa  (Kočí et al. , 2003). The ES is based on formal definitions, which are written as logical formulas in an editable script stored as a TXT file  (Tichý et al. , 2019). The ES script contains logical formulas of the Carici caryophylleae-Genistetea lobelii plant communities consisting of relational operators, which define individual assignment criteria, and the logical operators AND, OR, and NOT, which combine the individual assignment criteria  (Bruelheide, 1997). Similarly to  Mucina et al. (2016) , the ES that we built took into account discriminating species of each alliance and assigned each plot to that alliance whose discriminating species occurring in the plots had the highest sum of square-rooted percentage covers.
The ES was run using a software tool implemented in the JUICE 7 software  (Tichý, 2002). The species identified as diagnostic, constant, and dominant based on our TWINSPAN analysis were used as discriminating species groups; these groups of species were used to design the ES that could then be used to classify any vegetation plot from the Carici caryophylleae-Genistetea lobelii. The ES is based on the different species groups of the classification developed by  Mucina et al. (2016)  for the EuroVegChecklist classes, and it also takes into account the indicator species groups of all the alliances we have identified. Then it was applied to assign each plot to the plant communities for which the indicator species in the plot had the highest sum of square-rooted percentage covers. We merged the diagnostic species groups when two or more pools were interpreted as belonging to the same plant community.
Ordination analysis We used a Principal Component Analysis (PCA) to visualize the main environmental gradients. A PCA aims to analyze the variance in the multivariate data onto a few components  (Borcard et al. , 2011; Cornillon et al. , 2012). A standardised PCA was performed using the vegan package in R (version 1. 15-4, http://cc. oulu. fi/ jarioksa/softhelp/vegan. html). We used the WorldClim dataset  (Fick & Hijmans, 2017 ; accessed on 14 September 2019) to collect bioclimatic data characterizing each alliance. Bioclimatic variables (http://www. worldclim. org/bioclim) for the phytosociological plots were obtained through the overlay of the vegetation plot coordinates with the QGIS application, version 2. 18. 14 (open source; www. qgis. org/en/site/). The bioclimatic variables were plotted on the PCA diagrams to help interpret the ecological differences among the plant communities.
Species groups and formal definitions We have formulated formal definitions for one class, one order, three alliances, eight plant associations, and three subassociations. We have also added formal definitions for the classes which are very specific to these plant communities: the Cisto ladaniferi-Lavanduletea stoechadis and the Saginetea piliferae. Besides, we also integrated three other groups of 'Tree', 'Shrub', and 'Low-Shrub' species, which allow us to better distinguish scrub and related grasslands within the Carici caryophylleae-Genistetea lobelii. An expert system based on the modified Twinspan classification was developed and applied to the complete dataset of 189 vegetation plots of which 155 (82%) were classified (Appendix S3). For the vegetation plots that were not assigned to a plant association: 25 vegetation plots contain maquis dominated by Erica arborea, and nine belong to the Anthyllidion hermanniae and correspond to transitional vegetation between the supramediterranean and oromediterranean belts.
Advantages and limits of the method used The main advantage of the methodological approach used in our study is that it centralizes all of the phytosociological data for a specific type of vegetation within one database. As a result, we were able to gather, under Turboveg, all the bibliographical vegetation plots, holotypes, original tables, and vegetation plots resulting from new field investigations. The second advantage is the definition of diagnostic, constant, and dominant species for each level of synsystem from plant communities to class. With this data, we were able to develop an expert system for all French vegetation in the Carici caryophylleae-Genistetea salzmannii (Appendix  S3 ). This expert system includes a group of diagnostic species for each plant association as well as a group of diagnostic species for the higher levels (alliance, order, and class).
Our expert system also integrates groups of 'trees', 'scrubs' and 'low scrubs'. This increases the accuracy when recognizing vegetation plots belonging to the Carici caryophylleae-Genistetea salzmannii plant community and avoids confusion with vegetation that is dominated by woody species because they are often found near thickets or forests and are colonized by species from these plant communities. To better define the Carici caryophylleae-Genistetea salzmannii plant communities, we also include lists of species in the expert system for the classes that are similar to the Carici caryophylleae-Genistetea salzmannii such as the Cisto ladaniferi-Lavanduletea stoechadis (de  Foucault et al. , 2012)  and the Saginetea piliferae. Some errors are still possible between the Saginetea piliferae and the Plantaginion insularis grasslands in the dataset including both types of vegetation because we have proposed a formal definition for this class without considering all the Saginetea piliferae vegetation.
It is therefore advisable to follow two methodological steps, as we have done in our study: first, select vegetation plots belonging to the target vegetation to be studied from the expert system provided by  Mucina et al. (2016)  for the class level, and then second, apply our expert system to assign vegetation plots to the Carici caryophylleae-Genistetea salzmannii plant communities. Errors can occur when formal definitions are based on a small number of vegetation plots. The significant advantages of an expert system are that it can be re-adjusted and can evolve as new vegetation plots are added to the database. This is also the case for species lists and formal definitions which can be modified according to new data. Vegetation typology is an essential approach for describing vegetation communities and more broadly for describing habitats listed under the Habitats Directive  (Gigante et al.
Acknowledgments The authors would like to thank  Thierry Fernez  for his help collecting bibliographic data,  Bruno de Foucault  for his recommendations regarding the syntaxonomic nomenclature,  Olivier Argagnon  for his advice on the description of vegetation units, and  Guilhan Paradis  for his suggestions on the taxonomic nomenclature and for reviewing this manuscript. Thank to  Ladislav Mucina  for their suggestions to improve this manuscript. The authors also thank  Catherine Davies  and  Sara Mullin , from  Brest University , for the revision of the English translation.
( 23 ) The scalar-field solution on the other hands reads φ = 1 - r - r -4/13. ( 24 ) The solution (  20 )-(  24 ) has been verified via Mathematica, the code is accessible on GitHub  [37]. It is therefore the first known black hole solution of entangled relativity. r -→ 0 corresponds to a near vacuum situation described in the introduction. In this limit, the scalar-field tends to a constant field and the metric in Eq. (  20 ) tends to the Schwarzschild solution in a near vacuum situation. This represents the first example for which an exact solution of entangled relativity is shown to be well approximated in a near vacuum situation by the usual Schwarzschild solution in vacuum. This is an indication that the outside metric of the Schwarzschild solution can be an accurate mathematical idealisation of a non-rotating astrophysical black hole in entangled relativity.
Most neonates are nursed on the post-natal ward but if an elevated level of neonatal care is required e. g. phototherapy, intravenous antibiotics, nasogastric feeding or oxygen, they are transferred to the Special Care Baby Unit (SCBU), another department within the SMRU facilities  [16]. data, as stated, is available on request from scientists with a genuine interest in neonatal jaundice, which can be easily verified by the Mahidol Oxford Tropical Medicine Data Access Committee established in 2016, for data sharing purposes. We prefer to maintain the data access as already stated i. e Data Sharing Bioethics & Engagement-MORU Tropical Health Network (tropmedres. ac). The contact information is Rita Chanviriyavuth. Email rita@tropmedres. ac In addition, the data is still under analysis for a DPhil student enrolled at Oxford (details can be provided if needed).
Statistical analysis Statistical analyses were performed using SPSS 23. 0 (IBM SPSS Statistics, IBM Corporation) and STATA 14 (Stata Corp 2015, Version 14. 1. College Station, Texas, StataCorp LP). Moderate and severe NH incidence was calculated by survival analysis using data from neonates who had a complete regular follow up in the first week of life as defined in the Methods. One TSB per neonate with complete regular follow up measured at, or the nearest to 24 h (12-30 h), 48 h (31-60 h), 72 h (61-80 h) and 144 h (81-168 h) was used to describe TSB levels trend. Only TSB measurements prior to the initiation of PT were included. Time-point TSB median values were compared using Kruskal-Wallis Test. Potential risk factors for developing NH were evaluated using a Cox proportional hazard mixed model, clustered by site.
As 6 in 10 neonates <38 weeks developed NH within 24 h, preventive PT for neonates <35 weeks, and for those born 35 to 37 weeks with risk factors, was implemented using a simple checklist (S1 File). For those born 38 weeks or more the checklist aims to alert the staff to neonates with an increased risk to develop NH so they can plan for the follow-up. The strength of the results presented relies on a large dataset of routinely collected clinical and laboratory variables and a low proportion of missing information. Notwithstanding, there are limitations: neonates with potentially high NH risk (e. g. , born by caesarean section after a rupture of membranes �18 hours) were excluded and results likely underestimate NH incidence and proportion of severe jaundice. Exclusive breastfeeding was universal including in preterm neonates and its association with NH could not be measured.
Both methods resulted in similar estimates of organic nitrogen export, although those from the satellite were slightly lower (Supplementary Discussion and Supplementary Fig. 5 ). As the UVPbased estimates were carried out simultaneously to the water sampling, they capture the local variability of organic nitrogen export more precisely, and therefore we focus on the UVP dataset for comparison to the anammox rates. Based on the UVP method, organic nitrogen export from the photic zone ranged between 6. 5 and 61. 7 mmol N m -2 day -1 onshore, and 6. 9 and 45. 7 mmol N m -2 day -1 offshore (Fig. 2c , Supplementary Fig. 2d ), and was always at least 1. 8-fold higher than depth-integrated anammox rates (Supplementary Table  2  and Supplementary Fig. 6 ). As such, the export of organic nitrogen was sufficient to support the measured N-loss, which is in accordance with previous results from the Peruvian OMZ  5.
This dataset was not included in the linear regression but is included in Supplementary Table  1c. Correlations with the particle abundance in number per liter yielded similar results (see Supplementary Table  5 ). (see Supplementary Table  6  for more details). The slope of the correlation between anammox rates and particles in the smallest size class (128-256 µm) was 390 nmol N 2 mm -3 day -1. Intriguingly, we also found a significant linear correlation between anammox rates and the volume of the smallest particle size class, during a previous cruise (M93) to the same region in February 2013 (Fig. 4a , Supplementary Fig. 9 ), although the slope was higher (~590). It should be noted that in contrast to the dataset presented here, the M93 cruise occurred in austral summer when productivity is relatively high and the water column was sulfidic at some stations.
e nitrate reduction to nitrite, denitrification and dissimilatory nitrate/nitrite reduction to ammonium, DNRA). Nitrate reduction to nitrite, which is suggested to be the main remineralization process, has typical onshore rates of 0. 2 µmol N L -1 day -1 (refs. 5, 55 ). Remineralization associated with nitrate reduction to nitrite would therefore lead to the release of around 0. 015 µmol NH 4 + L -1 day -1 , around 40% of our estimated ammonium release (0. 04 µmol N L -1 day -1 ), which is likely underestimated. Preferential N-mineralization within particles and particle fragmentation (which cannot be fully resolved via modelling with this dataset) could both theoretically lead to higher ammonium release (see Supplementary Discussion). Furthermore, our modelling approach only takes sinking particles into account, whereas it is possible that some fraction of the smaller particles are suspended in the water column  27.
Furthermore, the negative intercept implies that a minimum volume of small particles (0. 04 mm 3 L -1 ) is required to fuel a significant anammox rate. This is supported by the observation that anammox is undetectable in the OMZ waters containing very few particles. Based on our mechanistic modelling, the cessation in anammox rates at low particle volumes likely results from ammonium release and encounter rates becoming too low (see Supplementary Fig. 17 ). The relationship from the linear regression was applied to a UVP dataset which covered a large area of the Peruvian OMZ and was collected during March-July 2017 (cruises M135-M138). UVP measurements were separated for the "inner" and "outer" OMZ, based on distance from the coast (175 km, as in refs. 5, 41, 80 ), which led to an estimated average nitrogen loss within the anoxic waters of around 6.
1 and 1. 5 mmol N m 2 day -1 for the inner and outer OMZ, respectively (Fig. 6 ). Subsequently, we extrapolated these rates over the area of the inner Peruvian OMZ (3. 2 × 10 5 km 2 , as in refs. 41, 80 ) and the outer Peruvian OMZ (12 × 10 5 km 2 as in ref. 5  ). This resulted in an estimated monthly N-loss of 1. 0 Tg N, and 0. 6 Tg N for the inner and outer OMZ, respectively, during the period covered by this dataset. If we extrapolate the monthly rates across an entire year, they would lead to an N-loss estimate of 19 Tg N yr -1 for the anoxic part of the Peruvian OMZ. 1] [82]  ). This annual extrapolation would be improved by additional data from the early winter to early summer seasons, sulfidic events and also by the inclusion of anammox activity from the oxycline, which we did not investigate in this study.