dataesr/scientific-paragraphs-categorization huggingface dataset:
Gomez et al. (2018)16) two contrasting agroecosystems datasets denotes what is achievable from S2A data in terms of predictive capacities for a single considered date. The soils considered in this study are located in French regions but widely develop abroad, across the temperate and Mediterranean areas. Assessment of Sentinel-2 performance is developing for other French regions with other soil types and further for tropical soils. notablycoarsefragmentcontentandvegetation. This distinguishes our models from those constructed from simulated MSI spectra derived from lab spectral libraries, as anticipated byCastaldi et al. (2016)for a number of forthcoming or newly launched satellites, including Sentinel-2. However, with the addition of noise and atmospheric effects and from the use of untransformed lab reflectance spectra sampled from central and southern Italy, these authors obtained validation results similar to our performance results for clay) that are inferior to those found for the Versailles Plain in terms of SOC content levels (R² 0.
Acknowledgment This study was carried out in the framework of the TOSCA " Cartographie Numérique des Sols (CNS)" program  of the  French Space Agency (CNES). It also benefited support from the  TOSCA-PLEIADES-CO program  of the  CNES  for the Versailles Plain. Special thanks to  Dalila Hadjar ,  Arthur Scriban ,  Paulina Michura , for technical assistance in the field. We are.
Results In Fig. 1 , we show results of typical QENS datasets and their analyses for WT and PR (500 MPa and 750 MPa) S. oneidensis bacteria at ambient (0. 1 MPa), 200 MPa and 500 MPa, obtained at TOFTOF (FRM-II, Germany), IN6 (ILL, France), and IRIS (ISIS, UK)). Details of the three instruments and data analysis procedures are provided below in Methods and the full set of datasets is provided in Supplementary Information (SI). Further details of the analysis are given in our previous communication  25. The data presented here correspond to water dynamics in the intracellular medium (Im) obtained from the isotopic contrast dataset combination Hc/Db -Db, using data recorded from "normal" hydrogenated cells (Hc) resuspended in perdeuterated buffer (Db), after subtracting the Db buffer contribution (Fig.
The larger number of experimental runs that we could conduct at TOFTOF (FRMII) allowed us to examine a wider range of isotopic contrasts for WT samples at 1 atm and 200MPa  25. Those data allowed construction of a further [(Dc/ Hb -Dc/Db) -Hb] contrast that distinguishes dynamics within the cytoplasm alone (Imc) from those occurring within the cell envel' (Fig. 1 ). That work allowed us to correlate the "dip" observed near 1 Å -2 in some of the Γ T (Q 2 ) datasets with transmembrane water transport via Aquaporin channels  25  (Fig. 2 ). However, the overall D T values for intracellular water motions extracted from the different datasets were identical within the systematic errors associated with each measurement (Table  2 ). We do note, however, that the D T values for the cytoplasm only (Imc) appear to be systematically lower (by ~5-6%) than those recorded for the full set of species contained within the cell envelope, including contributions from the membrane structures, proteins, nucleic acids etc, represented by the Im isotopic contrast subtraction (Table  1 ).
Discussion The intracellular water diffusion rates determined for WT bacteria at ambient pressure obtained at the three neutron scattering facilities overlapped closely with D T = 2. 43-2. 57 × 10 -5 cm 2 s -1 (Fig. 2 , Table  1 ). The consistency between these results provides confidence in our analysis and interpretation of the QENS datasets. The D T values obtained coincide with the lower limit of measurements recorded for bulk aqueous phases, and are similar to data obtained for nanoconfined water in porous inorganic matrices  [40] [41] [42] [43] [44] [45] [46]  (Fig. 3 ). We do note that one early QENS result reported a slowdown in water dynamics for the extreme halophile Haloarcula marismortua with high intracellular Cl -content  47. However, that result was not supported by more recent 2 H NMR spin relaxation rate studies  30.
1. Diffusion parameters obtained from fits by applying the jump model  38  to Γ Τ (Q 2 ) data obtained at all three instruments for Hb, Db, WT and PR bacterial samples at 0. 1, 200 and 500 MPa. The derived D T value and jump frequency (τ o ) are provided for the translational diffusion obtained by analysis of the narrow Lorentzian QENS component, and the rotational relaxational time (τ R ) was extracted from the fit of the dynamic structure factor to the broader Lorentzian function that was used to fit some of the datasets. In cases where the data did not require fitting using this additional component, S(Q,ω) was modelled using a single Lorentzian function and no information on the rotational relaxational times was obtained. Hc/Db refers to H cells resuspended in D-buffer, and the isotopic contrast combination and dataset subtraction Hc/Db-Db was designed to focus on water dynamics within the intracellular medium (Im), which includes everything contained within the cell envelope (e.
Data were also collected at 0. 1 MPa at ILL-IN6 using a flat plate Al liquid cell. Diagrams and photographs of the HP cell arrangements are given in Supplementary Fig. 11. QENS data obtained over momentum transfers of between approximately 0. 1 and 1. 8 Å -1 provided information on diffusional and rotational water relaxation dynamics over real space correlation lengths ~3-60 Å. The large difference in incoherent neutron scattering cross section between H and D (80. 27 vs 2. 05barn, respectively) meant that D scattering was almost invisible relative to H when both were present. In our previous report of work during several experimental sessions at TOFTOF (FRM-II) we were able to examine a wide range of Hc, Dc, Hb, Db isotopic contrast combinations and separate out contributions from transmembrane vs purely intracellular (Imc) water dynamics.
In this study we focused mainly on water dynamics within the overall intracellular environment derived from the (Hc/Db -Db) isotopic contrast combination (Im), that did not distinguish between contributions from the cytoplasm and cell envelope  25. Our initial experiments focused on obtaining data for Hb and Db aqueous buffer solutions, followed by QENS studies of Hc cells resuspended in perdeuterated buffer (Db). The QENS datasets were typically fit using two Lorentzian components. In agreement with previous work, we assigned the narrow component to translational diffusion with a HWHM linewidth Γ T (Q), and the broader (faster relaxing) component to a convolution of translational and rotational contributions (Γ T + Γ R )  5, 25, 31, 38, 39, 67. The relative amplitudes of the two components were taken as free parameters to fit the lineshapes.
Right: (C) Representative datasets and analysis of the neutron dynamic scattering function S(Q,ω) for the intracellular medium Im (isotopic dataset contrast [Hc/Db -Db]). Data are shown here for a pressure-resistant S. oneidensis population that had been previously exposed to to 500 MPa (500 MPa-PR) and subsequently cultured at ambient conditions, then examined by neutron scattering using the IN6 instrument at ILL (instrumental resolution 85 μeV; λ = 5. 12 Å). Data were recorded at room temperature at pressures of 0. 1 and 500 MPa for momentum transfers between 0. 2-1. 7 Å -1. The raw data and lineshape fits are shown with a logarithmic intensity scale to highlight QENS contributions. The central line (grey) due to elastic scattering is modelled by a delta function convoluted with the instrumental resolution giving rise to a Gaussian.
The narrow QENS Lorentzian signal (blue line) indicates the translational diffusion component with a linewidth (Γ) that varies as a function of Q. The broader (olive-green) Lorentzian represents the faster rotational relaxation that is Q-independent. The global fit (red continuous curve) is overlain on the data points (black open squares). A full set of datasets obtained and their analyses is provided in Supplementary Figs 1-5.
Acknowledgements This study was supported by grants from the  Leverhulme Trust  ( RPG-350 ) and the  Deep Life program  of the  Deep Carbon Observatory  ( Sloan Foundation ) to PFM. VTF acknowledges UK EPSRC support via grants  GR/ R99393/01  and  EP/C015452/1  for creation of the  Deuteration Laboratory in ILL's Life Sciences Group  and  EU  contracts  RII3-CT-2003-505925  and  NMP4-CT-2006-033256. We thank  Mohamed Zbiri  at  ILL  for help with beamline support. This project has received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under the NMI3-II Grant number  283883  to provide access to experiments at FRM-II. LEB gratefully acknowledges financial support from the  Swiss National Science Foundation  under grant number  200021-149847  and from the  French ANRwithin the Blanc International programme PACS  under reference  ANR-13-IS04-0006-01.
We also thank the sample environment teams at all neutron facilities. FF also thanks  ISIS (Didcot, UK : grant  RB1410406 ) for beamtime (doi:  10. 5286/ ISIS. E. RB1410406 ) and for financial support for experimental consumables (Grant  RB1410406 ). We are grateful to the  Institut Laue Langevin (Grenoble, France)  for neutron beamtime (doi: 10. 5291/ILL-DATA. 8-04-785 ). The open access fee was covered by  FILL2030 , a  European Union  project within the European Commision's  Horizon2020 Research and Innovation programme  under grant agreement No  731096.
Introduction and study aims Accurate real-time endoscopic characterization of colorectal polyps is key to choosing the most appropriate treatment. Mastering the currently available classifications is challenging. We used validated criteria for these classifications to create a single table, named CONECCT, and evaluated the impact of a teaching program based on this tool. Methods A prospective multicenter study involving GI fellows and attending physicians was conducted. During the first session, each trainee completed a pretest consisting in histological prediction and choice of treatment of 20 colorectal polyps still frames. This was followed by a 30minute course on the CONECCT table, before taking a post-test using the same still frames reshuffled. During a second session at 3 -6 months, a last test (T3 M) was performed, including these same still frames and 20 new ones.
Results A total 419 participants followed the teaching program between April 2017 and April 2018. The mean proportion of correctly predicted/treated lesions improved significantly from pretest to post-test and to T3 M, from 51. 0 % to 74. 0 % and to 66. 6 % respectively (P < 0. 001). Between pretest and post-test, 343 (86. 6 %) trainees improved, and 153 (75. 4 %) at T3 M. Significant improvement occurred for each subtype of polyp for fellows and attending physicians. Between the two sessions, trainees continued to progress in the histology prediction and treatment choice of polyps CONECCT IIA. Over-treatment decreased significantly from 30. 1 % to 15. 5 % at post-test and to 18. 5 % at T3 M (P < 0. 001).
For each subtype of colorectal polyp, this table suggested a treatment, based on the latest guidelines from the ESGE  [3, 12]. HP (CONECCT IH) are mostly seen in the rectum and the sigmoid. These lesions have the following features based on the NICE classification  [7] : color is same or lighter than background, vessels are lacking or isolated lacy vessels coursing across the lesion that do not surround the pits and the surface pattern has dark or white spots of uniform size or homogeneous absence of pattern. IH are usually small and numerous. Risk of progression to cancer is null and guidelines do not recommend resection of these polyps after proper identification Conclusion The CONECCT teaching program is effective to improve the histology prediction and the treatment choice by gastroenterologists, for each subtype of colorectal polyp.
Statistical analysis Baseline characteristics and outcome variables were described by the mean and range for continuous variables, and by frequencies and percentages for categorical ones. Comparisons of proportions between time points were performed using a mixed logistic regression model to take into account the fact that an investigator classified multiple lesions, and that lesions were classified at different time points. Comparisons of proportions between investigators (fellows and attending physicians) were also performed by mixed logistic regression models to take into account the fact that the same investigator classified multiple lesions. P < 0. 05 was considered statistically significant. All analyses were performed using Excel software (Office, Microsoft, United States) or the R software (R Core Team 2018.
Discussion The current study found that a teaching program of the CON-ECCT table is effective in improving histological prediction and treatment choice for colorectal polyps in both fellows and attending physicians specializing in gastroenterology. The benefits of this program were found regardless of the type of lesion and personal experience. In clinical practice, this improvement yielded a reduction of under-and overtreatment of colorectal polyps and could thus potentially impact treatment of these lesions. Furthermore, there was a persistent statistically significant improvement after 3 to 6 months. For each subtype of polyps, there was a statistically significant improvement between pretest and post-test in histological prediction and treatment choice. These results are encouraging, particularly for CONECCT IH lesions, because the minimal 95 % threshold of correct characterization required for the "notresect" strategy of the ESGE guidelines is almost reached in the post-test  [12].
On the other hand, performance for characterization of the lesions CONECCT IIA are still far from the same 95 % threshold of correct characterization using NBI to introduce the "Resect and Discard" strategy of the ESGE guidelines in routine practice  [12]. SSL were the least correctly characterized before the teaching course and a minority of trainees reported using the recent WASP classification  [10]. The teaching program CONECCT allowed them to make statistically significant progress in histology prediction of and treatment choice for these lesions. Endoscopic recognition of the landmarks of superficial and invasive carcinoma is crucial. In cases of invasive adenocarcinomas, potential resection is surgical to allow resection of both the invaded colon and the potentially metastatic lymph nodes.
In the current study, CONECCT teaching program led to an improvement in histology prediction and treatment choice for superficial adenocarcinomas. This diagnostic performance is far from sufficient in this setting despite being an encouraging first step. Based on all these considerations and also because participants regressed for each subtype of polyp outside the lesions CONECCT IIA for which there is indeed a statistically significantly progression, multiple training sessions with polyp recognition seem warranted to achieve better diagnostic rates. The current study found that fewer than 5 % of participants use all the classifications necessary to predict histology of a polyp and thus choose the appropriate treatment. Merging all these classifications as does the CONECCT table therefore seems important even if having five types of lesions in one table may appear more complex.
Introduction In this paper, we present the fourth edition 1 of the Bacteria Biotope (BB) task. The task was introduced in 2011. It has the ambition of promoting large-scale information extraction (IE) from scientific documents in order to automatically fill knowledge bases in the microbial diversity field  (Bossy et al. , 2012). BB 2019 is part of BioNLP Open Shared Tasks 2019 2. BioNLP-OST is a community-wide effort for the comparison and evaluation of biomedical text mining technologies on manually curated benchmarks. A large amount of information about microbes and their properties that is critical for microbiology research and development is scattered among millions of publications and databases  (Chaix et al. , 2019). Information extraction as framed by the Bacteria Biotope task identifies relevant entities and interrelationships in the text and map them to reference categories from existing knowledge 1 https://sites.
google. com/view/bb-2019 2 https://2019. bionlp-ost. org/ resources. This information can thus be combined with information from other sources referring to the same knowledge resources. The knowledge resources used in the BB task are the NCBI taxonomy 3   (Federhen, 2011)  for microbial taxa and the OntoBiotope ontology 4   (Nédellec et al. , 2018)  for microbial habitats and phenotypes. The large size of these resources relative to the small number of training examples reflects the real conditions of IE application development, whilst it challenges current IE methods. The lexical richness of the two resources partially offsets the difficulty. Compared to the 2016 corpus that contained only scientific paper abstracts from the PubMed database  (Deléger et al. , 2016) , the 2019 corpus is enriched with extracts from full-text articles.
Supporting Resources Supporting resources were made available to participants. They consist of outputs from state-ofthe-art tools applied to the BB data sets (e. g. , POS tagging, syntactic parsing, NER, word embeddings). We proposed in-house embeddings trained on selected relevant PubMed abstracts, and links to external embeddings  (Pyysalo et al. , 2013; Li et al. , 2017)  trained on PubMed and Wikipedia. The full list of tools and resources is available on the website.
Here, by analyzing anomalies in light intensity and temperature data recorded by geolocation loggers carried by 130 individuals of ten long-distance Palearctic migrant songbird species during their migration, we studied species diurnal migration patterns when crossing deserts in autumn (134 tracks) and spring (80 tracks). Based on conflicting earlier evidence and the diversity of species we studied, we expect to find a variety of strategies among these species, with no single rule for desert crossing in migratory songbirds, ranging from complete diurnal stopover to continuous non-stop flight. We further aim at broadly estimating relative flying altitudes of seven species from temperature differentials recorded during barrier crossings, and discuss the implication of migration altitude in the context of climate change.
Looking at light intensity and temperature data recorded by the loggers, we searched for patterns showing that individual birds prolonged a nocturnal migration flight into the day. A prolonged flight is revealed by a full light pattern (FLP) at least in the morning  9  , and generally (if recorded) a lower minimal temperature recorded during the four previous hours. This is followed by an abrupt change in the light intensity pattern and an increase in temperature after the bird has landed, as the tag's light sensor experiences greater, more variable shading compared to in flight and the temperature sensor responds to warmer ambient temperatures on the ground and a reduction in wind chill (Figs. 1 & 2). A flight prolonged over a complete day is revealed by a full-day FLP and low minimal and maximal temperatures during the whole day, including at noon (Fig.
Willow warblers revealed the most diverse strategies in autumn, with four individuals performing only nocturnal flights (no FLP), seven individuals prolonging nocturnal flights into the morning (FLP), and four individuals performing non-stop flights (FLP over a complete day). We also observed these three main strategies for at least one individual of four other species in autumn (whinchat, spotted flycatcher, tree pipit and nightingale). third and fourth days with obvious FLPs; no temperature data available. (f) nightingale BE506: two nights with large drops in minimal and maximal temperatures, the second followed by a short FLP, corresponding to a low minimal temperature saved at 9:39, so recorded during the four previous hours (5:39-9:39), while sunrise occurred at 6:00. Temperature differentials.
8%), and 1 rufous-tailed scrub-robin logger (return rate 46%)  34. As we retrieved some loggers after birds completed two migration cycles, in a few cases we analyzed more autumn tracks than the number of tracked individuals. On some tags, temperature was sampled by tags every 5-minutes, with the minimum and maximum values saved every 4-hour interval. Light intensity data and fLps. We visually explored the light intensity data to detect FLPs (Figs. 1  and S1 ), as reported by previous studies  5, 9. We also identified potential prolonged flights in the day by the lower minimal temperature recorded in the morning after sunrise when a potential FLP was short (Fig. S1 ). When detected, we reported the date (Table  S2 ), and the light intensity and temperature (examples shown in Fig. 1 ). To estimate the duration of prolonged flight during daylight, we defined sunrise as the first hour when the recorded light intensity was >2.
S2 ). Temperature data recorded may be correlated with weather, but can also indicate potential changes in altitude, especially when birds fly at high altitude. We expected low minimal and/or maximal temperatures recorded during a migration flight bout if it lasted during the four preceding hours (temperature data being stored every four hours). After identifying potential consecutive nights with relatively low temperatures in a long time series (see Fig. S2  for examples), we checked for the pattern of light data of the same days, and estimated the stationary area of each individual before and after the presumed barrier crossing migration flight. We estimated temperature differentials between days with and without prolonged nocturnal flights, as large differentials might reveal higher than usual flight altitudes.
estimating stationary areas. We used different approaches to estimate coordinates of stationary areas used before and after detected FLP days, according to species. For willow warblers, we reported stationary areas published in a previous study for the same individuals  34. For Mediterranean flycatchers, we estimated stationary areas as periods of stable latitude and longitude estimates as calculated with GeoLight v2. 0 with default parameters, including a -6° sun elevation angle. For ortolan buntings, we used the GeoLight v2. 0. 1 package to estimate twilight times using a threshold method  13. We used the 'LoessFilter' function to validate twilight events and to identify and remove those influenced by shading events at dawn and dusk. For English spotted flycatchers and wood warblers, we used on-bird in-habitat calibration during breeding in the deployment year as the method of estimating the sun elevation angle.
Acknowledgements This research was funded by  Conseil Général des Landes ,  Région Aquitaine ,  Région Nouvelle Aquitaine, Fédération Départementale des Chasseurs des Landes  ( FDC40 ),  Association Départementale des Chasses Traditionnelles à la Matole (ADCTM) ,  French Ministry  in charge of the Environment. The  Polish National Science Centre (NCN ) partially promoted the research in Poland -MS was funded by grant no. N N304 0198 40. MB and JC received funding from  Devon Birds  with field assistance from  Amanada Proud ,  Martin Ketcher ,  Stephen Westerberg ,  Tina Wiffin ,  Judit Mateos ,  Mark Lawrence ,  Emma Inzani ,  Irene Benedicto ,  James Kennerley  and  David Hunter. Research by the  British Trust  for Ornithology was funded by  Anglian Water ,  Mark Constantine ,  Dulverton Trust, Hampshire Ornithological Society, African Bird Club  ( Tanji Birders ) and donations to the  BTO 's Spotted Flycatcher Appeal.