dataesr/scientific-paragraphs-categorization huggingface dataset:
Search strategy and data source Two investigators (FR, VH) searched the literature through the following databases: PsycInfo-Esbco (Psycinfo, Eric, PsycARTICLES, Psychology and Behavioral Sciences Collection), PubMed and the revue collection Science Direct (Fig. 1 ). The review regarded organization and structure of training of CAP and GAP in Europe and was performed using subject headings with the following algorithm: (Psychiatr* AND Training AND Europ*); and (Psychiatr* AND Training AND [Name of 39 European countries]). These two algorithms were used in the following search sections: in "abstract" for PsycInfo-Esbco; in "title and abstract" for PubMed; in "Title, abstract and keywords" for Science Direct. Only references published after January 2000 were considered because there was no point in considering older articles due to reforms regularly implemented in psychiatry training.
Our review also suffers from database and language biases because certain national journals may have been underrepresented in the databases we used and because of exclusion of a limited amount of studies in other languages that English or Spanish. Some data were not available for all countries, making comparisons difficult when exploring the harmonization process. In addition, the number of references on CAP and GAP training varied widely between countries, from one to more than six references per discipline and country. Most countries (68% for CAP and 86% for GAP) had between two to five references per discipline (Additional file 2: Table  S3 , Additional file 3: Table  S4 , Additional file 4: Table  S5  and Additional file 5: Table  S6 ). More specifically, scarce (information obtained for < 5/19 items) or no data was available for 9/35 1 countries regarding GAP, and for 6/35 2 countries regarding CAP.
Acknowledgements Current core members of the  MILESTONE Consortium :  Swaran Singh ,  Helena Tuomainen ,  Jason Madan ,  Jane Warwick ,  Cathy Street ,  Dieter Wolke ,  Moli Paul ,  Priya Tah ,  Rebecca Appleton ,  Alastair Canaway ,  James Griffin  ( University of Warwick, UK ),  Giovanni de Girolamo ,  Giulia Signorini  ( Saint John  of  God Clinical Research Center, Italy) ,  Santosh Paramala ,  Ilyas Sagar-Ouriaghli ,  Natalie Heaney ,  Federico Fiori  ( Kings College London, UK ),  Diane Purper-Ouakil ,  Frédérick Russet ,  Virginie Maurice ,  Véronique Humbertclaude  ( Hôpital Saint Eloi, France ),  Athanasios Maras ,  Larissa van Bodegom ,  Mathilde Overbeek ,  Esther Kooymans  ( Yulius Academie, the Netherlands ),  Ulrike Schulze ,  Melanie Saam ,  Ulrike Breuninger  ( Universität, Germany ),  Sabine Tremmery ,  Gaëlle Hendrickx  ( KU Leuven, Belgium ),  Fiona McNicholas ,  Aleksandra Gronostaj  ( University College Dublin, Ireland ),  Tomislav Franić ,  Nikolina Davidović  ( University Hospital Split, Croatia ),  Frank Verhulst ,  Gwen Dieleman ,  Suzanne Gerritsen  ( Erasmus MC, The Netherlands ),  Kate Lievesley (HealthTracker, UK) ,  Amanda Tuffrey ,  Anna Wilson ,  Charlotte Gatherer ,  Leanne Walker  ( Young  project advisors).
Funding The  MILESTONE  project received funding from the  European Union 's  Seventh Framework Programme  for research, technological development, and demonstration under grant agreement no  602442. The  European Commission  ( FP7 programme ) had no any role in our manuscript, no involvement in the writing of the manuscript or in the decision to submit the manuscript for publication. This Health Policy reflects only the authors' views and the  EU  is not liable for any use that might be made of the information contained therein.
CAP is organized as an autonomous speciality (since 1959) with its specific training programme, rules and guidelines, as well as practice domain. Current programme developed and disseminated as from 1 January 2011. -Backbone of the system: only one specialty Methods Expert opinion Narrative review A literature search performed using MEDLINE, Spanish journals, reference lists, national databases, and European and Spanish official documents Expert opinion Expert opinion Aim Medical Education (CME) in France To describe the training and examination requirements of the new system in place in 2007 in the Psychiatric training in UK To describe the current state of the Mental HealthCare Services in Spain To describe the panorama of psychiatry in Portugal, including training of professionals To describe the state of psychiatry in the Netherlands Study Javed et al.
Ethics statements All participants gave consent after being informed of the purposes, methodology and potential risks of the study. This study was conducted in accordance with the guidelines of the Declaration of Helsinki of 1975 as revised in 2013 and was approved by the Caen ethics committee (Comité de Protection des personnes Nord-Ouest III)  (ref. 2013-15). This study was registered on the ClinicalTrials. gov website: NTC02284776.
Acknowledgements The authors would like to thank the biostatistician,  A. Pinon  and all physicians implicated in volunteers enrolment:  Dr G. Breteau ,  Dr M. Chedal ,  Dr C. Derousseaux ,  Dr B. Friggeri ,  Dr J. Guerin  and  Dr D. Stutz. The authors also gratefully acknowledge  Dr A. Foote  for critically reading the manuscript and editing our English. This work was funded by the  "Association Française pour la Recherche Thermale -AFRETH" (Paris, France).
= (1) were accumulated overnight in order to increase the signal-to-noise ratio. Dmfit program  (Massiot et al. , 2002)  was used to fit peaks and areas under curves were integrated for each unit and expressed in percent. In order to determine the atomic composition and the API disposition within particles, flurbiprofen-loaded HMPs were studied by energy dispersive X-ray (EDX, FEI Quanta 200 FEG SEM). One micrometer cube was analyzed at each dot and backscattered-electrons were recorded (Oxford Instruments, X-Max N Silicon Drift Detector). Flurbiprofen as well as ibuprofen is a nonsteroidal anti-inflammatory drug belonging to aryl carboxylic family (Fig. A. 1). It was selected for its fluorine atom that can be mapped by EDX within HMPs. The mineral part of HMPs was also estimated by thermogravimetric analysis (TGA; STA 6000, PerkinElmer) from 25 to 900 °C at 10 °C.
To confirm the influence of the acetic medium on the efficiency of crosslinking, infrared spectra were recorded on HMPs formulated in deionized water (HMPw) or in acetic buffer (HMPa) using ICO as reference (Fig. 6 ). The absorbances at 952, 1075 and 1102 cm -1 were assigned to the ethoxysilanes (Si-O-CH 2 - CH 3 )  (Leyden and Atwater, 1991; Silverstein et al. , 2005, p. 124 ). An enhanced hydrolysis of the ethoxysilanes moieties was observed for HMPa related to HMPw. In addition, the broadband around 1000 cm -1 attributed to overlapping of the -Si-O-Si-and -C-Si-O-stretching peaks  (Allauddin et al. , 2013)  underscores the efficiency of the condensation in HMPa spectrum. To ensure that the acidic pH did not alter the triglyceride structure, especially the ester bond between glycerol and ricinoleate, microdroplets of CO formulated in the same conditions were analyzed by 1 H NMR spectroscopy and the result showed that the ester bond remained stable despite the low pH (data not shown).
226). 3 8 457 = 4I J -I H 7 × K = 4I J -I H 7 4:5 L 3 (B. 2) It is important to note that 3467 and 3 8 are both R dependent. As the amount of released ibuprofen is additive, then the total of released ibuprofen depends on the size distribution of HMPs at a given radius (M457): 3467 = 345, 67 = N 345, 67 M457 d5 The size distribution of HMPs (N(R)) can be obtained experimentally by Laser diffraction particle sizing technique, and used to calculate the 5 L and 5 The eq. (B. 6) was used to fit the experimental data points, using the non-linear least square method, and the GNU Octave software (leasqr function). To work out the eq. (B. 6), we used the experimental size distribution of particles and the trapeze method to estimate integrals in the eqs. (B. 7) and (B. 8). Finally, the solver was used in order to extract the diffusion coefficient 568 (D) of ibuprofen in each HMP.
ACKNOWLEDGEMENTS Authors are willing to thank  Laurent Mercier  for his technical assistance,  Emmanuel Fernandez ,  Aurélien Lebrun  and  Karine Parra  for their technical assistance and advices in NMR,  Didier Cot  for Scanning Electronic Microscopy photographs and  Caroline Laurent  for kindly supplying the Caco-2 cells. Authors thank the  Algerian government  for the PhD grant and the  Franco-Algerian steering committee  for its support.
Acknowledgements: We thank the  University of Southampton , the  Leverhulme Trust  (grant  RPG-2015-211 ), and the  European Community  ( INTERREG IVa Channel Programme, IS:CE-Chem , project  4061 ) for funding, and the  EPSRC  for a core capability grant ( EP/K039466/1 ). The  CCIPL  ( Centre de Calcul Intensif des Pays de Loire ) also is acknowledged for provision of computer time. Prof Philip Kuchel  and  Dr Dmitry Shishmarev  are acknowledged for stimulating discussions.
Docking studies All the compounds were docked into the minimised average structure of MbtI complexed with the lead compound I 14. The software Gold with the four fitness functions implemented (i. e. GoldScore, ChemScore, Astex Statistical Potential, and ChemPLP) and plants were employed in this study as previously reported  14, 25  , since they have been already used showing good results in the previous virtual screening study on MbtI inhibitors performed in our laboratory  15. The docking site was defined as the region comprising all residues that stayed within 10 Å from and DTT (yellow diamonds) (B) confirm that the compound is not a PAIN. The Universal CAS assay performed on culture media of M. bovis BCG cells grown in the presence of 1h (C), together with the determination of the mycobactins in the above-mentioned cells (D), confirm that the antimycobacterial activity is related to iron uptake inhibition.
All data are mean ± SD of three replicates. the reference compound I. By applying the five docking methods, five different binding dispositions (best-scored docking pose) resulted from the docking of each ligand into the protein binding site. The RMSD of these docking poses against the remaining four was evaluated by using the rms_analysis software of the Gold suite. On this basis, for each ligand docked into the protein binding site, a 5 Â 5 matrix was generated reporting the RMSD results. By using an in-house programme, these results were clustered, so that among the five results, all of the similar docking poses were grouped together  26. We selected an RMSD clustering threshold of 2. 0 Å; therefore, the so-obtained clusters contained the group of poses that were less than 2. 0 Å away from all others poses belonging to the same cluster.
MD simulations All simulations were performed using AMBER 16  27. General amber force field (GAFF) parameters were assigned to the ligands, whereas partial charges were determined using the AM1-BCC method as implemented in the Antechamber suite of AMBER16. MD simulations were carried out employing the ff14SB force field at 300 K. Magnesium ion was inserted considering its disposition and interaction into the 2FN1 PDB code. Ligand-protein complexes were placed in a rectangular parallelepiped water-box and solvated with a 20 Å water cap by using the TIP3P explicit solvent model. Sodium ions were added as counterions in order to neutralise the system. Before MD simulations, two steps of minimisation were performed; in the first stage, a position constraint of 500 kcal/(molÁÅ 2 ) was applied to keep the protein fixed thus minimising only water molecules.
Funding: This research received no external funding. Acknowledgments: JZsM is grateful for the support of the  National Research, Development and Innovation Fund of Hungary , under the  K18 funding scheme  with project No. K 128621. IFS acknowledges support from  Agence Nationale de la Recherche  via the project  MONA , from the  CNRS  via the GdR TheMS, from  La Région Normandie ,  FEDER  and  LabEx EMC 3 via the projects Bioengine, PicoLIBS, EMoPlaF  and  CO 2 -VIRIDIS  and from the  Programme National "Physique et Chimie du Milieu Interstellaire" (PCMI)  of  CNRS/INSU  with  INC/INP  co-funded by  CEA  and  CNES.
EDS and EDXA a b s t r a c t Coconut kernel shell (CKS) and palm kernel shell (PKS) powders were analyzed using Surface Electron Microcopy (SEM) and Transmission Electron Microscopy (TEM). The SEM and TEM were combined with Energy Dispersive X-ray Spectroscopy Analysis for elemental composition of the sample materials. The micrographs of all samples were thoroughly examined and explained. The dataset presented herein helps to elucidate the ultrastructure and could suggest expanding traditional applications of the PKS/CKS to novel ones. The data are related to the research article "Insight on the Ultrastructure, Physicochemical and Thermal Characteristics and Applications of the Palm Kernel Shells"  (Ntenga et al. , 2018).
Dense core properties and accretion timescales We determined the temperatures of the dense cores (from Paper II) located within the filaments by fitting the spectral lines of different molecular species with the software XCLASS  (Möller et al. in prep). All values are in the range of 50-200 K and listed in Table  2. These high temperatures suggest the presence of already formed stars inside the cores 5. The stellar content can 5 Other mechanisms such as external or shock heating can be excluded. For a typical density of 10 6 cm -3 and temperature of 100 K, a heating source would need to see the core as optically thin around the peak (∼ 30 µm) of the black body emission. The dust absorption coefficient be derived from the luminosity of the dense cores. Considering them as spherical black bodies, the stellar luminosity is given by the Stefan-Boltzmann equation L = 4πr 2 σT 4 (5) where r is the radius of the dense cores, σ the Stefan-Boltzmann constant and T the temperature.
Molecular species like CH 3 OCH 3 , CH 3 OCHO, CH 3 OH, or H 2 CS show a filamentary network similar to the distribution of the dust continuum emission at 242 GHz. Contrary to that, species like OCS or C 2 H 5 CN show a spherical or bubble-like distribution that will be further analyzed in forthcoming papers. -We have identified eight filaments, which converge toward the central massive core or hub. All but one filament are traced in multiple molecules, including rare isotopologues. Filament F02 is detected in our dataset in only one molecule, H 2 CS. The filaments extent for about 0. 1 pc (some up to 0. 5 pc) and have masses of a few hundred M. The structure and distribution of the filaments, together with the presence of a massive central region (∼2000 M ), suggest that these filaments play an important role in the accretion process and transport mass from the outer regions to the central hub.
in prep). An accurate fit of the observed data to derive the best temperature, column densities and velocities is helpful but not mandatory. Reasonable assumptions are enough to determine which frequency transitions are detected in the observations, since the synthetic spectrum is used for the identification of bright transitions. For example, for the case of CH 3 OCHO, we identified 250 bright lines above a 10 σ threshold in the frequency range 211 to 275 GHz. This selection prevents us from including transitions that are included in the catalog entries of the CDMS and JPL databases, but are too weak and most likely non detected, in our source of interest. Moreover, the exclusion of the weak transitions, reduces the addition of components highly dominated by noise or by the presence of (bright) transitions from other species.
Second (step B in Fig. A. 1), we cut out all the identified transitions and produce subspectra centered at them. These spectra are transformed from frequency to velocity by applying the Doppler equation. The velocity at 0 km/s (see Fig. ), all spectra are averaged by taking the the arithmetic mean. In the final stacked spectra, the signal-to-noise ratio has increased, while at the same time line blendings are averaged out. This simplifies ensuing the analysis of the kinematic properties like velocity, linewidth, lineshape or number of components. The stacking process can be applied to a subsample of transitions, selected for example, by excitation energy level (E upper ) or Einstein A coefficient, parameters included in the molecular line databases CDMS and JPL. This selection of transitions will be used in a forthcoming paper to characterize the excitation and physical conditions of the filaments in Sgr B2(N).
We performed tests with synthetic spectra to demonstrate the reliability of the line stacking method. We have used the XCLASS software to generate a synthetic spectrum of the molecular species C 2 H 3 CN (Acrylonitrile), which is a good candidate since it has approximately 300 clearly detectable transitions in the observed frequency range (211-275 GHz). The synthetic spectrum of C 2 H 3 CN is produced including two different velocity components with velocities of 0 and -5 km s -1 , and linewidths of 4 and 2 km s -1. In Fig. A. 2, we show the results. In the top panel we have stacked the transitions of the synthetic spectrum. The stacked spectrum shows a clear two-velocity component profile. We fit Gaussian distributions and recover the velocities and linewidths with an accuracy of 98%. In a second run (see  Fig.
A. 2, bottom panel)  we combine the synthetic spectrum with the observed data of Sgr B2(N). We note that the molecule C 2 H 3 CN is not detected in our data and therefore the only transitions that should be found are those include in the synthetic spectrum. After performing line stacking, we recovered the velocities of the two components with a high accuracy (about 98%). The derived linewidths are slightly larger than the original ones, resulting in an accuracy of 82%. This increase in the linewidth is likely produced by the presence of neighboring transitions of other molecular species, which act like noise and result in the broadening effect. Therefore, line-stacking of chemically rich regions results in slightly broader lines. We also note that the presence of this additional transitions artificial increases the continuum level, while not affecting the velocity information of the lines.
Acknowledgements. This work was supported by the  Deutsche Forschungsgemeinschaft (DFG)  through grant  Collaborative Research Centre 956  (subproject  A6  and  C3 , project  ID 184018867 ) and from  BMBF/Verbundforschung  through the projects  ALMA-ARC 05A11PK3  and  05A14PK1. This paper makes use of the following ALMA data: ADS/JAO. ALMA# 2013. 1. 00332. S. ALMA is a partnership of  ESO  (representing its member states),  NSF (USA)  and  NINS (Japan) , together with  NRC (Canada)  and  NSC and ASIAA (Taiwan)  and  KASI (Republic of Korea) , in cooperation with the  Republic of Chile. The Joint ALMA Observatory is operated by  ESO ,  AUI/NRAO  and  NAOJ. DCL acknowledges support of the  Scientific Council of the Paris Observatory. Part of this research was carried out at the  Jet Propulsion Laboratory, California Institute of Technology , under a contract with the  National Aeronautics and Space Administration.
The assignment of transitions to molecular species is done using the software XCLASS: eXtended CASA Line Analysis Software Suite: Möller et al. (2017) , which make uses of the Cologne Database for Molecular Spectroscopy(CDMS, Müller et al. 2001, 2005)  and Jet Propulsion Laboratory(JPL, Picket et al. 1991)  catalogs, via the Virtual Atomic and Molecular Data Centre (VAMDC, Endres et al. 2016).
Discovery of protein modification sites relies on protein digestion by proteases and mass spectrometry (MS) identification of the modified peptides. Depending on proteases used and target protein sequence, this method yields highly variable coverage of modification sites. We introduce PTMselect, a digestionsimulating software which tailors the optimal set of proteases for discovery of global or targeted modification from any single or multiple proteins. Post-translational modifications (PTMs) play a crucial role in the regulation of all cellular processes in eukaryotic cells, and over 300 eukaryotic PTMs including phosphorylation, glycosylation, glycation, oxidation, are currently known 1. PTMs are emerging as important markers of aging and age-related diseases such as Alzheimer's and Parkinson's diseases, cancer or diabetes 2.
Results and Discussion PTMselect was optimized to eliminate the tedious work of manually sorting and selecting peptides to choose digestion settings before performing any MS-driven PTM analysis. This software is designed for (1) optimization of global coverage of protein PTM sites, (2) optimization of protein PTM sites coverage with the highest probability to be modified and (3) optimization of target PTM positions coverage. PTMselect needs one or more protein sequences imported in Fasta format from protein databases, the identity of the amino-acids carrying PTMs, and the cleavages sites of the proteases (Fig. 1a ). It computes all proteases combinations and the peptides released by these combinations. Peptides are further filtered by PTM sites and by size, compatible with LC-MS. A set of scores is then calculated, based on the number of PTM sites of the filtered peptides (Fig.
In case of multiple protein analysis, the software is able to merge the score table of each protein into a final score table. PTMselect can analyze any number of proteins, PTM types and combinations. PTMselect simulations are based on protease specificities, peptide lengths and amino acids carrying the protein modifications. The eight proteases mostly used in MS (and CNBr) are available by default in PTMselect, but the user can add or remove proteases. PTMselect is compatible with any protein modifications, since only the amino acids linked to the modifications are necessary for the simulations, and can easily be changed in the PTMselect configuration file. We chose protein phosphorylations to illustrate PTMselect capabilities. To estimate the real impact of PTMselect on the total number of phosphosites identifiable in a MS experiment, we selected six phosphoproteins with sizes ranging from 31.
• The maximal score is the total number of modified sites in the protein. • The ETD score is the total number of modified sites in the peptides after digestion and filtering. Indeed, any labile modified site can be attributed unambiguously by electro-transfer dissociation  19, 20. • The CID score. Labile modified sites cannot always be attributed unambiguously when modified peptides are analyzed by collision induced dissociation  19, 20  because spectra are often dominated by large neutral loss peaks compromising reliable site-specific identification  21. That is why PTMselect gives more weight to mono modified peptides in the CID score calculation. The CID score of a peptide with n modified sites is: = p n 1 CID The score of the entire protein with k modified peptides is: ∑ = = P p CID i k CID 1 i • The predicted matched score is the sum of each individual modified site score predicted by a prediction software for all peptides selected after digestion and filtering.
• The predicted unmatched score is the sum of each individual modified site score predicted by a prediction software for all peptides rejected after digestion and filtering. Results output. The five modification scores (maximal, ETD, CID, predicted matched and unmatched) for each protease combination are exported in a table. PTMselect also calculates the number of mono-modified peptides, the number of target peptides accessible or not accessible and the corresponding lists of target site positions. A graphical map representing modified peptides and modification site positions is generated for each protease combination (Fig. 1d ). The details of the modified sites in each peptide sequence and in the entire protein sequence are exported in a text file. PTMselect includes a summarizer able to process an unlimited number of score tables to calculate the sum of all the scores.