dataesr/scientific-paragraphs-categorization huggingface dataset:
Simulating the diffusion process In Caballero and Hill (1992), the authors provide explicit formulas for the probabilities of fixation as well as approximations for the times to loss or fixation of an allele. Due to the bi-dimensionality of our model which largely increases the difficulty of mathematical calculations, fixation probabilities as well as laws of times to fixation, loss and absorption (either loss or fixation) of allele a are determined using simulations of Eqs. (1a) and (1b). These simulations are run using a script written in C++ (which is available from Dryad). The stochastic elements of the equations, B 1 t and B 2 t are obtained by successive samplings from a normal distribution with mean 0 and variance dt. dt is the size of the time step and is a parameter fixed at the beginning of the simulation, which we have set to 10 -4 for a carrying capacity K ¼ 100 and and 10 -5 for K ¼ 10 and 1.
Acknowledgements We thank  Sylvain Billiard ,  Emmanuelle Porcher ,  Sally Otto , and Whitlock for the helpful discussions. Numerical results presented in this paper were carried out using France Grille, CNRS and on the Biomed virtual organization of the  European Grid Infrastructure  (http://www. egi. eu)via DIRAC (http://diracgrid. org). This work was partially funded by the Chair " Modélisation Mathématique et Biodiversité " of VEOLIA-Ecole Polytechnique-MNHN-F. X. , and was also supported by the  Mission for Interdisciplinarity at CNRS  and by a public grant as part of the  Investissement d'avenir project , reference  ANR-11-LABX-0056-LMH ,  LabEx LMH. Diala Abu Awad  was funded by the  Agence National de la Recherche  ( ANR SEAD -ANR-13-ADAP-0011 ).
Samples The Hustedt diatom collection (herbarium code BRM) was the main source of material for this research (Table  1 ) and allowed us to include the slides observed by F. Hustedt (including the type slide of Fragilariopsis ritscheri) and by G. Hasle for the publications which laid the foundations for current species concepts of the three target taxa  (Hustedt 1958 , Hasle 1965). Meta-data on BRM slides can be obtained on-line via http://hustedt. awi. de. In addition, several slides from sediment core PS1768-8 from the South Atlantic (https://doi. pangaea. de/10. 1594/PANGAEA. 108079) and three slides from East Antarctica that contained problematic forms were included in the analyses (Table  1 ). With the exception of slides from sediment core PS1768-8, each image can be traced back to its slide of origin by file name.
Imaging Imaging and image analyses were performed as described in  Kloster et al. (2017) , with the exception that for high resolution imaging, valves were selected manually after a low-resolution pre-scan of the slides. This manual selection was necessary because of our focus on taxa that tend to occur in low abundances. A manually marked area of each slide was scanned with a 20x objective (ZEISS plan neofluar, NA=0. 5) in overlapping fields-of-view using a Metafer slide scanning system (MetaSystems, Altlussheim, Germany; individual field-of-view images had 1360 x 1024 pixels at 3. 1 pixels • µm -1 ). Field-of-view images were combined into virtual slides (large overview images zoomable to full original resolution) using the VSlide software (MetaSystems, Altlussheim, Germany). Target valves were located and marked manually in these virtual slides.
These positions were then imaged in a second step with a 63x oil immersion objective (ZEISS plan apochromat, NA=1. 40; again 1360 x 1024 pixels, at 9. 8 pixels • µm -1 ) at 20 focus positions in 0. 2 µm distances with the Metafer system. The 20 focus plane images were combined to produce an extended depth-of-focus image (performed as part of image processing by the Metafer image acquisition software). Figure  1  provides a schematic overview of the process.
Image analysis Segmentation and initial extraction of morphometric features from extended focus images was performed using SHERPA  (Kloster et al. 2014). Additional features which were considered taxonomically informative in the target group were quantified from the outlines as segmented by SHERPA using R 3. 2. 0 (R Core Team 2015) and the package Momocs  (Claude 2014). Although SHERPA calculates elliptic Fourier descriptors (EFDs), these were re-calculated using Momocs after an alignment procedure. The reason for this recalculation was that, during initial data exploration, it was noticed that the heteropolarity of several valve outlines in the data set led to bimodal withingroup distributions of EFDs, which could be remedied by aligning outlines accounting for heteropolarity. For this, the 60 points exported by SHERPA along each valve outline were aligned with their major axis to the X-axis of the coordinate system, centered on the midpoint of their major axis, and the slope of the regression line of absolute y-values against the x-values of the outline points was determined.
If this was negative, the outline was flipped around the y-axis and the starting point of the chain code was shifted accordingly. The coordinates of 60 points on each valve outli e a e fou d i the file Frag-3spp-all-Gabor-2. txt as a ia les X1-X60 and Y1-Y60, whereas the original outline coordinates preceding the alignment procedure can be found in the files called *. XY_EFA. csv i the su folde "HERPA output i the a o pa i g PANGAEA data a hi e. Aligned outline coordinates were used for calculating EFDs (the values of which can be also be found.
Accepted Article This article is protected by copyright. All rights reserved. i the ai data file Frag-3spp-all-Gabor-2. txt i the a o pa i g PANGAEA data a hi e. Fourteen EFDs (corresponding to 14 x 4 = 56 variables in total) were kept for further analyses because these captured 99. 9% in cumulated harmonic power in the data set as determined by the function calibrate_harmonicpower() from the Momocs package. Aspect ratio, the ratio between valve length and width, was among the features quantified using SHERPA. Heteropolarity was quantified by dividing each object outline on the minor axis of their best fitting ellipse, and dividing the difference in the areas of these two nearly-half-valves by total valve area; this number is referred to as the heteropolarity index or simply as heteropolarity in the following text, although it only partially captures heteropolarity as perceived by a diatomist.
Statistical analysis Statistical analyses were performed in R 3. 2. 0 (R Core Team 2015). Univariate analyses of variance (ANOVA), as well as bivariate analyses of covariance (ANCOVA), were performed using the lm() function; p-values associated with individual coefficients are reported as provided by summary. lm() and a p-value significance limit of 0. 05 is used. For visualizing group-wise distributions of individual variables, the sinaplot package  (Sidiropoulos et al. 2015)  was used. For multivariate classification, the functions naiveBayes() and svm() from the R package e1071  (Meyer et al. 2015) ; lda() and qda() from MASS  (Venables and Ripley 2002) ; and randomForest() from package randomForest  (Liaw and Wiener 2002)  were used. Three sets of features were used in three sets of classification experiments.
The first feature set referred to as non-EFD features included area, perimeter, length and width of valves; the heuristic shape descriptors rectangularity, compactness, ellipticity, triangularity, and roundness; the convexity indices convexity by perimeter, convexity by area, CDF, PCAF, CHMDF; and aspect ratio, stria density, stria orientation, and relative location of broadest position. The second set of features included the 56 coefficients of the 14 EFDs. The third set of features was a combination of the previous two. Images, data and analysis scripts for each substantial step of the study are provided in a Supplementary archive available from PANGAEA under https://doi. org/10. 1594/PANGAEA. 879785.
For transparency, in spite of having removed these duplicate images from our analyses, they were kept in Appendix S1, marked as duplicates. R code applicable for identifying such multiply imaged specimens automatically is now also available  (Kloster et al. 2017). In spite of these drawbacks, automated diatom slide imaging procedures  (Pech-Pacheco and Cristóbal 2002, Kloster et al. 2017 ) are now coming close to a level of maturity for routine use. However, the everyday diatom analysis workflows will still require further rethinking to fully harvest the potential of these methods, not only for automatic identification but also for alpha taxonomy of diatoms. Our study takes a step in that direction.
Acknowledgements Fu di g to Beszte i, Kloste a d Kaue as p o ided the  DFG p io it p og a e 11 8 A ta ti Resea h ith o pa ati e i estigatio s i A ti i e a eas u de fu di g odes   BE 1 / -1 | KA1655/3-1. Leventer was supported by  NSF  grant # 1143836. Barcena was supported by  University of Salamanca  grant  ID2014/0019 , The  Scientific Committee on Antarctic Research (PAIS and AnT-ERA ), The  International Arctic Science Committee ,  The Palaeontological Association  and  The Micropalaeontological Society  in the organization of the 5 th Polar Marine Diatom Workshop.
GBIF facilitates collaboration between nodes at different levels through its Capacity Enhancement Support Programme (CESP) [https://www. gbif. org/programme/82219/ capacity-enhancement-support-programme]. One of the actions included in the CESP guidelines is called 'Mentoring activities'. Its main goal is the transfer of knowledge between partners such as information, technologies, experience, and best practices. Sharing architecture and development is the key solution to solve some technical challenges or impediments (hosting, staff turnover, etc. ) that GBIF nodes could face. The Atlas of Living Australia (ALA) team developed a functionality called 'data hub'. It gives the possibility to create a standalone website with a dedicated occurrence search engine that seeks among a range of data (e.
g. specific genus, geographic area). In 2017, GBIF Benin and GBIF France wanted to strengthen their partnership and started a CESP project. One of the core objectives of this project is the creation of the Atlas of Living Benin using ALA modules. GBIF France developers, with the help of the GBIF Benin team, are in the process of configuring a data hub that will give access to Beninese data only, ‡ ‡ ‡ § ‡ § © Lecoq M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. while at the same time Atlas of Living France will give access to French data only. Both data portals will use the same back end, therefore the same databases.
Circular Dichroism. CD spectra were recorded on a Jasco J-815 CD spectrometer at 20 °C using a quartz cuvette of 10-mm optical path length. The reported spectra of DNA samples at 5 μM concentration in potassium phosphate buffer (pH 7) were the average of 3 scans over the 220-320 nm wavelength range, at the scanning speed of 50 nm/min, baseline-corrected for buffer contribution. Thermal Denaturing. Thermal denaturing experiments were performed on Jasco V-650 UV spectrometer. DNA samples at 5 μM or 100 μM strand concentration were initially heated to 95 °C for 5 min and cooled to 20 °C by a temperature ramping rate of 0. 1 °C/min, followed by heating from 20 to 95 °C at the same rate. UV absorbance at 295 nm was measured every 0. 5 °C. Obtained data were plotted as folded fraction against temperature and the melting temperature was determined as the value at which the folded fraction was 0.
5 °C and independent of the DNA strand concentration (5 to 100 μM), consistent with the formation of a monomeric G-quadruplex structure. Additionally, on a native gel the migration of LTR-III was similar to that of a monomeric threelayered G-quadruplex structure  35  (Figure  S1B ). Overall, these data support the formation of an intramolecular monomeric G-quadruplex structure. LTR-III G-Quadruplex Adopts a (3 + 1) Folding Topology Containing a Diagonal Stem-Loop. To elucidate the folding topology of LTR-III, NMR spectral assignment was performed using well-established protocols. 36 Imino protons (H1) involved in base-pairing formation were assigned using site-specific low-enrichment (2-4%)  15  N-labeling (Figure  3A ),  37  except for G11 for which H1 was assigned using NOE connectivities observed at low temperature (10 °C) (Figure  S2 ).
■ DISCUSSION In this work, we demonstrated that LTR-III folds in a hybrid quadruplex-duplex conformation with a three-layered G-tetrad core arranged in a (3 + 1) topology and a long 12-nt loop forming a hairpin structure. NMR analysis of the sequence named LTR-III+IV and able to form both LTR-III and LTR-IV G-quadruplexes showed that the folding topology of LTR-III is still conserved, suggesting the preferential folding of LTR-III G-quadruplex within the dynamic context of multiple conformations. Hybrid quadruplex-duplex structures have been described previously as artificial constructs with different relative quadruplex-duplex orientations, exploring junction and connection varieties. 32 Our structure of LTR-III G-quadruplex containing a duplex hairpin across a diagonal loop reveals a significant tilting between the helical axis of the duplex and that of the quadruplex, contrasting the feature observed for an artificial hybrid quadruplex-duplex also containing a duplex hairpin across a diagonal loop (PDB code 2M91) (Figure  S12 ).
Establishing reference values for MRI biomarkers will be important and complex MRI datasets (especially if multiparametric) will require detailed analysis plans with input from both imaging and biostatistics experts. Recommendation 5: The biological validity of renal MRI needs to be determined through cross-sectional studies in which MRI biomarkers are compared against renal biopsy In clearly defined patient cohorts (both CKD and renal transplantation), individual or combinations of MRI biomarkers should be compared against quantitative renal histology techniques that measure important biological processes such as fibrosis (glomerulosclerosis score, extent of interstitial fibrosis, collagen accumulation), inflammation (density of inflammatory cells and cell subtypes), peritubular capillary density and podocyte loss.
Given the weight of evidence that albuminuria is a marker of kidney damage and an independent predictor of adverse outcomes associated with CKD  [67] , studies should correlate MRI measures with the magnitude of albuminuria and changes in albuminuria over time. In cross-sectional studies, fasting and hydration should be documented, as these are known to modulate MRI biomarkers and estimates of renal function. Recommendation 10: Biosample storage, data storage and matched image banking should be built into prospective MRI studies to generate linked clinical data, biosamples and imaging biomarkers Imaging biobanks will permit assessments of combinations of genetic, molecular and imaging biomarkers, the use of additional filtration markers that may help improve the accuracy of eGFR equations or the use of a panel of urine and blood injury markers to provide an additional way of establishing biological validity (e.
F U N D I N G P. B. is supported by the  Deutsche Forschungsgemeinschaft (DFG ;  BO 3755/6-1 ,  SFB/TRR57 ,  SFB/TRR219 ) and by the  German Ministry of Education and Research (BMBF Consortium STOP -FSGS number  01GM1518A ). Alberto Ortiz is supported by  Instituto de Salud Carlos III  ( PI16/ 2057 ,  RETIC REDINREN RD16/0009 ),  FEDER  funds and  Comunidad de Madrid   B2017/BMD-3686 CIFRA2-CM. Aghogho Odudu  is supported by an  Academy of Medical Sciences  starter grant ( SGL015/1019 ) and  National Insitute for Health Research Lectureship  ( CL-2014-06-003 ). S. S. is partly funded by the  BEAt-DKD  project through the  IMI 2 JU  under grant agreement  115974  (www. beat-dkd. eu). J. P. V. and H. C. T. are partially supported by  Swiss National Foundation  grants  FNS 32003B_159714/1  ( ME10250 ) and IZCOZ0_177140/1.
Microbiological investigations WGS of Salmonella isolates has been performed routinely at the French NRC since April 2017. DNA extraction, libraries and high-throughput genome sequencing for our cases were carried out at PIBnet, Institut Pasteur, Paris on the Illumina NextSeq500 platform. Molecular serotyping was done by in-house scripts based on MLST-7, fliC and fliB gene databases. For all 88 S. Agona isolates received in the NRC between 1 January and 31 December 2017, the filtered pairedend reads were aligned with the Agona SL483 reference genome (GenBank accession number NC_011149)  [2]. Phylogenetic analysis was performed on the single nucleotide polymorphism (SNP) filtered alignment using the maximum-likelihood method, and the final tree was visualised as previously described  [3]. Raw reads of a representative strain are available under the European Nucleotide Archive number ERR2219379 and under Enterobase name SAL_NA11229AA.
Acknowledgements We thank all French medical laboratories participating to the clinical network of Salmonella. We acknowledge all the team of the  NRC  for their excellent work in Salmonella processing. We warmly thank  Edith Laurent ,  Isabelle Billecoq  and epidemiologists located in  Agence Régionale de Santé  and in Regional offices of SPF in interviewing parents of cases. We thank  Silvia Herrera Leon  for sending the Spanish strains, and  Kassiani Mellou  for sharing information about the Greek strain.
| Molecular coordinates In this research, we used the coordinates of a GABA A receptor model from the work of  Mokrab et al. 11  This model used as template the nicotinic acetylcholine receptor (nAChR) structure from the work of Unwin,  12  where five intracellular helices were resolved (Protein Data Bank code: 2BG9). Thus, this is the only model of the GABA A receptor that includes part of the intracellular domain. The subunit composition of this receptor is (α1) 2 (β2) 2 γ2. There exist five stand-alone structures of GABARAP, and their Protein Data Bank codes are, respectively, 1GNU, 1KJT, 1KOT, 1KLV, and 1KM7. 1GNU and 1KJT come from X-ray crystallography experiments, and we chose 1GNU because of its higher resolution of 1. 75 Å. 1KOT, 1KLV, and 1KM7 all come from NMR experiments; 1KM7 contains only one conformer, while residues 1-17 in 1KLV could not be located and so we chose 1KOT with 15 conformers.
| Docking There are 15 slightly different conformations in the NMR structure 1KOT. They will hereafter be called 1KOT model 1 to 1KOT model 15. The X-ray structure 1GNU contains only one coordinate set, but Ser 16, Ser 53, and Arg 65 have been resolved with two alternative conformations, each with occupancy 1/2. We thus generated eight structures from the 1GNU coordinate set, each with slightly different conformations. They will hereafter be called 1GNU-aaa to 1GNU-bbb, depending on whether the A-form or the B-form from the Protein Data Bank was chosen. Twenty-three coordinate sets, 15 from NMR experiments, and eight from X-ray crystallography experiments, were used as the ligand for SwarmDock. 14, 15 This docking method allows for flexibility of the molecules using normal modes,  16  and the use of the program is available on a public server (as of the time of writing this article, the SwarmDock server resides on https://bmm.
The van der Waals cut-off was 12 Å, and Ewald summation was used for long-range electrostatics. The time-step was lengthened to 2 fs over 30 000 time-steps, while all main-chain nitrogen atoms of the three helices were tethered with a force constant of 2 kJ/mol/Å 2. A 40-ns equilibration was carried out on the initialised system, followed by a data collection period of 100 ns. Configurations were output every 2 ps. We calculated the r. m. s. deviation of the simulated structures from the original starting structure. We also evaluated the distance between the γ2-subunit helix Asp 423 and GABARAP Lys 46, and γ2-subunit Ile 438 and GABARAP Gln 59. As can be seen in Figure  2 , Asp 423 is at the membrane end of the intracellular helix, and Ile 438 is at the cytoplasmic end of the helix. We monitor these distances to see if GABARAP stays bound to the GABA A receptor throughout the simulations.
| Free energy change calculations The molecules were prepared using the CHARMM-GUI freely available on the web (as of the time of writing this article, the address of the CHARMM-GUI is http://charmm-gui. org). 17 The molecular dynamics package NAMD 2  18  was used in this work. In the simulation of the intracellular helices of the GABA A receptor we first selected atoms from the following amino acids: α1-subunit Lys 391-Leu 422, β2-subunit His 421-Ile 449 and γ2-subunit Asp 413-Ser 443. The helices were placed in a periodic box with at least 10 Å between the protein and its image. The system consisted of 19 708 water molecules, 56 K + ions and 73 Cl -ions to achieve a [KCl] of 0. 15 mM. The system comprised a total of 61 857 atoms. The system was minimized for 10 000 steps with all the protein atoms frozen.
The van der Waals cut-off was 12 Å, and Ewald summation was used for longrange electrostatics. The time-step was lengthened to 2 fs over 40 000 time-steps. The system was then equilibrated for 2 ns. Data collection was carried out for 5 ns, again with all main-chain nitrogen atoms frozen, with configurations output every 0. 5 ps. We obtained a total of 10 000 configurations for each model of the hydrated GABARAP. The MD trajectory for the GABA A receptor was processed as described by Vukovi c et al. 10  First, hydration sites as defined by Haider and Huggins  19  were created on all surface regions of the GABA A receptor. The hydration sites were time averaged water molecules assigned positions, densities and occupancies. 20, 21 Hydration sites with a radius of 1. 2 Å were picked starting from the densest patch of water in order of decreasing density and no sites were picked within 2.
There are a large number of hydration sites not involved in the binding of these three proteins. However, when we examine the crystallographic datasets, we find that these sites are involved in dimerisation or trimerisation. It is still unknown how GABARAP dimerises in the cell, so it is uncertain if these crystallographic oligomers represent the natural state of oligomerisation. Table  6  also shows the sites involved in GABARAP-GABARAP interfaces ("self-interaction"). Note that Coyle et al  4  suggested a dimerisation face for GABARAP, but since no related PDB dataset has been reported, we have deduced the overlapping site from Figure  1  of the paper by Coyle et al. 4  Moreover, the dimerisation suggested involves the N-terminal amino acids "swinging out" to produce the "open" form of GABARAP; this "open" form of GABARAP is in a dimer form, and also simultaneously binds tubulin and the GABA A receptor.
30  Diagram showing the GABA A receptor red and orange hydration sites on the surface of its γ2-subunit. In this diagram, the GABA A receptor "close," "regular" and "far" red hydration sites, as described in Table  3  are combined to give the red sites, and the "close," "regular," and "far" orange sites are combined to give the orange sites. The GABARAP residues are colored to correspond to their nearest sites according to the convention in The interaction between the glycine receptor and gephyrin has been studied experimentally. Gephyrin was first identified as a protein which bridged the glycine receptor and tubulin. 31 Sola et al. 32  cocrystallized a segment of the glycine receptor β-subunit and a partial dimer of the cytoplasmic protein gephyrin (Protein Data Bank code: 1T3E). They were able to resolve the structure of a pentapeptide portion of the glycine receptor β-subunit and the gephyrin domain E dimer.