dataesr/scientific-paragraphs-categorization huggingface dataset:
Fibre orientation estimation and tractography Prior to "XTRACT", the crossing fibre model described in  (Jbabdi et al. , 2012)  was applied to the diffusion data using FSL's bedpostx and used to estimate orientations to inform tractography. This is a parametric spherical deconvolution model that accounts for the non-monoexponential decay of the dMRI signal with higher b-values. Up to three fibre orientations were estimated in each voxel along with their uncertainty. The XTRACT toolbox read the standard space tractography protocols and performed probabilistic tractography  (Behrens et al. , 2007). As discussed before, tractography protocols were defined for each bundle using a unique combination of seed, target, exclusion and stop masks, along with a seeding strategy (see Table  1 ). A number of default tractography termination criteria were also used in all protocols (curvature threshold: AE80 , max streamline steps: 2000, subsidiary fibre volume threshold: 1%, randomly sampled initial fibres in case of fibre crossings in a seed location, no minimum length constraint, loop-checking and termination).
WM tract and WGB termination atlases of the human brain We applied the prescribed tractography protocols to ~1000 HCP and 1000 UK Biobank subjects. Fig. 3  presents the tract atlases, obtained from the HCP datasets. To obtain these atlases, the subject-specific MNItransformed tracts were binarised and subsequently averaged to produce the population percent coverage for every tract, shown in the Figure. The atlases obtained using the UK Biobank data are shown in Supplementary Figure  1. Connectivity blueprints were also derived for each HCP subject and averaged to obtain an atlas. Examples of columns of this average Fig. 11. Examples of tractography results for a subset of the subjects found to have anatomical abnormalities, demonstrating that cohort-averaged tracts do not respect underlying anatomical abnormalities.
0. 2 and later (www. fmrib. ox. ac. uk/fsl/XTRACT). Tract atlases will be made available in the next release of FSL and are currently available via GitHub (https://github. com/SPMIC-UoN/XTRACT_atlases). connectivity blueprint across all HCP subjects are shown in Fig. 4 , representing atlases of termination points of each tract on the white-grey matter boundary (WGB) surface. We also investigated the effect of sample size on tract atlas creation. For each of the HCP and UK Biobank cohorts, we produced tract atlases with increasing numbers of subjects and cross correlated, tract-wise, each set of atlases to a 1000-subject atlas set. Supplementary Figure  2  shows the distributions of the tract-wise correlations for each of the sample size atlases. The top plot includes an atlas set with a sample size of 10 subjects which, whilst already showing high correlations (>0.
Robustness against datasets To explore robustness against varying data quality, we compared tract atlases and inter-subject variability of the tract reconstructions within and across cohorts. To compare atlases, each tract from the HCP atlas set was cross correlated with its corresponding UK Biobank tract atlas (population threshold of 30% applied to each tract atlas). The average correlation across tracts was 0. 80 (standard deviation ¼ 0. 07). Inter-subject correlations were obtained by cross correlating random subject pairs tract-wise (i. e. correlating the normalised path distributions in MNI space for each tract) and averaging the correlation across tracts for each subject pair. This was repeated for many subject pairs within and across cohorts. To avoid possible family structure-induced bias in the HCP, we restricted our subjects to the 339 unrelated subjects.
We matched the number of subjects in the UK Biobank data by randomly selecting 339 (gender matched) subjects. The across-cohort comparison was made by correlating a random subject in the unrelated HCP subject pool with a random UK Biobank subject, giving a distribution of 339 correlations per tract. Within-cohort comparisons gave average correlation values of 0. 51 (standard deviation ¼ 0. 03) and 0. 54 (standard deviation ¼ 0. 03) for the HCP and UK Biobank respectively (p ¼ 8 Â 10^-46) (Fig. 5 ). Across-cohort comparison gave an average correlation of 0. 41 (standard deviation ¼ 0. 03) which is lower than within-cohort comparisons (p ¼ 1 Â 10^-110 and 2 Â 10^-110), yet it is comparable enough, particularly given the differences in data quality and the age difference of subjects in the two cohorts (HCP: 22-35 years old, UK Biobank: 40-69 years old, mean age for our chosen subjects in HCP ¼ 28.
Discussion We have presented a new toolbox (XTRACT) for automated probabilistic tractography along with standardised protocols for extracting white matter bundles in the human and the macaque brain. We have demonstrated that the protocols are robust when applied to data of varying image quality and to data from a non-human primate species. We have generated human WM tract atlases using an order of magnitude more data than previous efforts, as well as macaque atlases using a small number of, however high-quality ex vivo, datasets. We have performed indirect validation illustrating that reconstructed tracts are left/right asymmetric when they are expected to be based on previous literature. We have also shown that despite automatically generating tracts using standard-space protocols, the protocols respect the underlying individual variability, as reflected in twinship-induced similarities and in respecting anatomical abnormalities.
The toolbox, tractography protocols and atlases are freely and openly available as a part of FMRIB's software library (FSL) (version 6. 0. 2 and later). A current issue in the field of tractography is that protocol definitions in the literature often lack detail or are designed without data-sharing in mind. Here, we offer a platform for direct sharing of standardised protocol masks and tract atlases, allowing for the standardisation of tractography protocols across studies and aiding reproducibility. Moreover, we made the protocol definitions generalisable across species to directly facilitate comparative anatomy studies. Anatomists/tractographers may exchange their tract definitions/methods and hopefully converge on consensus protocols, as is the focus of a current multi-centre consortium on defining and standardising WM tractography (cf.
Schilling, Landman, Descoteaux et al. ). We believe that XTRACT can contribute to these efforts. A platform for tractography protocol definitions is also presented in  (Wassermann et al. , 2016) , where a white matter query language (WMQL) is devised. Our approach uses a similar logic to WMQL, in the sense that it also relies on masks and Boolean operations on streamlines going through those masks. However, our protocols are generalisable and their utility in both the human and non-human primate brain as has been demonstrated here. Also, a main conceptual difference is that we don't rely on an automated grey matter (GM) parcellation, such as WMQL, but instead on hand-defined WM masks. WMQL relies on seeding in WM and defining cortical endpoints through subject-wise brain parcellations. Using this approach for tracking into GM has challenges; bottlenecks exist in the cortical gyrus, after which fibres fan out, and most tractography algorithms have issues resolving this fanning  (Maier-Hein et al.
, 2017). To mitigate these issues, our protocols are not dependent on GM masks. We instead focus on reconstructing the main body of the tracts of interest using ROIs mostly in WM. In order to obtain cortical termination points of WM tracts, we take the opposite approach of tracking from the GM surface towards the WM, thus following the direction in which the fibres are expected to merge, rather than to fan out. We then multiply the surface-to-WM tractrogram with that of the body of the tract to create the WM by GM surface projections of the tract (connectivity blueprint). This avoids some of the major problems associated with tracking towards the surface  (Eichert et al. , 2019b; Mars et al. , 2018b). We reconstructed tracts using imaging datasets of different quality and we generated atlases for both the Human Connectome Project (HCP) and the UK Biobank cohorts.
Comparisons of tract reconstructions within and across the human cohorts demonstrate that the method and protocols are robust across subjects and against data quality. The HCP and UK Biobank cohorts provide examples of high-quality data and more typical quality data respectively. Within cohort comparisons reveal similar intersubject tract correlations across the varying quality data, with greater inter-subject tract correlations observed in the UK Biobank. This may reflect a reduced level of detail in the lower resolution UK Biobank data compared to the HCP data, but also differences in the mean age of subjects in the two cohorts. In addition, we have generated atlases using a smaller cohort of macaques. To compensate for the small number of subjects, we used high-quality and high-resolution ex vivo data.
Conclusions In conclusion, we have developed and demonstrated a set of robust and standardised tractography protocols for cross-species automated delineation of white matter bundles, along with a platform to use them. The demonstrated toolbox (XTRACT) is freely available along with the tractography protocols and human/macaque tract atlases as a part of FMRIB's software library (FSL version 6. 0. 2 and later). Given the benefits with regards to data and protocol sharing, we expect that this toolbox will aid reproducibility in the field of tractography and facilitate comparative neuroanatomy studies.
Acknowledgements S. W. is supported by a  Medical Research Council PhD Studentship UK  [ MR/N013913/1 ]. K. L. B. was supported by a  Marie Skłodowska-Curie Individual Fellowship Grant   MSCA -IF [750026 ]. R. B. M. is supported by the  Biotechnology and Biological Sciences Research Council (BBSRC)   UK [BB/N019814/1 ] and the  Netherlands Organization for Scientific Research NWO Netherlands  [ 452-13-015 ]. J. S. was supported by a  Sir Henry Dale Wellcome Trust Fellowship UK  ( 105651/Z/14/Z ). G. D. is supported by an  MRC Career Development Fellowship   UK [MR/ K006673/1 ]. S. J. was supported by a  Wellcome Trust   Collaborative Award   UK [215573/Z/19/Z ]. The work was also supported by grant  EP/ L023067/1  from the  UK Engineering and Physical Sciences Research Council (EPSRC)  and by a  Wellcome Trust  grant  UK [217266/Z/19/Z ].
Human datasets were provided in part by a) The Human Connectome Project,  WU-Minn Consortium  (Principal Investigators:  David Van Essen  and  Kamil Ugurbil ;  1U54MH091657 ) funded by the 16  NIH Institutes  and Centers that support the  NIH Blueprint for Neuroscience Research ; and by the  McDonnell Center for Systems Neuroscience at Washington University  and b) The  UK Biobank Resource  under Application Number  43822. The computations described in this paper were performed using the  University of Nottingham's Augusta HPC  service and the  Precision Imaging Beacon Cluster , which provide High Performance Computing service to the  University's research community. The  Wellcome Centre for Integrative Neuroimaging  is supported by core funding from the  Wellcome Trust  [ 203139/Z/16/Z ].
[29] , as well as the lack of consensus concerning conceptual bases of body image disturbances (BIDs)  [28]. The alternative-the paper-based FRS-can be criticized for its unrealistic representations of one's own body-its lack of ecological validity due to the exclusive use of frontal views of bodies, and the incomplete representation of the full range of body sizes in the population, such as obesogenic body types  [30]. In regard to the lack of ecological validity due to the 2D visual perspective, in the last two decades, virtual reality (VR) technology has increasingly been used to better understand the concept of body image and to assess and treat BIDs. The research team led by Riva conducted the first pioneering studies of the application of VR to assess and treat BIDs  [31, 32]. They developed a software package, the BIVRS (Body Image Virtual Reality Scale;  [31, 33] ), with a 3D graphical interface representing nine male or nine female figures ranging from underweight to overweight.
All figures were represented in an allocentric (i. e. , third person) perspective, as in the classical paper-based FRS. This perspective corresponded to a non-immersive VR modality. Participants could choose the figures that best represented their mental representation of their actual and ideal body size. The discrepancy between perceived and ideal body size was adopted as a measure of body image dissatisfaction  [31, 33]. The BIVRS software was used by Riva and colleagues in several studies for assessing changes in BIDs after treatment  [13]. In Spain, Perpiña and colleagues  [34]  designed and developed another VR software for the assessment and treatment of BIDs in EDs. Their VR application consisted of a 3D virtual human body, presented in an allocentric perspective, whose body parts could be modified by the participant using a slider bar.
Statistical Analysis The participants with missing data (n = 2) were excluded from the analysis. To document the potential impact of gender on the results, all statistical analyses were also performed separately for females and males. The results did not differ when analyzed separately for each sex (i. e. , significant differences remained significant, and non-significant differences remained non-significant). Therefore, to maximize statistical power, results for the aggregated sample were reported (results analyzed by sex are available upon request). Parametric variables were represented as mean ± standard deviation (SD). Statistical analysis was performed using Stata 16. 1 software. In the paper-based FRS and eLoriCorps conditions, score amplitude indicated the severity of BIDs, with a score of zero indicating no BIDs.
Funding: This research was funded by  RBC Royal Bank, Lemaire family, Fond. UQTR-RBC Banque Royale-PI-Loricorps ,  2017-2021 , and by the  Fonds de Recherche du Québec-Société  et culture,  FRQSC-2014-NP-17646 ,  2013-2020. Acknowledgments: Special thanks go to  RBC Royal Bank, Lemaire family , and  Fonds de Recherche du Québec-Société  et culture, whose patronage helped finance the completion of this study. Special thanks to  Kate Finegan  for helping with the language review.
ASTEC-Na model development The three ASTEC-Na modules that focussed on the modelling efforts were CESAR, ICARE-SFR and CPA*. The final in-vessel and ex-vessel modelling capabilities listing the models that were developed are displayed in Figure  7. The ICARE module development particularly benefited from accurate fuel thermomechanical and fission gas models issued from SCANAIR  1  for describing the pin behaviour during accidental transients which makes it very promising for assessing future SFR designs  [9]. A highly flexible point-kinetics model was also implemented with the possibility to use time-dependent reactivity coefficient provided by neutron physics codes  [10]. The in-containment source term modelling in CPA* was focused on the Na-particle generation from pool fires and their chemical ageing.
ASTEC-Na model verification and validation The CESAR thermos-hydraulic module, where the models developed most, pointed out good performances (i. e. boiling onset) for the single phase where the quality of ASTEC-Na results were found similar to what exhibited by more mature codes. For two-phase thermal-hydraulics, the pressure drop calculated by the 5-equations model was generally too large and some deviations were found in the calculation of the two-phase front radial propagation inherent to the 2D axial-symmetric model. In ICARE, though the RIA model showed its capability to reproduce the dynamics of the physical phenomena (i. e. internal pressure built-up, gap closure, clad straining, etc. ), some deviations from data trends during PCMI 2  (i. e. axial fuel expansion, clad deformation) were observed that could prevent from an adequate molten fuel pressurization and clad failure calculation.
Recommendations for the future The ASTEC-Na tool, though offering great opportunities was still far from being mature at the end of the project The SWOT analysis performed in analysing the code weaknesses and threats allowed to point out the priorities in future development of the missing models and, beyond ASTEC-Na, to make some key recommendations for any forthcoming development and validation of a safety analytical tool: extend the validation of prototypic MOX fuel thermosmechanical and fission gas models to the high temperature domain covered in SFR transients; perform further analytical work on in-containment and in-vessel fission product behaviour to alleviate the scarcity of experimental data in the open literature. As for ASTEC-Na, the development of an interface with a fuel irradiation and a neutron physics codes to minimize as far as possible the user work was strongly recommended and the continuation of the sensitivity studies on the RIA model key parameter warmly advised.
Pool thermal hydraulics Although it is recognized that pool thermal-hydraulics as such is highly design dependent, the development and validation of modelling approaches for pool thermalhydraulics is not. In order to improve the validation base, liquid metal experiments were performed at different scales. Firstly, an experiment in the TALL-3D facility which includes a small pool in which thermal stratification and mixing phenomena can be studied. Four large scale experiments have been performed in the CIRCE facility using the so-called ICE test section which has been instrumented such that relevant data for thermal stratification and flow patterns can be extracted. The ESCAPE facility, a scaled down mock-up of MYRRHA, is instrumented such that relevant data for thermal stratification and flow patterns can be extracted.
System thermal hydraulics Traditionally, the analysis of nuclear system behaviour is performed using system thermal-hydraulics codes. Such analyses are validated using integral design specific experiments or reactor data from prototype, test, or demonstration reactors. In recent years, the traditional approach of using system thermal-hydraulic codes is supplemented with new multi-scale approaches in which system thermal hydraulics codes are coupled to detailed three-dimensional CFD approaches. SESAME project aimed at extending the validation base by providing reference data at different levels. The validation data were provided in loop scale by experiments in the NACIE-UP facility, focused on the multi-scale coupling of the behaviour in the fuel assemblies and the loop system. Scaling up, the CIRCE facility in the so-called HERO configuration is used to provide experimental validation data.
WP2 determines experimentally all safety-related data of the fuel salt. WP3 investigates experimentally and numerically the natural circulation dynamics of the fuel salt in the primary vessel and emergency drain tanks, and the behaviour of the salt in the freeze plugs during a drain transient. WP4 assesses numerically the accident scenarios identified in WP1, which include the normal operation transients and the off-normal accident scenarios. WP5 assesses experimentally and numerically the safety aspects of the chemical extraction processes, and the interaction between the chemical plant and the reactor. WP6 covers the dissemination and exploitation of knowledge and results, e. g. by education and training of young scientists. SAMOFAR is the latest MSR-related project in a successful series (MOST, ALISIA, EVOL) and started in August 2015.
The design and construction of the SWATH facility and the test sections in which the experiments will be carried out have been completed. SWATH uses a molten salt between 500 °C and 700 °C to perform thermal hydraulics measurements, including phase change phenomena and experiments on freeze plugs. In WP4, transient calculations based on the scenarios identified in WP1 will be performed based on leading-edge multi-physics codes including uncertainty propagation. Verification and validation of these code systems has been done via code-to-code comparison and by using the experimental data generated in WP3. In WP5, the fuel salt processing scheme has been updated, and thermochemical calculations have revealed the transfer coefficients. This data has been used to calculate the radionuclide inventory at each stage using new software, as well as the radioactivity, the decay heat production and the shielding requirements.
6), regarding the design of the seismic isolation systems of the ASTRID and ALFRED reactors. The ALLIANCE project is helping to realise the vision of a next-generation GFR in one of four central European countries during the next decade. Outcomes will help meet EU energy and climate targets. The JASMIN project has fostered a collaborative work on the integral Beyond Design Basis Accident (BDBA) ASTEC-Na code development and validation. The project, relied on the PIRTs produced within the previous CP-ESFR FP7 project, capitalized the large amount of knowledge produced since 40 years in this field in the ASTEC-Na code development by collecting and sharing some past experimental program results, and disseminated it to end users. JASMIN end-products were the final version of the ASTEC-Na code and the associated validation experimental matrices.
Obviously, such a problem cannot be resolved by a small, C&S action; however, VINCO contributes to its solving by building a research platform able to cope with one of the future concepts, gas-cooled nuclear reactors, in Visegrad countries. Within the SESAME project, new analytical and simulation methods are being validated with reference data. Most of these reference data are based on experimental results and, when not feasible, are complemented or replaced by high fidelity simulation data (typically DNS or LES). As such, within these projects, experiments, high fidelity reference simulations and pragmatic engineering simulation will go hand-in-hand providing not only the international liquid metal fast reactor designers, but also the light water community with valuable new reference data and modelling approaches.
Introduction Accurately identifying organisms observed in the wild is an essential step in ecological studies. Unfortunately, observing and identifying living organisms requires high levels of expertise. For instance, plants alone account for more than 400,000 different species and the distinctions between them can be quite subtle. Since the Rio Conference of 1992, this taxonomic gap has been recognized as one of the major obstacles to the global implementation of the Convention on Biological Diversity  [6]. In 2004, Gaston and O'Neill  [27]  discussed the potential of automated approaches for species identification. They suggested that, if the scientific community were able to (i) produce large training datasets, (ii) precisely evaluate error rates, (iii) scale up automated approaches, and (iv) detect novel species, then it would be possible to develop a generic automated species identification system that would open up new vistas for research in biology and related fields.
Data Collection: The task will rely on a large collection of more than 60,000 herbarium sheets that were collected in French Guyana (The "Herbier IRD de Guyane", CAY  [14] ) and digitized in the context of the e-ReColNat project  [8]. iDigBio  [11]  hosts millions of images of herbarium specimens. Several tens of thousands of these images, illustrating the French Guyana flora, will be used for the PlantCLEF task this year. A valuable asset of this collection is that several herbarium sheets are accompanied by a few pictures of the same specimen in the field. For the test set, we will use in-the-field pictures coming different sources including Pl@ntNet  [20]  and Encyclopedia of Life  [9]. Task Description: The challenge will be evaluated as a cross-domain classification task. The training set will consist of herbarium sheets whereas the test set will be composed of field pictures.