dataesr/scientific-paragraphs-categorization huggingface dataset:
Unfortunately, the data generated by these activities and institutions have not been harmonized and centralized. National atlases of tsetse and AAT are considered indispensable tools for efficient disease management in the context of the progressive control pathway (PCP) for AAT  [15]. In 2013, the Food and Agriculture Organization of the United Nations (FAO) launched a multinational project to support six AAT-affected countries (i. e. Burkina Faso, Mali, Ghana, Kenya, Ethiopia and Uganda), and one of its goals was to promote the development of the national atlases. The Insectary of Bobo Dioulasso-Tsetse and Trypanosomosis Eradication Campaign (Insectarium de Bobo Dioulasso-Campagne d'Eradication de la mouche Tsé-tsé et de la Trypanosomose-IBD-CETT, formerly PATTEC Burkina Faso), implemented the FAO project in Burkina Faso as the specialized national structure in charge of tsetse and AAT control.
Input data Input data were collected either in the framework of tsetse and trypanosomosis control operations or in the context of research activities. Control operations were mostly carried out by PATTEC Burkina Faso by using impregnated targets and traps and animal treatment. Data included both baseline cross-sectional surveys (i. e. pre-intervention) and longitudinal surveys (i. e. during or post-intervention), and provided a large amount of unpublished information. The raw data from research activities were obtained from the authors of published articles, using as a basis the systematic review of the literature carried out by FAO for the continental atlas. The full list of publications that contributed to the national atlas in Burkina Faso is provided in Additional file 1: Text S1. When the raw data underpinning publications could not be retrieved, information on AAT and tsetse occurrence was extracted directly from the papers, as done for the continental atlas.
Tsetse data In Burkina Faso, entomological surveys are mainly carried out with biconical traps  [23] , which may or may not be boosted with odour attractants  [24]. However, other traps such as monoconical Vavoua trap  [25]   [26, 27] , N'Zi traps, adhesive targets and electric targets were also occasionally used in experimental settings  [28]. The trapping duration was usually 3 days for the surveys carried out in the framework of control activities, and 1 to 3 days for research activities. All traps were geo-referenced with GPS. Entomological data were recorded at the level of individual traps. Data were initially captured in hard-copy recording sheets, which were subsequently converted into digital format (e. g. Microsoft Excel or Access). Field recording sheets include information such as the name of the surveyed location, its coordinates and administrative units (which in Burkina Faso are called regions, provinces and departments), the date of the survey, the time of trap deployment and removal (and the corresponding duration of trapping), and the number, species and sex of trapped tsetse flies.
African animal trypanosomosis data As for tsetse, AAT data were mainly collected in the framework of control activities, thus including both baseline and monitoring/longitudinal investigations. Supplementary data were generated in the context of research. AAT surveys in Burkina Faso target the main susceptible animal species such as cattle, sheep, goats and donkeys, but data on horses and camels are also occasionally collected. In most surveys, the sampling locations and the animals are selected randomly. However, a non-random sampling was sometimes performed, for example in studies of trypanocidal drug resistance  [29, 30] , or for the isolation of trypanosomes. Cross-sectional surveys provided the majority of datasets included in the atlas, but longitudinal investigations were also included  [14].
Field data recording sheets for AAT include the data source and the institution in charge, the name, geographical coordinates and administrative units pertaining to the survey village or site, the date of the survey and the sample size (i. e. the number of animals tested). The sheets also include parasitological results such as the number of AAT-positive animals by trypanosome species, the haematocrit (packed cell volume-PCV) and the possible use of trypanocidal drugs (including the type of drug). AAT data are recorded at the level of individual animal in the parasitological recording sheets, and information at the animal level was retained in the atlas. When the animal level data were not available, aggregated information at the herd/site level was recorded.
Data repository The data repository includes digital copies of all the input files used to build the atlas, i. e. spreadsheets, databases, reports, thesis and scientific articles. At a first level, the repository is organized by type of data (i. e. tsetse or AAT), at a second level by geographical area (i. e. province), and last by individual data source or publication. File names for scientific publications are standardized as author name and year of publication (i. e. Surname_ YEAR. pdf ), and for unpublished works as title of activity and year.
Tsetse database Entomological data recorded in the tsetse database are organized in six tables: 1) data sources; 2) geographical data; 3) entomological surveys (trap level); 4) tsetse catches (trap level); 5) entomological surveys (site level); and 6) tsetse catches (site level). As in all relational databases, records in each table are given a unique identifier, the 'primary key' , which allows them to be linked to records in other tables through 'foreign keys'. The table on 'data sources' summarizes information on the input files stored in the repository. In particular, it records the following information: institution, author's name, title, year of production/publication, presence of information on tsetse or AAT, availability of raw data and whether the source is published or not. The 'geographical data' table includes the location or village name, its geographical coordinates and the corresponding administrative units.
The table on 'entomological surveys' (trap level) includes the code of the trap (as per survey recording sheet), the type of trap, the attractant used (if any), the geographical coordinates of the trapping site (latitude and longitude in decimal degrees on WGS84 datum), the trapping period and its duration. Information on the possible presence of tsetse control activities in the surveyed area is also recorded. The table on 'tsetse catches' (trap level) summarizes the results of the trapping and includes the tsetse species, sex and the number of flies caught. The tables on 'entomological surveys' and 'tsetse catches' (site level) record data that were directly extracted from scientific publications when raw data at the trap level could not be obtained. These site-level tables of the national atlas for Burkina Faso have a similar structure to those of the continental atlas  [17].
African animal trypanosomosis database The database for AAT contains seven tables: (1) data sources; (2) geographical data; (3) animal species; (4) diagnostic method;  (5)  AAT data (animal level);  (6)  AAT data (herd level); and (7) chemotherapy. The tables 'data sources' and 'geographical data' are similar to those of the tsetse database. The table 'animal species' records the species and breed of tested animals, and the table 'diagnostic method' provides details on the diagnostic test used to detect AAT. The table ' AAT data' (animal level) includes the code of the animal (as per survey recording sheet), its age, sex, haematocrit/ PCV, health status, treatment with trypanocidal drugs, date of last treatment, husbandry system, date of survey, presence or absence of trypanosomes, species of trypanosomes (including subspecies/groups), type of animal sampling (random or purposeful), type of survey (longitudinal or cross-sectional) and possible presence of vector control operations during the survey.
The table ' AAT data' (herd level) is used to capture data extracted from scientific publications when the raw data at the animal level could not be obtained; as such, it follows the structure of the continental atlas  [16]. The last table (chemotherapy) provides details on the possible treatment of animals with anti-trypanosomal drugs before the survey. It includes the date and cause of treatment, the drug used, the doses and the person who administered the treatment. The detailed structure of the AAT database, including the relationships between the tables, is provided in Additional file 3: Text S3.
Development of the atlas The first step in the development of the atlas was to collect input data from all partner institutions. Workshops and meetings were organized to facilitate the process. When input data could only be retrieved as hard copy, Microsoft Excel was used to enter data in digital format. Merging data from a variety of sources into the atlas databases required a systematic process of verification and harmonization. Geographical coordinates were standardized as latitude and longitude (decimal degrees on WGS84 datum). When Universal Transverse Mercator (UTM) coordinates were reported in the input files, coordinate transformation was performed. Extensive harmonization was also needed for data on animal breeds, husbandry systems, names of geographical locations and the related administrative units.
For tsetse data, the names of locations were often missing. For AAT data, a high proportion of epidemiological records lacked geographic coordinates; in these cases, the names of the survey sites were used to extract geographic coordinates from other sources (i. e. Geographical Institute of Burkina Faso, Google Earth and Google Maps). Also, input data sheets often lacked information on whether interventions against tsetse were taking place in the study area at the time of the survey, or whether trypanocidal drugs were being used. In these cases, reports and publications were often useful to fill the gaps. When raw data could not be retrieved, information was extracted directly from the papers; for example, the maps included in the publication were imported in the GIS and georeferenced to estimate the geographical coordinates of the study sites.
Results A total of 2261 data recording sheets were included in the atlas repository ( 723 for the tsetse component and 1538 for the AAT component). The review of the published and grey literature also enabled us to identify 105 eligible documents, including scientific papers, PhD and MSc theses, and activity reports. The results of the atlas are summarized in Fig. 1 , which shows the locations where tsetse flies and AAT were detected in Burkina Faso during the period 1990-2019. Locations where surveys were conducted but tsetse and AAT were not detected are not shown in Fig. 1 , although they are included in the database of the atlas.
Tsetse fly distribution Entomological data on tsetse fly distribution were assembled for a total of 19,960 tsetse trapping events in 10,022 distinct trapping locations, including 9768 locations at the trap level and 254 locations at the site level. 'Site' locations normally refer to groups of traps, and they were used to map data from publications when the underlying trap-level data could not be obtained. The overall trapping intensity was 48,345 trap days. The bulk of the entomological data included in the atlas are from the western and south-western part of the country. In particular, intensive baseline and monitoring surveys were conducted between 2007 and 2013 in the region at the Loop of the Mouhoun River (Boucle du Mouhoun), in the framework of an attempted large-scale elimination campaign  [14, 24].
African animal trypanosomosis distribution In the AAT component of the atlas, the results of AAT diagnosis for 54,948 animal's blood samples were included, originating from 218 distinct geographic locations. Cattle account for 90. 37% of animals tested (n = 49,654), followed by sheep (5. 20%; n = 2859), goats (2. 29%; n = 1258) and donkeys (2. 10%; n = 1154). Very limited data were found on horses (n = 21) and camels (n = 2). AAT was confirmed to be present in all the tsetseinfested areas, in particular in the southern and southwestern parts of the country. Hotspots of transmission appear to be located in the areas bordering Côte d'Ivoire and Mali, and in the Mouhoun River basin. To a lesser extent, transmission occurs in the eastern part of the country, especially in the areas bordering Togo and Benin near the Arli National Park (Fig.
Database completeness A high level of completeness was achieved in the atlas database. Regarding the tsetse component, the required information items could be found for the vast majority of the entomological records, in particular trap coordinates (83. 57%), administrative units (100%) [i. e. region, province, department], location names (89. 69%), date of trapping (99. 52%), duration of trapping (97. 25%), type of trap (99. 25%), tsetse species (98. 65%), tsetse apparent densities (97. 25%) and control interventions against tsetse (76. 34%). The majority of trap coordinates were in UTM (75. 72%), so they had to be converted into geographical coordinates (Decimal Degrees). Regarding the AAT component, a similarly high level of completeness was achieved for geographical coordinates (87. 12%), administrative units (90.
The gaps are related to the inherent limitations of the existing datasets, and in particular to the geographical coverage, range of animal species tested and diagnostic methods. With regard to the geographical coverage, the main gap in the atlas is the severe lack of information from the north, north-east, north-west, centre and extreme east of the country. This situation is explained by the fact that institutions involved in tsetse and AAT research and control in Burkina Faso focus their investigations and efforts on the regions of highest tsetse infestation  [14, 38] ). On the other hand, the northern and eastern regions are plagued by insecurity, which severely limits field data collection activities in these areas. As already observed in Mali  [20] , this lack of information for a large part of the national territory hides the true extent of the AAT problem in the country.
Conversely, T. congolense and T. brucei are more frequently transmitted by tsetse of the morsitans group, which in Burkina Faso are now restricted to a few protected areas. Mechanical transmission also plays a role in the relative abundance of trypanosome species because, even though mechanical transmission of T. congolense is possible  [45] , this mode of transmission is normally much more important for T. vivax. Indeed, in some contexts, mechanical transmission is known to act as an amplifier of AAT transmission  [46] [47] [48]. As to T. brucei, it was found mainly confined to protected areas in the west, south-west and centre-east of the country. These areas are of economic interest to the country, as they include pastoral areas, a park and a reserve. In the development of our atlas, no data on T.
The development of the atlas also helped to develop capacities for data management of all the involved partners. It promoted synergies among national institutions for data collection and sharing, and the establishment of mechanisms for regular updating and upgrading. With a view to filling the present geographical gaps, AAT data collection could include the east, northeast and the centre where data are not available. Entomological surveys could also include the Batié area to update the status of G. longipalpis. Additional work may be carried out to include tsetse fly infections in the atlas.
Acknowledgements We thank the  FAO  and the  Government of Burkina Faso  for the unlimited support given to the  IBD-CETT  which enabled the compilation of all the data presented in this paper. We also thank all the institutions involving in Tsetse and AAT control and research in Burkina Faso, CIRDES,  IRD ,  CIRAD, ELAT, University of Dedougou , for their availability and their raw data sharing. Participation of integrated pest and vectors management staff of the  General Direction of IBD-CETT  in the data collection process is gratefully acknowledged. The assistance offered by the  FAO , including training of staff, scientific visits and supervision of atlas development, is greatly appreciated.
Funding The national atlas of tsetse and AAT in Burkina Faso is an initiative of the Government of Burkina Faso, through its General direction IBD-CETT. FAO assistance to this study was provided in the framework of the Programme against African Trypanosomosis (PAAT), and supported by the Government of Italy (Project 'Improving food security in sub-Saharan Africa by supporting the progressive reduction of tsetse-transmitted trypanosomosis in the framework of the NEPAD' , codes GTFS/RAF/474/ITA and GCP/RAF/502/ITA). Financial support was also provided by the IAEA.
Form of fluvial sediment In this work, we made use of 63 digitized grains that were obtained via computer tomography scanning  [44]. The scanned samples are fluvial gravels collected from the Rhine River in Germany and randomly selected from seven different size fractions, i. e. , 2. 8-4 mm, 4-5. From such a scan, we obtained the subset of the equally spaced three dimensional sample points that are contained inside the grain. We then constructed the convex hull of this point cloud as a robust measure to determine a triangulated surface mesh. With the help of the Python library trimesh  [45] , we moved the mesh's center of mass into the origin of the coordinate system, rotated it such that the principal axes are aligned with the coordinate axes, and computed the moments of inertia. As mentioned before, these moments determine the equivalent ellipsoid and, consequently, L, I, and S.
These steps are shown in Fig. 1  and Appendix provides the details about this procedure. Next, we evaluated the size, flatness, and elongation of all 63 available grains in this way (Fig. 2 ). The two latter form factors were deliberately selected from the set of available ones, see Table  1 , as they are the most commonly used and reported ones in the context of sedimentology. Some exemplary grains are visualized in Fig. 3 , also stating their flatness and elongation. The complete analysis is shown in Fig. 2    This observation is in line with other studies, e. g. , of granite rock aggregates by Zhao et al. [30]. Additionally, we gathered and visually extracted sets of flatness-elongation data from the literature, checked them for normality and extracted values of mean and standard deviation of the respective sample.
Appendix: Determination of mass-equivalent ellipsoid Given a closed surface mesh that represents the geometry of a particle, we first move its center of mass into the origin of the coordinate system. Then, the mesh is rotated such that its principal axes of inertia are oriented along the three coordinate axes. Consequently, the inertia tensor of this mesh is a diagonal matrix where the non-zero entries are the three moments of inertia I x , I y , and I z. The semi- axes of an ellipsoid with the same mass m p and moments of inertia are then given as: From them, the form parameters are given as L = 2a , I = 2b , S = 2c , assuming a ≥ b ≥ c. In our case, these operations and evaluations are carried out using trimesh, a Python library  [45]. Acknowledgements The authors want to thank Axel Winterscheid for fruitful discussions that helped to shape the research.
5 • and the presence of POAG as a dependent variable, all variables associated with glaucoma in the bivariate analysis with a p-value < 0. 20 were included in the model. The smoking status variable was forced in the model. Then, a final model adjusted for age, sex, smoking status, lens status, plasma alpha-linoleic acid (ALA), and eicosapentaenoic acid (EPA) n-3 polyunsaturated fatty acids (PUFAs) was obtained by manual backward selection. For all analyses, the tests were two-tailed and the results were considered significant when p-values were less than 0. 05. Analyses were performed using SAS software (version 9. 4; SAS Institute, Inc. , Cary, NC, USA).
We used a semiquantitative food frequency questionnaire to quantify the dietary intake in terms of carotenoid among participants in order to control for any disparity in MPOD caused by diet. In our study, there was no significant difference between the two groups in term of carotenoids intake (data not shown). One school of thought suggests from preclinical studies of the glaucoma model that MP could operate as a neuroprotective agent. MP could regulate the production of prooxidant stressors in the early ischemic retinal injury and protect the inner retina from the neurodegenerative process  [41, 42]. Another school of thought strengthened by the results of the present study found no association between MP and glaucoma  [19, 34, 36]. Hence, positive results could be explained by many confounders (healthy diet and lifetime exposure) and not independently by carotenoids and MP.
We acknowledge several limitations of this study. First, we analyzed only 611 eyes of 1153 participants in the Montrachet study due to imaging quality and availability of MP evaluation. Thus, missing data could decrease the power of our analysis even though there was no difference between participants and non-participants. Second, these findings are based on a Caucasian European population and cannot be extrapolated to other parts of the world and other ethnicities. Third, this exploratory cross-sectional study only enhanced a potential absence of association between MPOD, MP spatial distribution, and glaucomatous optic neuropathy. This should be confirmed by a longitudinal study to validate our findings. Fourth, it is also important to acknowledge that our two groups are unequal (n = 48 versus n = 553) with a small sample size of glaucomatous patients, which could lead to statistical bias and lower statistical power.
Supplementary Materials: The following supporting information can be downloaded at: https: //www. mdpi. com/article/10. 3390/jcm11071830/s1, Figure  S1 : A digital subtraction image with intensity corresponding to MPOD (right) and their measurements plotted from center to periphery of fovea corresponding to the mean MPOD at each eccentricity (left). Funding: National Research Institute for Agriculture, Food and Environment (INRAE); Regional Council of Burgundy (PARI Grant); European Regional Development Fund (FEDER); Agence Nationale de la Recherche (ANR-11-LABX-0021-01).
This cross-cohort study aimed to (1) determine a network-based molecular signature that predicts the likelihood of inadequate response to the tumor necrosis factor-ɑ inhibitor (TNFi) therapy, infliximab, in ulcerative colitis (UC) patients and (2) address biomarker irreproducibility across different cohort studies. Whole-transcriptome microarray data were derived from biopsies of affected colon tissue from 2 cohorts of infliximab-treated UC patients (training N = 24 and validation N = 22). Response was defined as endoscopic and histologic healing at 4À6 weeks and 8 weeks, respectively. From the training cohort, genes with RNA expression that significantly correlated with clinical response outcomes were mapped onto the Human Interactome network map of protein-protein interactions to identify a largest connected component (LCC) of proteins indicative of infliximab response status in UC.