dataesr/scientific-paragraphs-categorization huggingface dataset:
Efforts to quantify canopy texture features and their link to AGC had limited to no success. Our analysis provides insights into the rate at which deforestation and reforestation has taken place over a multi-decadal scale in the central Congo Basin. As such, it provides a useful historical context while interpreting past and ongoing forest research in the area. Zenodo: https://doi. org/10. 5281/zenodo. 3547767. All data not included in the latter repository can be found bundled with the analysis code as listed below. Proprietary datasets (i. e. , Geo-Eye data) are not shared, but purchase order numbers allow for acquisition of these datasets to ensure reproducibility.
Code Availability All analysis code is available as R/python  [65]  projects (https://khufkens. github. io/orthodrc and https://khufkens. github. io/orthodrc_cnn/). The analysis relied heavily on the "raster"  [66] , "RStoolbox"  [67] , and "landscapemetrics"  [43]  packages, while post-processing and plotting was facilitated by the "tidyverse" ecosystem  [68] , "ggthemes"  [69] , "scales"  [70] , and "cowplot"  [71]. Additional plotting elements were formatted or provided by "sf"  [72]  and "rnaturalearth" [73] packages. I am grateful for the contributions to the scientific community by the developers of these packages.
adolescents of the IMAGEN sample, the NEO-FFI was acquired at three measurement occasions across five years. Based on a partial measurement invariance second-order latent growth curve model we conducted whole-brain analyses on structural MRI data at age 14 years, predicting change in neuroticism over time. We observed that a reduced volume in the pituitary gland was associated with the slope of neuroticism over time. However, no relations with prefrontal areas emerged. Both findings are discussed against the background of possible genetic and social influences that may account for this result. The search for neural correlates as underlying foundation of personality has received reasonable attention in the field of personality neuroscience, where traits as one core aspect of personality are linked to underlying brain areas and function in order to understand personality and individual differences on 'biological' level  1.
Results Measurement invariance. As a first step, the 12 neuroticism-items of the NEO-FFI serving as manifest indicators of the measurement model were tested for different degrees of measurement invariance (see Fig. 1  for the development of mean scores). Configural invariance was tested, that is, all 12 indicators were forced to load on the one latent factor at each time-point. The model fitted the data well (adjusted χ 2 = 1134. 62, df = 534, p < 0. 001, RMSEA = 0. 025 (90% CI: 023-0. 027), CFI = 0. 96). In a second step, weak measurement invariance was tested, that is factor loadings were constrained to be equal across time. This model did not result in a substantial loss of model fit, although the chi-square-difference was significant (adjusted χ 2 = 1,208. 75, df = 556, p < 0. 001, RMSEA = 0.
Methods Participants. We used data from 1,808 healthy 14-year old adolescents (mean age = 14. 4 years, SD = 0. 46 years; 884 males) who were recruited within the scope of the IMAGEN project, a European multi-center genetic-neuroimaging study in adolescence  45. The selection of the participants was based on the availability of structural imaging data at age of 14 years additionally to self-report personality data. Self-report retest data at age 16-17 years was available for 1,414 participants (mean age = 16. 4 years, SD = 0. 65 years; 692 males) and at age 19 years for 1,282 participants (mean age = 19. 0, SD = 0. 74 years; 609 males). We had three different patterns of dropout: dropout after baseline, dropout after second measurement occasion, and intermittent dropout after second measurement occasion with return for the third measurement occasion.
12 Items describing neuroticism from the 60-item-scale were selected for the present analyses. The NEO-FFI represents a short form of the extensive 240-item NEO-PI-R. Items were assessed on a 5-point-Likert scale from strongly disagree to strongly agree. Four items had to be reverse coded. Scanning procedure. Structural MRI was performed on 3 Tesla scanners from three manufacturers (Siemens: 5 sites; Philips: 2 sites; and General Electric: 2 sites). The details of the entire MR protocol are described elsewhere. In this study, we used the T1-weighted images. These high-resolution anatomical MRIs were obtained using a three-dimensional sequence based on the ADNI protocol (http://adni. loni. ucla. edu/research/protocols/ mri-protocols/). Voxel-based morphometry. In order to evaluate if and how structural data from baseline predict developmental changes at following measurement occasions, we applied whole-brain voxel-wise analyses.
52. As time-invariant covariates measured at baseline, sex, age, scanner-site, puberty stage, depression at baseline and, finally, voxelwise whole-brain MRI-data were added. We chose time-invariant covariates over time-varying covariates as the former are well suited for explaining variation of intercept and slope, whereas the latter rather address occasion-specific variance in the dependent variables, which was not the focus of our paper  53. Sex was dummy-coded with 1 = female and 0 = male. Age was assessed as days since birth. The nine different scanner-sites were dummy-coded each with Berlin as reference. Puberty was assessed with the Pubertal Development Scale  54. Depression was extracted from the Development and Well-Being Assessment Interview (DAWBA)  36. Throughout the analyses we used R (3.
Acknowledgements S. K. has been funded by a  Heisenberg grant  from the  German Science Foundation  ( DFG KU 3322/1-1 ), the  European Union  ( ERC-2016-StG-Self-Control-677804 ) and the  Jacobs Foundation  ( JRF 2016-2018 ). FN has been funded by a  Heisenberg grant  from the  German Science Foundation  ( NE 1383/14-1 ). Thanks to  Micha Kraus  for the programming support.
Methods This revision is based on detailed work during the last 25 years on the orchid flora of Madagascar and neighbouring islands. J. & C. Hermans (in Du Puy et al. 1999)  published a comprehensive bibliography which was revised  (Hermans in Hermans et al. 2007)  and has been kept up-to-date since then. At the same time, photographs, drawings and data were assembled from herbaria (including BM, BR, BRLU, CGE, DUB, G, HEID, K, M, MO, P, SZU, TAN, TEF, W, WU, M, SZL, ZSS). The authors visited many type and other localities during extensive fieldwork and visits to Madagascar and Réunion. A new checklist was compiled, based upon examination of herbarium and photographic material in all the major collections. Species were typified or retypified as necessary, a provisional key to the species was also prepared.
Conservation status Using the IUCN Red List Categories and Criteria (IUCN 2012), we produced preliminary risk of extinction assessments for each species. In order to gather the most comprehensive georeferenced distribution dataset, historical collections were georeferenced post facto when locality information was sufficiently precise and if not, these specimens were not taken into account in the preliminary assessments. We imported georeferenced specimen data into the dedicated R package, ConR  (Dauby et al. 2017)  to calculate the Extent of Occurrence (EOO) and Area of Occurrence (AOO). Minimal AOO was calculated using a cell area set to 4 km 2 (cell size = 2 × 2 km) as recommended by  IUCN (2017). The number of locations (sensu  IUCN)  were estimated with regard to the size of the main threat, in which a single location may encompass more than one adjacent subpopulation.
Schlechter added a total of 18 new Malaxideae to the flora of Madagascar (Liparis andringitrana Schltr. (Schlechter 1924: 135) , L. bathiei Schltr. (Schlechter 1924: 135) , L. cladophylax Schltr. (Schlechter 1916: 321) , L. densa Schltr. (Schlechter 1924: 137) , L. dryadum Schltr. (Schlechter 1924: 138) , L. gracilipes Schltr. (Schlechter 1924: 138) , L. henrici Schltr. (Schlechter 1924: 139) , L. hildebrandtiana Schltr. (Schlechter 1924: 140) , L. imerinensis Schltr. (Schlechter 1924: 141) , L. jumelleana Schltr. (Schlechter 1916: 320) , L. latilabris Schltr. (Schlechter 1924: 142) , L. listeroides Schltr. (Schlechter 1924: 143) , L. microcharis, L. perrieri Schltr. (Schlechter 1913: 164) , L. rivalis Schltr. (Schlechter 1924: 146) , L. sambiranoensis Schltr. (Schlechter 1924: 147) , L. stenophylla Schltr.
Most species are terrestrials or moss-humus dwellers but many can also grow as epiphytes, generally at the base of trees or on lower branches. The only exclusive epiphytes are Liparis bulbophylloides, L. cladophylax, L. dryadum, L. foliosa, L. parva (Kuntze) Ridl. (Ridley 1885: 462)  and Oberonia disticha. All true epiphytes, except Oberonia disticha, are only recorded from the lower parts of trees. None are true lithophytes except perhaps Liparis andringitrana which has watery young pseudobulbs as a xerophytic adaptation to its environment. Several species can be found on rocks but are usually rooted in the humus-rich and mossy substrate and not onto the rock itself. The vast majority are found in the Eastern forests of Madagascar and the higher elevation forests of the Comoros and Réunion.
Distribution mapping Georeferenced maps with WGS 84 projection have been used as a background for the distribution maps. They have been freely downloaded from the following websites: www. fao. org/geonetwork/srv/en (land cover of Madagascar, dated 2009), https://www. data. gouv. fr (Mayotte and Réunion islands) , https://gadm. org (country outlines of  Comoros, Mauritius and Seychelles). Similar data can be found at www. diva-gis. org. The locality coordinates come from the authors' own observations, made with Garmin etrex 10 GPS using the WGS 84 projection, or from the Tropicos website gazetteer to Malagasy botanical collecting localities: www. tropicos. org. All the positions of specimens have been double-checked with Google Earth: https:// earth. google. com. A relational database with two tables: localities and observed species, has been built with the database management system 4D version  11 (www.
4d. com) , storing a total of about 500 observations or collected specimens. A computer program was then written in 4D programming language to automatically produce one CSV file per species (ASCII files with commaseparated values), every file containing a list of coordinates for a given species. Eventually the open source Geographical Information System QGIS version 2. 18. 10 (www. qgis. org) was used to compose the final pictures in jpeg format, combining the countries' outlines, Madagascar land cover and the location spots for every species. Distribution is only shown for the area under review in this paper. A simple underlying vegetation map was used as a background for each species, a map of the whole area covered and the distribution of all Malaxideae, as well as maps showing the different provinces and regions of Madagascar are included for reference  (Maps 1, 2, 3 and 4).
ILLUSTRATIONS. Figs 19, 20. Schlechter (1932: T. 52) ;  Perrier (1939: 283) ;  Guérin & Hervouet (2013: 326) ;  Hervouet (2018: 408). Liparis dryadum Schltr. (Schlechter 1924: 138) ;  Perrier (1939: 278) ;  Hermans et al. (2007: 218) ;  Cribb & Hermans (2009: 152)  Platystyliparis dryadum (Schltr. ) Margonska (2009: 94)  synon. nov. RECOGNITION. Liparis dryadum is one of the smallest species of the genus. The inflorescence is somewhat longer than the lanceolate leaves, of which it has two to three leaves with wavy margins and a short petiole. The lip disk has a short, bilobed callus at the base. The broadly inverse-trapezoid lip with rounded corners is also characteristic. Liparis dryadum is similar to L. xanthina but the leaves are shorter and narrower, the differences in flower characteristics are difficult to ascertain with only Deans Cowan's rudimentary watercolour as evidence.
It is somewhat different from L. cladophylax which has wider leaves that are not corrugate at the margins and an narrower lip with an 'M' shaped callus vs shortly bilobed. Schlechter mentioned a similarity with L. epiphytica Schltr. (Schlechter 1905b)  from West Africa, but it is easily distinguished by being more than half the size both in plant and flower and a bilobed lip callus vs rectangular. Perrier seems to have made another collection in the same locality one month after collecting the type specimen and gave it the same collection number. The later collection is a topotype of the species (P00094978). It is also possible that an error was made on the specimen labels. The species was re-classified as Platystyliparis dryadum (Schltr. ) Marg. by  Margonska in Richardiana (2009: 94)  but there is no evidence or necessity for this.
DISTRIBUTION. Endemic to Madagascar: Antsiranana, Fianarantsoa, Mahajanga, Toamasina Provinces (Map 20). Confusingly Perrier indicated 'Centre' on collection labels; the Tsaratanana mountain range is in Antsiranana province in Northern Madagascar. Szelengowicz & Tamon (2013: 355) ; reported this species from Réunion but there is no evidence for this. Their description transcribes Perrier's original text and is accompanied by a fuzzy photograph of an unidentifiable plant. HABITAT. Epiphyte in lichen forest, or dense humid evergreen forest, moss and lichen-covered trees. Altitude: 660 -1600 m. CONSERVATION STATUS. Category EN: the extent of occurrence (EOO) of Liparis dryadum is estimated to be 151,497 km 2 (far exceeding the limits for Vulnerable status under criterion B1) whereas its minimal area of occupancy (AOO) is estimated to be 20 km 2 (which falls within the limits for Endangered status under the criterion B2).
With only four known subpopulations representing four locations (sensu  IUCN) , this species has been preliminarily assessed as EN using the green listing method. This species is threatened by selective logging, timber harvesting for small-scale subsistence and tavy (slash-and-burn farming), resulting in habitat reduction and habitat quality reduction. FLOWERING TIME. January to March. ETYMOLOGY. Referring to the Dryads, tree dwelling mythological nymphs. ILLUSTRATIONS. Figs 21, 22; Perrier (1939: 283) ;  Cribb & Hermans (2009: 151). Very small to small, terrestrial or epiphytic plant, squat, 6 -11 cm, rhizome very short, older pseudobulb leafless and porrect to horizontal, the flowering one erect, roots glabrous, thin and wiry. Pseudobulbs 1 -5 cm, 8 -19 mm diam. , covered by membranous leaf sheaths, carrying 2 -4 erectly-spreading leaves but generally with 2 prominent leaves.
1 -5. 1 × 3 -3. 6 mm. Column thick, semiterete, wings broad, angular and strongly incurved, c. 4 × 1 mm. Anther with a short sharp apicule at the front, c. 1 × 0. 8 mm. Pollinia ovate, c. 0. 3 mm diam. RECOGNITION. Liparis parva is a very small two-leaved plant with relatively large flowers, orbicular pseudobulbs, long and narrow leaves, a loosely flowered and zig-zag inflorescence, and flowers with a lip with a large sub-rectangular callus at the base, wide and angular, incurved column wings, a pedicellate ovary and column at an acute angle. The species has some similarities with Liparis cladophyllax and L. dryadum but neither have the distinct globular pseudobulbs and have a column that is indistinctly winged vs distinctly angular, and a lip almost half the size. Liparis parva bears some similarity to L.
The plants flowered at Kew on several occasions, a plant and flower were painted in 1906 (in the style of Matilda Smith, Fig. 70 ) and a flower without a lip is also preserved on a herbarium sheet in 1907, both are annotated with the Kew accession number 437. Rolfe finally described the new species in 1908. The herbarium sheet and watercolour are both annotated by Rolfe as being 'close to L. parva'. Rolfe, in his description, just referred to 'Warpur' as the type specimen but mentioned that the plant was 'introduced about 7 years ago'. The K herbarium sheet Warpur from 'Tananabe' 10 June 1900 is chosen here as the lectotype with the single imperfect flower Warpur 437 (K0002452145) being an lectoparatype plus the watercolour of Warpur 437 of September 1906 being an additional lectoparatype.
He returned it to the Paris herbarium in October of the same year and published the description a year later. There are two sheets from the same locality, one has a collecting date of October (X) and the other December, this could be an error but could equally be a collection from a later date. Perrier made another collection in 1924, from a different area of Mt Tsaratanana of a somewhat different form with a wider lip and more linear anther beak. No other reliable records exist of the species. ILLUSTRATION. Perrier (1939: 271). The photographs in  Cribb & Hermans (2009: 149)    RECOGNITION. Liparis xanthina has an inflorescence that is longer than its leaves; two fairly broad leaves, small flowers and fairly long floral bracts. It is similar in its inflorescence and flowers to Liparis dryadum but it has broader and larger leaves.
Acknowledgements We are most grateful to the directors and staff at  BM, BR, BRLU, CBDM, DUB, G, HEID, K, M, MAU, MO, P, REU, SZU , TAN, TEF, W, WU, M, SZL, ZSS and their relevant libraries. Marc Pignal at P for many years of hospitality. The botanical artists and especially  Juliet Beentje ,  Judi Stone  and  Oliver Whalley. Clare Hermans  for processing huge amounts of data. Simon Verlynde & Tariq Stévart  for making the Ambatovy herbarium available. Patrice Bernet  for providing material from  Réunion. Justin Moat  for general advice on mapping. Michael Kiehn  for his advice and help. Daniel Geiger  for reviewing  Oberonia. Brian Fisher  of the  California Academy of Sciences  for help in ant identification. We are also most grateful to the brave anonymous reviewers. In the context of the description of Liparis laurentii,  Louis Nusbaumer  thanks  Laurent Gautier  for the specimens and for initiating and leading the botanical researches in  Loky-Manambato ,  Rodolphe Spichiger  and  Pierre-André Loizeau  for supporting the project,  Nicolas Spitznagel  for the treatment of the field picture, the institutions which funded the researches in Loky-Manambato: CJBG,  Université de Genève ,  Conservation International  ( CBC fund ),  Malagasy NGO Fanamby ,  Fondation Jean-Marcel Aubert , and  Vontobel Stiftung  as well as the  Direction Générale des Eaux et Forêts de Madagascar  and the  Département de Biologie et Ecologie Végétale de l'Université d'Antananarivo  for supporting our project.
We introduce Multiple Interface String Alignment (MISA), a visualization tool to display coherently various sequence and structure based statistics at protein-protein interfaces (SSE elements, buried surface area, ∆ASA, B factor values, etc). The amino-acids supporting these annotations are obtained from Voronoi interface models. The benefit of MISA is to collate annotated sequences of (homologous) chains found in different biological contexts i. e. bound with different partners or unbound. The aggregated views MISA/SSE, MISA/BSA, MISA/∆ ASAetc make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. As such, they should prove of key relevance for knowledge based annotations of protein databases such as the Protein Data Bank.
Availability and practical matters MISAs are implemented within the Multiple_interface_string_alignment package of the Structural Bioinformatics Library (  [13] , http://sbl. inria. fr), see https://sbl. inria. fr/doc/Multiple_interface_string_alignment-user-manual. html. The calculation and the analysis of MISAs is based on four scripts-see online documentation: • sbl-misa. py: building MISAs from a description of complexes and possibly unbound structures. • sbl-misa-mix. py: mixing selected colored MISAs into a single (html) file. • sbl-misa-bsa. py: displaying the BSA of all (or selected user defined) residues. • sbl-misa-diff. py: comparing i-strings and associated properties (in particular BSA) of two interfaces. Has two modes: comparing two i-strings; comparing one i-string and a list of interface residues typically coming from a publication.
As we shall see, even such a simple study sheds new light on a number of published facts. 3. 2 Comparing the RBD of SARS-Cov-1 and SARS-Cov-2 in complex with ACE2 Baseline. The spikes of SARS-Cov-1 and SARS-Cov-2 are highly homologous proteins binding ACE2. Pairwise alignment shows that the overall percent protein sequence identity is about 76%  [34]. The S1 subunit is less conserved (64% identity) than S2 (90% identity). Within S1, the receptor-binding domain (RBD) is 74% identical. The initial analysis of the complex between the RBM of SARS-Cov-1 and its target ACE2 was first carried out in  [35]. In this work, it is noted that the BSA at the interface is ∼ 1700Å. These recent publications take the 14 a. a. identified in  [35]  for granted. Note that in furthering these analysis, we sometimes refer to the jupyter notebook which accompanies our software, and propose selected analysis using the four scripts of the Multiple_interface_string_alignment package.
Whole Voronoi interfaces. The Voronoi interface calculation yields comparable results (Figs. 1  and 2 ). For SARS-Cov-1 (PDB: 2ajf, RBD: chain E, ACE2: chain A), one obtains 246 interface atoms making up 2 binding patches, and defining overall 414 pairwise contacts. For SARS-Cov-2 (PDB 6m0j, RBD: chain E, ACE2: chain A), one gets 212 interface atoms also disposed on two binding patches, and defining overall 371 pairwise contacts. The two interface patches correspond to the transition between a beta sheet and loops on the RBD (Fig. 1(B, C )), dotted line-segments). Moving to interface strings (Fig. 2 , we note that the RBD contribution is is characterized by five main stretches along the backbone. Interestingly, two stretches (yellow and red) span the whole interface, crossing on top of one another in a X like figure (Fig.
8. 3 Coloring the MISA : script sbl-misa. py, modules Colored_MISA. py, MISA_ColorEngines. py Overview sbl-misa. py produces four colorings for each MISA, one for each of the following quantities (designated as coloring values): • the secondary structure (SSE) • the buried surface area (BSA) The cMISA_recorder creates the output files, by combining the Interface_string of each cMISA with the coloring legend provided by the color_engine of the cMISA. For each cMISA, the chains with the same output are grouped together to lighten the display. A. html file displaying simultaneously all the cMISA sharing the same MISA id is created in the odir/MISA directory. A sub-directory odir/MISA/single-coloring-figures is created, where each of the cMISA is stored individually, in both. pdf and. html format.
Script sbl-misa-mix. py Overview The sbl-misa-mix. py script allows, based on the individual colored MISA produced by sbl-misa. py, to display together several colored MISA for an easier comparison. Main steps Parse the mix_ifile • Parse the several. html files containing the MISA id / colorings of interest • Combine them into a mixed fig • The third is a matrix showing the number of atoms involved in the calculation of i-RMSD for each pair of chains.
Supplemental: formal specification of the method 23 8 Implementation details 24 8. 1 Overview. 24 8. 2 Computing the MISA : script sbl-misa. py, module Multiple_interface_string_alignment. py. 25 8. 3 Coloring the MISA : script sbl-misa. py, modules Colored_MISA. py, MISA_ColorEngines. py. 25 8. 3. 1 Coloring SSE. 28 8. 3. 2 Coloring BSA and ∆_ASA. 28 8. 3. 3 Coloring B-factor. 28 8. 4 Script sbl-misa-mix. py. 28 8. 5 Script sbl-misa-bsa. py. 29 8. 6 Script sbl-misa-diff. py. 29 8. 7 Structural comparison, script sbl-misa. py, module iRMSD. py. 29.