dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparison of FOD amplitude and AI Maximum amplitude of FODs and AI distribution within the peritumoral region obtained with COMPARI were compared to those extracted with the MSMT-CSD models (Fig. 6 ). Median amplitudes as well as median AI were higher in COMPARI than in MSMT-CSD in all patients of the clinical dataset, with average FOD amplitude of 0. 10 in MSMT-CSD compared to 0. 54 in COMPARI.
In this case, FODs fitted to the GM had an excessive number of peaks (Fig. 7 ), which could result in false positives in tractography connecting GM regions. As such, care should be taken to fit COMPARI only to the WM, or to restrict tractography to the WM and peritumoral area, such as with anatomically constrained tractography  [40, 41]. Third, while simulated results suggest that best results with COMPARI will be achieved with multi-shell datasets, COMPARI has not yet been tested in in vivo multi-shell datasets with a variety of b-values and direction sets. In clinical practice, tractography could be useful for clinicians treating patients with brain tumors, especially in the context of surgical planning. Indeed, tumor resection is the first treatment for most tumor types  [42] , and the quality of the resection (i.
our model performed poorly on a human data set with b=3000 s/mm 2 and 128 directions (S21 Fig), since it relies on an estimate of isotropic diffusivity. This effect was not seen in simulated data due to a limitation of the simulation model. Thus, from our experiments on simulated and human data, we concluded that best results with COMPARI would be achieved using a multi-shell dataset with a low b-value shell to capture isotropic diffusivity, and one or more high-b shells to resolve fiber directions, fit with l max = 12 with the super-CSD approach, if possible. a result, 2. As May 1, 2023 12/19.
9% (Icaronycteris index) to 5. 7% (Microchiropteryx foliae). Given the widely recognized beneficial impact in phylogenetics of combining and analyzing morphological and molecular data simultaneously,  [71] [72] [73] [74] [75] [76]  and the extensive DNA sequence data available for our extant terminals, we used a total evidence approach, combining our craniodental matrix with 36. 9 kb of DNA sequence data from 27 nuclear loci, taken directly from O'Leary et al. 61  The inclusion of temporal information has also been shown to increase phylogenetic accuracy,  54  and so our focal analysis was a dated Bayesian analysis of our total evidence dataset using a fossilized birth-death model implemented in MrBayes,  77, 78  with all tips and selected nodes assigned age priors and with separate Independent Gamma Rates clock models applied to the morphological and molecular partitions (see STAR Methods).
In addition to this focal analysis, we also carried out maximum parsimony (MP) analysis of the full craniodental dataset and MP analysis of a ''homoplasy-filtered'' version of the craniodental dataset in which characters that show homoplasy relative to the current consensus view of extant bat phylogeny (i. e. , with monophyletic Yangochiroptera and Yinpterochiroptera; e. g. , Shi and Rabosky  83  and Amador et al. 84  ) were excluded, and undated Bayesian analysis of the total evidence dataset (see STAR Methods and Figure  S2 ). These subsidiary analyses also support Vielasia as a stem bat, and a constrained position of Vielasia within the crown clade is rejected by Templeton tests (for the MP analyses) and Bayes factors (for the undated Bayesian analysis; see STAR Methods; Data S1E). The age of crown bats was poorly constrained in our dated total evidence analysis (Figure  2 ), stretching from the earliest Eocene to the late middle Eocene (95% highest probability density [HPD] interval: 53.
18  Relative cochlear size and an articulation between the tympanic bone in the middle ear and a cranially expanded stylohyal bone (part of the hyoid arch that supports the larynx) remain definitive and uncontested hallmarks of laryngeal echolocation in bats. 18, 48  The stylohyal and middle ear bones are not yet known for V. sigei, but its threedimensionally well-preserved cranium and petrosal (cochlea and semicircular canals) has enabled this early bat's inclusion in analyses of large datasets of cranial and inner ear attributes related to auditory and echolocation capabilities in extant bats. In these analyses, V. sigei grouped with LE rather than non-LE bats, and there is little to suggest that Vielasia used a type of echolocation different from that used by modern LE bats. This finding is congruent with previous studies suggesting that some non-crown bats may have had modern or near-modern echolocation capabilities  47  and contrasts with some proposals based on embryological and molecular analyses of extant bats that, if stem bats did use echolocation, it was of a primitive kind (such as tongue-clicking).
Materials availability The holotype and paratype specimens of Vielasia sigei are lodged in the collections of Universit e de Montpellier (Montpellier, France), where the specimen is permanently available for research. The 3D models of the cranium and bony labyrinth of the holotype UM-VIE-250 are available at https://morphomuseum. com (https://doi. org/10. 18563/journal. m3. 217). Comparative data for other fossil bat taxa/specimens included in our study were retrieved from personal observations and the literature (as indicated in the taxon list provided below), and from O'Leary et al. 61  Data and code availability d Data analyzed in our study are publicly available as of the date of publication. Fossil accession numbers are listed herein, and a 3D model of the cranium and bony labyrinth can be accessed from the data repository MorphoMuseuM (see key resources table ).
01 mm). Univariate and multivariate analyses of the dental sample were performed in the statistical program PAlaeontological STatistics (PAST 4. 05; Data S1A, and see below). One binning of the mCT dataset was applied prior to skull and bony labyrinth segmentation, resulting in a dataset with a 17. 86 mm resolution, using ImageJ v1. 48; segmentation was performed using Avizo Ò 9. 3 tools brush, lasso, and magic wand using varying threshold to remove sediment; model reconstruction was performed using Avizo Ò 9. 3, with an unconstrained smoothing value of 2. 75. Measurements of the bony labyrinth (linear and angles) were made on the virtual model using 3Matic (Materialise), following the methods of Spoor and Zonneveld,  124  Spoor et al. ,  64  Ekdale,  89  and Davies et al. 19, 63  (Data S1F, and see below); basilar membrane length was measured using 86 approximately equidistantly stationary points (as per  Davies et al.
Comparative material In the list below, an asterisk (*) denotes original material examined in addition to (otherwise) primary literature, supplementary photographs and/or scan data from MorphoSource and DigiMorph. Families listed alphabetically. List of institutional abbreviations for specimen numbers follows the taxon list. AEGYPTONYCTERIDAE: Aegyptonycteris knightae Simmons et al. 125   44  Murgon, Queensland, Australia QM F19147, QM F19149*; Jaegeria cambayensis  Bajpai et al. 132  Vastan lignite mine, Gujarat, India IITR/SB/VLM/585; Chiropteran in  Tejedor et al. 146  Laguna Frı ´a, Chubut Province, Argentina, LIEB-PV 999; Chiroptera indet. 2 in Marandat 147 Fournes, Minervois, France FNR-02*; Eochiroptera in Ravel et al. 29  El Kohol, Algeria UT-KD-02, UT-KD-03; Altaynycteris aurora Jones et al.
19  also inferred low and high limits of hearing frequencies at 30 dB and at 60 dB, using the methods of West 162 and Manoussaki et al. 163  They performed OLS regressions of (1) log 10 low limit of hearing frequencies against log 10 of the product of basilar membrane length and number of cochlear turns, and of (2) log 10 high limit of hearing frequencies against log 10 of relative basilar membrane length (i. e. , ratio between basilar membrane length and cube root of body mass). Davies et al. 19  used a dataset containing 38 mammal species but discarded two subterranean rodents and two marsupials for performing OLS regressions. The latter dataset contains 14 chiropteran species and 20 non-bat placental mammal species. Davies et al. 19  performed OLS regressions both with and without the 14 bat species, and therefore obtained two OLS regression lines for each of the four cases (low/high limit, 30/60 dB).
We re-analysed the data (Data S1K; Figure  S4 ) and estimated low and high limits of hearing frequencies at 30 dB and 60 dB for Vielasia sigei, comparing these also to values calculated by Davies et al. 19  for the theoretical ''chiropteran ancestor'' (Data S1L). Eye size -Eyeball size in Vielasia sigei was estimated as 2. 3 mm diameter or less, using the method of Brooke et al. 93  (and see Thiagavel et al. 22  for validation in bats). Using this method, a virtual spherical eye ball was fitted into the socket in a model of the holotype UM-VIE-250 without touching any part of the skull while the gap between bone and eyeball on the median side was maintained at 1 mm.
50  and described here as Vielasia sigei n. gen. et sp. A second, much smaller bat species is represented by rare teeth, also noted by  Legendre et al. 50  ; these teeth will be described separately and are not included in the sample analysed here. Univariate and multivariate analyses of 131 complete/measurable craniodental specimens were performed in the statistical program PAlaeontological STatistics (PAST  119, 168  ), with univariate summary statistics given in Data S1A. Coefficient of variation (CV) values lie within the range expected from a single population, i. e. , CV values between 4 to 10, 169 and PCA analysis (using iterative inputation for missing data) also found no evidence of clustering that would suggest the presence of more than one population/sexual dimorphism among isolated teeth referred to this species (Data S1A).
For most variables, mixture analysis  170, 171  showed no evidence of clustering or dimorphism in the sample of isolated teeth. However, for lower first molars (N=41), mixture analysis did detect two groupings in trigonid widths (m1WT) with means at 1. 30 mm and 1. 47 mm (prob. 0. 536 and 0. 464, respectively), and two groupings in talonid widths (m1Wt) with means at 1. 20 mm and 1. 33 mm (prob. 0. 541 and 0. 459, respectively) (Data S1A). The well-preserved Vielase fossil tooth sample provides an opportunity to further examine dental variation, including sexual dimorphism, in an early Eocene bat and is the subject of a separate analysis by additional authors.
We deleted all fossil taxa from the matrix, and then analysed the extant-only matrix using MP in TNT, using the same two-stage search strategy as before, and applying a ''molecular scaffold'' that enforced the monophyly of the following clades, based on recent molecular studies (e. g. , Meredith et al. ,  2  A ´lvarez-Carretero et al. ,  6 and Upham et al. 173  ): Eulipotyphla (our extant outgroup taxa Sorex, Solenodon and Erinaceus), crown Chiroptera (our six extant bat terminals), Yinpterochiroptera (Pteropus and Rhinopoma), Yangochiroptera (Saccopteryx, Nycteris, Myotis, and Pteronotus), and Emballonuroidea (Saccopteryx and Nycteris). This procedure resulted in a single most parsimonious tree. We then used the R package TreeSearch 174 to calculate the minimum possible length of each craniodental character on any tree (using the MinimumLength function), and its length on the single most parsimonious tree that resulted from the molecular scaffold analysis (using the CharacterLength function); if the latter was greater than the former (indicating some homoplasy relative to the molecular consensus), then that character was removed from the craniodental matrix.
The fossil bats are recovered in a single clade that is moderately strongly supported (bootstrap 73%), rather than as a paraphyletic assemblage as found in the MP analysis of the full craniodental matrix (Figure  S2A ); within this fossil clade, Vielasia and Cambaya form a weakly supported (boostrap < 50%) clade that is sister to another weakly supported (bootstrap < 50%) clade comprising the remaining fossil taxa. Although this analysis similarly supports the hypothesis that Vielasia is not a crown clade bat, it is incongruent with previous studies  9, 36  (and with our maximum parsimony of the full craniodental dataset [Figure  S2A ] and our Bayesian dated analysis of our total evidence data set [Figure  2 ]) in placing all Eocene fossil bats in a clade, with onychonycterids (species of Onychonycteris, Eppsinycteris, Ageina and Honrovits) in a nested position; these other analyses instead recover Eocene fossil bats as paraphyletic with respect to the crown clade, and place onychonycterids (including the well-preserved Onychonycteris, which shows a range of features that have been generally interpreted as plesiomorphic relative to other known fossil bats) in a basal position.
Templeton tests of alternative topologies To test whether our full and homoplasy-filtered craniodental matrices are compatible with Vielasia being a crown chiropteran, we carried out constrained MP analyses of both matrices with Vielasia enforced to fall within the crown-clade. As already noted, MP analysis of the full craniodental dataset placed extant laryngeally-echolocating bats in a single clade to the exclusion of Pteropus, which was sister to all other chiropterans (Figure  S2A ); within the extant echolocating clade, Myotis and Pteronotus formed one subclade, and Nycteris, Rhinopoma and Saccopteryx the other. For the constrained analyses of the full craniodental dataset, we therefore enforced Vielasia to either form a clade with Myotis and Pteronotus to the exclusion of all other taxa, or a clade with Nycteris, Rhinopoma and Saccopteryx to the exclusion of all other taxa.
MP analysis of the homoplasy-filtered craniodental dataset (Figure  S2B ) recovered monophyly of Yangochiroptera and Yinpterochiroptera, and so for the constrained analyses of this dataset, we enforced Vielasia to either form a clade with the extant yangochiropteran taxa (Saccopteryx, Nycteris, Myotis, and Pteronotus), or the yinpterochiropteran taxa (Pteropus and Rhinopoma), to the exclusion of all other taxa. The constrained maximum parsimony analyses used the same search settings in TNT as the unconstrained analyses. Templeton tests 179 comparing the most parsimonious topologies from the unconstrained and constrained analyses were then implemented in PAUP* 4. 0a169, 120 the resultant p-values converted from two-tailed to one-tailed (following  Goldman et al. 180  ) by dividing by two, and mean p-values were calculated from the MPTs for each constrained analysis.
191  An Independent Gamma Rates (IGR) clock model 192 was specified, with two separate clock models: one for the morphological characters, and one for the combined DNA sequence data. The prior on the clock rate was estimated using the custom R script of  Gunnell et al. 193  A vague prior -uniform (0. 001,200) -was specified for the variance of the IGR clock model, following  Matzke and Wright. 194  Diversity sampling was assumed, with a sample probability of 0. 00418, based on the inclusion of six extant bat species out of a currently recognised total of 1437. 195  Because our taxon set does not include any fossil terminals younger than 47. 4 Ma, we specified a shift in sampling at this time. 196  Priors on speciation, extinction and fossilisation were left as the MrBayes defaults. Extant terminals were assigned an age of 0 Ma, whilst fossil terminals were assigned a uniform age prior reflecting the stratigraphic uncertainty in their ages, following the recommendations of Pu ¨schel et al.
64  as the average of the diameters of the first and second cochlear turn and of the ''slant height'' of the cochlea) and found a difference between echolocating bats and other mammals (including non-echolocating bats) when plotting semicircular canal size against cochlea size (echolocating bats having larger cochlea/smaller canals). For both basilar membrane length vs body mass and semicircular canal size vs cochlear size, we tested whether we could discriminate between bats and non-bat placentals, and between different echolocation types in bats (non-laryngeal echolocating, oral-emitting, and nasal-emitting). We included cetaceans in both datasets because they represent a mammalian clade that includes species that have evolved to hear very high frequencies (odontocetes), similarly to bats, but also species that have evolved to hear very low frequencies (mysticetes).
These two additional classes may allow us to identify a functional signal in the traits tested and therefore increase the validity of our inferences. After controlling for potential effects of these ecological categories on the relationships we tested, our final goal was to include Vielasia and test whether it could be confidently assigned to a particular class (i. e. , non-LE bats, LE-bats, HF-hearing cetaceans, LF-hearing cetaceans, or other placental mammals). For the cochlear basilar membrane length vs body mass relationship, we simply added measurements for Vielasia to the dataset of Davies et al. (see table  S2 ),  19  with therefore 82 species included (44 extant bats, 37 extant mammals, and Vielasia sigei; Data S1G). The dataset of Davies et al. (see table  S1 )  63  included measurements of cochlear and semicircular canal sizes for chiropterans only; thus, we had to obtain the non-chiropteran data they used directly from various references,  64, 92, 112  to which we added additional measurements for cetaceans.
110, 111  The resulting dataset therefore includes 124 species, with 52 extant bats, 71 extant mammals, and Vielasia sigei (Data S1M). The phylogeny used by Davies et al. 63  for their comparative analyses does not include cetaceans, and so we instead used the dated mammalian phylogeny of A ´lvarez-Carretero et al. 6  as the starting tree for our own analyses. However, we replaced the bat clade in the A ´lvarez-Carretero et al. 6  phylogeny with the bat phylogenies derived from Shi and Rabosky,  83  Amador et al. ,  84  and the current study (see ''phylogenetic framework'' above). This requires that the age of Vielasia + crown Chiroptera is younger than that of the node uniting Chiroptera with its sister taxon, which in the A ´lvarez-Carretero et al. 6  phylogeny is Artiodactyla + Perissodactyla + Carnivora + Pholidota.
This was the case for 74 of the 104 trees derived from Shi and Rabosky 83 without rescaling, but was not the case for either of the two trees derived from Amador et al. 84  without rescaling (see ''phylogenetic framework'' above for details); for the rescaled phylogenies, this was the case for 971 of the 1001 trees derived from Shi and Rabosky,  83  and for 974 of the 1001 trees derived from Amador et al. 84  For each dataset (basilar membrane length vs body mass; semicircular canal size vs cochlear size), we then pruned the relevant phylogenies to retain only those species for which we had measurements. Basilar membrane length vs body mass -Regarding the allometric relationship of basilar membrane length to body mass, we first simply plotted all points, distinguishing them according to the following groups: high-frequency hearing cetaceans, low-frequency hearing cetaceans, non-laryngeally echolocating bats (pteropodids), laryngeally echolocatng bats (nasal-and oral-emitters), and other placentals.
We then performed phylogenetic generalized least squares (PGLS) regressions of (natural logarithm of) basilar membrane length against body mass, repeating the analysis for all phylogenies we created. To do so, we used functions and methodology from the packages phylolm 214 and sensiPhy 215 to implement PGLS regression of log basilar membrane length against log body mass, taking into account phylogenies with variation in their relationships (within Chiroptera) and in their branch lengths. The function phylolm from the eponym package 214 allows for performing PGLS regressions with several different possible evolutionary models (Brownian motion, Brownian motion with trend, Ornstein-Uhlenbeck with a fixed and estimated root value or with a stationary ancestral distribution, Pagel's lambda, kappa, and delta, and the early burst model).
The function tree_phylm from the sensiPhy package enables the PGLS regression to be repeated across multiple phylogenies, and outputs tables to compare averaged parameters between the tested models. We wrote a function named tree_phylm_full_results 123 which is a slightly modified version of the tree_phylm function (of the sensiPhy package). This custom function can be easily further modified to output more information than given by the standard tree_phylm function, such as regression residuals, fitted values etc. This custom function returns two important elements that are also returned by the standard tree_phylm function, namely: the estimated parameters for each PGLS regression (the $sensi. estimates element) and the averages of the parameters for each model (the $all. stats element). In tree_phylm_full_results however, the $sensi.
estimates element as well as other outputs from the regressions can be returned for all tested models, not just for the bestfitting model, the choice being up to the user (by turning the option output. all. models to TRUE or FALSE). Finally, we tested whether there were significant differences in the PGLS regression parameters between selected comparisons (bat versus non-bat placentals, laryngeally echolocating bats versus other placentals, high-frequency hearing mammals versus others, high-and low-frequency hearing mammals versus others). To perform these comparisons, an additional wrapper on the tree_phylm function, compare. tree_phylm 123 was written. This function takes the same input variables as the tree_phylm_full_results function, plus information regarding potential subsetting of the dataset.
If a subset is specified, the dataset is divided in two groups (i. e. , both the phylogenies and the morphometric data), PGLS is performed for both (using tree_phylm_full_results function), then the compare. tree_phylm function provides the results from a t-test contrasting average slopes and intercepts for the PGLS with bestfitting evolutionary models for each group, and finally it outputs average regression line parameters to be able to simply add them to an existing biplot. Overall, there are few differences between our comparisons (Data S1H), that aim to compare selected subsets of our dataset (LE bats, all bats, LE bats plus HF-hearing cetaceans, LE bats plus both HF-hearing and LF-hearing cetaceans) both to the remaining species (i. e. , non LE bat placentals, non-bat placentals etc.
) and to the whole dataset. There is no significant difference in regression slopes (p > 0. 4 for every comparison), and only some significant differences in regression intercepts. These differences generally contrast echolocating mammals and other species: LE bats seem to differ from other placentals, although this relationship is not significant (p = 0. 06), bats are significantly different from non-bat placentals (p = 0. 02), and placentals with extreme hearing abilities (i. e. , HF-hearing and LF-hearing mammals) in general differ markedly from other placentals (p = 0. 009). No selected subset differs significantly from the overall placental trend (i. e. , the regression for the whole placental dataset), and so we only added the placental regression line (i. e. , Pagel's delta with an average value of 2.