dataesr/scientific-paragraphs-categorization huggingface dataset:
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It would be crucial for the understanding of stromal remodeling during keratoconus and it may possibly improve its early diagnosis. In conclusion, we have taken advantage of the small coherence length in epi-detected SHG microscopy and of P-SHG sensitivity to collagen orientation in order to map the lamellar structure of human corneas with micrometric resolution. We have carefully assessed the precision of our orientation measurements and obtained 3D reconstructions in the center of 10 entire corneas over their full thickness. Quantitative analyses of these data show in a unique way the evolution of the lamellar structure along the depth of the cornea. A key advantage of our method is to use epi-detection and consequently to be compatible with any corneal chamber or with in vivo imaging. It could therefore be used to record stromal remodeling during inflation assays in ex vivo corneas, in order to measure advanced mechanical properties of cornea.
Acknowledgements The authors acknowledge funding from  Agence Nationale de la Recherche  ( ANR-10-INBS-04 ,  ANR-11-EQPX-0029 ,  ANR-21-CE19-0010-01 ), and  Banque Française des Yeux  ( BFY 2021  prize). The authors thank the  Banque Française des Yeux (BFY, Paris)  for providing human corneas,  Isabelle Lamarre-Jouenne ,  Caroline L'Hermitte-Stead ,  Lucille Melottee ,  Xavier Solinas  and  Jean-Marc Sintès  for technical support in the SHG setup and in cornea handling, and  Karsten Plamann ,  Maëlle Vilbert ,  Manuel Joffre ,  Willy Supatto  and  Emmanuel Beaurepaire  from LOB,  Jean-Marc Allain  and  Chloé Giraudet  from  LMS  ( IP Paris ) and  Vincent Borderie ,  Kate Grieve  and  Djida Ghoubay  from  CHNO 15-20  ( Inserm, Sorbonne University ) for fruitful discussions.
Phylogenetic Analyses. We performed a cladistic assessment of the morphological evidence (A1 analysis) to investigate the phylogenetic position of Ashaninkacebus in a highlevel phylogeny of basal anthropoids from the Old World (i. e. , Paleogene South Asian and North African known taxa), plus known extinct and extant New World platyrrhines (SI Appendix, Table  S1 ). The data matrix included 456 characters and 81 taxa (see Methods for character assumptions, data, and phylogenetic analyses; also, SI Appendix, Table  S2  and Text S2 ). We enforced a molecular backbone tree on the dataset to recover extant primate clades strongly supported by genomic sequences (see Methods). The analyses yielded a single most-parsimonious tree (2429. 49 steps, Consistency index = 0. 36; Retention index = 0. 56; Fig.
That Perupithecus or Ashaninkacebus is the oldest known stem platyrrhine remains probable, but the limited morpho-paleontological data so far assembled (very few dental evidence and no cranial or post-cranial data) do not allow formalizing either hypothesis. This means that rooting (technically) the Platyrrhini in an Old World anthropoid clade in which either Ashaninkacebus or Perupithecus is nested requires further morphological support than current data allow. Paleobiogeographic Implications. In addition to the Parapithecidae  (19)  and Oligopithecidae-like primates  (12)  of African origin, the eosimiid affinities of Ashaninkacebus point to a third clade of basal anthropoids involved in the Paleogene colonization of South America by primates. Eosimiids are well documented in the Paleogene of South Asia  (34, (46) (47) (48) (49) (50) , but have not been formally recorded in the Eocene of Africa.
(33) , modified from Allen et al. (67). We also used the platyrrhine dental measurement and diet dataset provided in Kay et al. (33). Phylogenetic Reconstructions and Divergence-Time Estimation Between Taxa. The phylogenetic position of Ashaninkacebus in a high-level phylogeny including basal anthropoids (Old World, i. e. , Paleogene South Asian and North African known taxa) and known extinct and extant platyrrhines was investigated (see SI Appendix, Table  S1 ). We performed a cladistic assessment of the dental evidence (plus cranial and postcranial characters for several other taxa), as well as Bayesian tip-dating (BTD) analyses on the same morphological dataset to estimate divergence times between taxa (and also both, i. e. , phylogeny and divergence times). A summary of the different types of analyses performed (A1 to A6) is provided in SI Appendix, Table  S2.
We employed and updated the morphological matrix provided in Marivaux et al. (13) , which itself was adapted and substantially modified from Kay  (37). We incorporated in the matrix early anthropoid primates from the Paleogene of South Asia (i. e. , Eosimiidae and Amphipithecidae) and North Africa (Parapithecidae, Oligopithecidae, and Propliopithecidae), as well as basal anthropoid taxa (Amamria, Phileosimias, Afrasia, and Talahpithecus), the phylogenetic status of some of which has not been formally established to date. The matrix also included primates recently discovered in South America (basal anthropoids and early platyrrhines), although some are poorly documented (Perupithecus, Canaanimico, Panamacebus, Parvimico, and Ucayalipithecus; SI Appendix, Table  S1 ). All characters for all taxa in the total matrix were re-examined, and some upper and lower dentition characters were reinterpreted, adjusted or added to better describe the extent and variation of character states within basal and advanced anthropoids, and extinct and extant platyrrhines (see SI Appendix, Dataset S1).
The final data matrix included 456 characters and 81 taxa (see SI Appendix, Datasets S2 and S3). We applied a molecular scaffold  (68)  on the datasets to recover those extant primate clades (Tarsiidae, Catarrhini, and Strepsirrhini) and notably Platyrrhini and within Platyrrhini clades that are strongly supported by genomic sequences. The gene-based tree of extant taxa used as a constraint derives from several consistent molecular phylogenetic results (e. g. ,  21, 22, 69). Among Platyrrhini, this backbone tree enforces the monophyly of the three main families (and sub-families within): Cebidae (including Cebinae, Callitrichinae, and Aotinae), Atelidae (including Atelinae and Alouattinae), and Pitheciidae (including Callicebinae and Pitheciinae), the latter family being the most basal platyrrhine diverging clade.
The matrix for the parsimony analyses is provided in SI Appendix, Dataset S2. The phylogenetic reconstructions were performed with PAUP 4. 0a 169 (  73 ) by heuristic searches (Hsearch) using random step-wise addition (1,000 replications with randomized input order of taxa) and tree-bisection-reconnection branch swapping options. Polymorphic versus uncertain character states (multistate taxa) were considered, and both were treated distinctly by PAUP (option MSTaxa= Variable). The clade robustness was measured by the Bremer Index (74) in equally weighted maximum-parsimony (after 1,000 iterations with randomized input order of taxa) (see SI Appendix, Fig. S5 ). Bayesian Tip-Dating (BTD) Analyses. This Bayesian approach considers both the ages of the fossil taxa (tips) and rates of character evolution  (75).
For all the BTD analyses performed (A3 to A6; SI Appendix, Table  S2 ), we selected the conditional version of the 1-parameter Markov-k model [Mkv  (76) ] for our total dataset, which includes only morphological data. The independent gamma rates (IGR) relaxed-clock model was applied to account for variation in morphological evolutionary rates among branches. The fossilized birth-death (FBD) process was used as a prior on branch lengths (in setting "samplestrat" to "fossiltip"), thus considering those tips left no descendant. Each fossil tip was calibrated with a uniform prior on age, corresponding to the minimum and maximum ages of each extinct taxon (i. e. , stratigraphic range of a taxon, or upper and lower bounds of geological stages or Land Mammal Ages to which a fossil has been assigned, or even the error range of an absolute radiometric age; see SI Appendix, Table  S1 ).
The matrix and command lines for the BTD analyses and their variants are provided in SI Appendix, Datasets S3 and S4. For each BTD analysis, two independent runs were performed simultaneously with four Monte Carlo Markov Chains (MCMC), with one cold and three heated (temp = 0. 01) for 50 million generations per run. The MCMC were sampled every 1,000 generations, with a burn-in percentage of 25%. Convergence was assessed by checking the effective sample size (ESS) and the average standard deviation of split frequencies in the final generation (see SI Appendix, Table  S3 ). For the A5 and A6 BTD analyses, an "allcompat" consensus tree was generated, summarizing all post-burn-in sampled trees. Several sensitivity analyses were performed with various perturbations of the priors, notably "igrvarpr", clockratepr" and "speciationpr" (see SI Appendix, Text S4), which returned similar age estimates.
Figures and Tables Figure Table  S1. Selected primate taxa for the phylogenetic analyses (A1 to A6) with information regarding their provenance and age range. S1 ). We performed a cladistic assessment of the morphological evidence, as well as Bayesian tip-dating (BTD) analyses on the same morphological dataset to estimate divergence times between taxa (and also both, i. e. , phylogeny and divergence times). Below are summarized the topological constraints applied to the analyses. Text S2. The Bayesian tip-dating (BTD) approach was performed primarily to estimate divergence times between taxa (notably for A3 and A4, in which the parsimony-based topologies of A1 and A2 were applied as hard constraints, respectively). However, we also performed a BTD analysis (A5) with no topological constraints employed within the Anthropoidea clade, other than those of a molecular scaffold for extant primates, and those of the Anthropoidea branchinggroups and outgroups.
We duplicated the latter BTD analysis (A5), in evaluating the impact of considering (as in A4) the Amphipithecidae clade as stem Anthropoidea (A6). In our matrix, "multistate taxa" were considered for some characters. In these cases, characters were scored primarily as polymorphic (e. g. , 0 and 1; i. e. , 0+1: morphological variability in a given species) or as uncertain (e. g. , 0 or 1; i. e. , 0/1: when a character state observed in a species/individual was ambiguous). Unlike PAUP, which treats distinctly polymorphic ( (01) under PAUP) versus uncertain ( {01} under PAUP), character states (options MSTaxa = Variable), MrBayes (v. 3. 2. 7a) treats all cases of polymorphism and uncertainty in the matrix as missing data (i. e. , "?"). In our matrix, more than 4% of scores for the dental characters are polymorphic (418) and uncertain (560) states, dental scores that are then lost in the different BTD analyses.
Results of the A5 analysis: With this BTD analysis, we estimated simultaneously phylogenetic topology and divergence times of taxa (but see our comments above regarding our reluctance to incorporate fossil ages into phylogenetic reconstruction). MrBayes treats all cases of polymorphism and uncertainty as missing data (see Text S2). In that context, several morphological scores were then discarded, a loss of information that can have impacted the phylogenetic reconstruction, and provided irrelevant position of some taxa. Although the overall tree topology of these results (Fig. S9 ) is not in conflict with that deriving from the PAUP results (A1, Fig. S5 ), there are, however, phylogenetic changes regarding a number of taxa. Ashaninkacebus is retrieved among the Eosimiiformes, but occupying a more basal position, resolved as the earliest offshoot of the Eosimiidae clade.
Acknowledgments We are very grateful to  Adolpho Herbert Augustin  ( Institute of Petroleum and Natural Resources, Porto Alegre, Brazil ) and  Anne-Lise Charruault  ( ISE-M, France ) for μCT-scan acquisitions, treatments and reconstructions. We also thank  Juliana Charão Marques  and  Daniel Triboli  ( LGI, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ) for SEM microphotographs. We extend our gratitude to our Brazilian colleagues and students from the  Universidade Federal do Acre¸ Cruzeiro do Sul and Universidade de São Paulo , who have contributed to some of the fieldwork seasons on the Rio Juruá. Special thanks go to the waterway staff (pirogues) and assistants for the logistics of the camps, as well as to the local people along the  Rio Juruá  for their hospitality and help in facilitating the fieldwork.
We thank the  Specialized Police Company  of the 6 th  Military Police Unit of Cruzeiro do Sul (Acre) , which ensured our security during the last field campaign on the  Rio Juruá (August 2022 ). Chris Beard  (guest Editor), as well as  Erik Seiffert  and two other anonymous reviewers provided formal reviews of this manuscript that enhanced the revised version. This research was supported by the  Brazilian Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq ,  306951/2017-7 ,  312941/2018-8 ,  140773/2019-3 ,  310023/2021-1 , and  310948/2021-5; CNPq/MCTI/CONFAP-FAPS PROTAX 22/2020 441626/2020-3 , and  FAPERGS 21/2551-0000781-8 ),  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior  ( CAPES, COFECUB program  Te  924/18 ,  88881. 143095/2017-01 ), the  São Paulo Research Foundation  ( FAPESP , process  2011/14080-0  and  2019/14153-0 ), and the  French Agence Nationale de la Recherche (ANR)  in the framework of the  LabEx CEBA  ( ANR-10-LABX-25-01 ; strategic project  EMERGENCE ).
We used a large (34 species, 63 specimens; Figure  1 ) MRI dataset alongside phylogenetic comparative methods to evidence isometric scaling between the cerebellum and cerebrum  50, 51, 77  and assess ansiform area hyperscaling  13, 36. Where possible, we explored intraspecific variability, which is substantial among brain traits  72, [78] [79] [80] [81] [82]  and an inherent challenge for comparative primatology  83. Our analyses confirmed isometric scaling between the cerebellum and cerebrum. Reanalysis of Stephan collection 84 data indicated this relation may be hypo-allometric. Conversely, the ansiform area scaled hyper-allometrically versus the cerebellum and   S1 ). Extant species included in the current study are given on the right and colored by their clade membership. Additionally, the numbers of specimens per species are given, and species with multiple specimens are marked with asterisks.
Data Primate comparative data are rare and sizable datasets are difficult to obtain. We used the collection of primate species collated from different sources in the Brain Catalogue Primates project  85  , available on BrainBox  83. It included 35 species (N=66), which covered the primate phylogenetic tree relatively well, with 9 infraorders from Strepsirrhini and Haplorhini suborders. The red howler monkey was excluded due to irreparable damage. Cerebellar damage was also noted in other specimens, whose volumetric estimates need to be treated with due diligence. Cebidae (7 species), Hominoidea (7), Lemuriformes (6), and Papionini (5) were most extensively sampled (Figure  1 ). Scans included both fully abstracted brains and in situ brains, either full body scans or only including the skull.
T1-or T2-weighted (T1w or T2w) MRI anatomical scans were obtained at either 1. 5, 3T, 7T or 11. 4T for up to 12 hours. See Supplemental Methods for basic data acquisition, provenance  [85] [86] [87] [88] [89]  and damage description, and Supplemental File S1 for quality-control data including signal-to-noise ratios and resolutions.
Ansiform area Segmentation (Figure  2c ) relied on identification of superior posterior (SPF) and ansoparamedian (APMF) fissures  13, 92, 93. Since data quality was variable, segmentation was performed in a subset of specimens representative of the sample that allowed fissure identification with reasonable certainty: 5 apes (N=22; including 10 humans and 9 chimpanzees) and 8 non-apes. Segmentations were again iteratively performed to satisfaction. An interobserver strategy validated segmentations made by NM. For six species, a secondary observer (MA) provided blinded segmentations alongside NM. Additionally, a tertiary observer (VS) segmented the remaining human and chimpanzee ansiform areas in consultation with NM. All segmentations were checked by KH and SLV.
Statistical analyses and reproducibility Consensus phylogenetic trees for the 34-(Figure  1 ) and 13-species analyses were obtained from the 10kTrees 66 primate database (10ktrees. nunn-lab. org; version 3). They were constructed from 17 genes and 7 different loci 66 (10ktrees. nunn- lab. org/downloads/10kTrees_Documentation. pdf). We used R version R 4. 1. 0 for statistical analyses  98. Fit of extant phenotypes in the current and previous 85 studies were tested with three common evolutionary models of trait evolution using Rphylopars  99. Models included Brownian Motion Extant primate traits are not statistically independent, but share variable amounts of evolutionary history 103. Substantial phylogenetic signal was detected, necessitating correction. Corroboratively, correlations between current and previously  85  recorded phenotypes illustrated severe collinearity (Figure  3 ).
The cerebellum and cerebrum scale isometrically Our study supports primate isometric cerebello-cerebral  50, 51, 89, 118, 126  evolution, tending towards hypo-allometry. A recent study reported similar and significant hypo-allometric cerebello-cerebral scaling across mammals 118. When we reran PGLS in the Stephan sample, we observed the same cerebello-cerebral scaling coefficient as this study did (. 92) 118. We found no support for distinct scaling patterns in apes. Lemurs and apes displayed the highest cerebellum-to-cerebrum ratios. Corroboratively, lemurs may have large brains for their bodies 118 , a trait shared with hominoids and especially humans. High relative volumes (Figure  4c ) and positive deviations above the slope of the primate dataset (Figure  5a  and Supplemental Figure  S6b ) evidence relatively large lemur and hominoid cerebella.
Small sample sizes warrant caution Range of absolute and relative volumes across even the 13-species data was substantial, as expected  [80] [81] [82]   29. 58%)  13, 130  , but illustrate how intraspecific variability cannot be ignored. Reanalysis of ansiform area scaling in larger datasets will be necessary to confirm our observations as they may be partially driven by an underpowered sample and influenced by specimen-specific idiosyncrasies  83, 141, 142.
Community-wide sharing accelerates comparative neurosciences Reanalysis in the Stephan dataset 84 offered the following: 1) there is potential for sizable intraspecific samples; 2) but integrating datasets comes with great challenges due to methodological differences, incomplete descriptions, lack of individual observations, or missing provenances; and 3) intraspecific variability is substantial and likely one of the primary drivers of spurious results  [80] [81] [82] [83] 141. Notable discrepancies in volumetric data between the current study and previous datasets  13, 72, 84, 126, 143  underline the pressing need for intraspecific data in comparative analyses. Community-wide guidelines for data collection and statistical handling need to be created to facilitate integration of data from primate studies  7, [144] [145] [146].
Data must be shared openly and completely. Most studies  9, 50, 70, 72, 126, 143  contain data provenance but studies describing specimen-specific observations are still rare  72. Online databases and catalogs for primate brain datasuch as PRIMatE Data Exchange (PRIME-DE)  147  and BrainBox  91  can be used to earmark all primate brains with a unique identification number, linked to relevant metadata including sex, age, body weight, captivity status, data availability, and inclusion in specific studies. This would help interpret contradictory results 141 , and test their statistical significance  148, 149. Access to individual observations allows incorporation of intraspecific variability. There is a pressing need to incorporate this statistical uncertainty  80, 83  , and statistical methods to do this exist  99, 111, 121.
Larger comparative datasets are necessary: exchange platforms have been initiated. Such datasets in combination with relevant metadata and sizable intraspecific samples will facilitate evolutionary analyses sensitive to intraspecific variability. The primate cerebello-cerebral system is a strong functional neuroanatomical scaffold  7. Within it, the ansiform area is characterized by strong positive allometry  13, 130  , unique functional activations  14, 15  and involvement in functional networks  [16] [17] [18] 42, 43. It furthermore has a distinct developmental trajectory 150 and structural properties  150, 151  , and a characteristic role in disorders  7. Concludingly, the ansiform area should be a primary area of interest for the study of human and comparative cognitive correlates in the future  7.
intermediate text files and figures, are uploaded to the repository accompanying this project: github. com/NevMagi/34primates-evo-cerebellum. Input files necessary to replicate our results can also be found here, alongside full-size figures to aid legibility. MRI data have been collated from different sources, and published Open Access  85. The Stephan collection (DOI: 10. 1159/000155963) was not published Open Access. Therefore, access to the data was requested by the authors through the Copy Clearance Center Marketplace and facilitated through the Central Library of Forschungszentrum Jülich GmbH. Reuse permission for these data may be requested from the publisher.