dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition, the average expression levels of HLA-DRB4 and HLA-DRB5 were 1. 4-1. 5fold higher than HLA-DRB3 (Figure  1  and Table  1 ). The lowest reads were for HLA-DQA1 and HLA-DQB1. The ratio of hinges (third quartile reads/first quartile reads) in the box-and-whisker diagram confirmed that locus-specific variations of the read numbers for the HLA-DQ RNA levels (2. 8 for HLA-DQA1 and 3. 6 for HLA-DQB1) were much higher than 1. 3-1. 4 for the class I RNA levels and 1. 7-2. 0 for the HLA-DP and HLA-DR RNA levels (Table  1 ). The RNA levels expressed at each allele were analyzed using the read numbers obtained from at least three different samples. Figure  2  shows box-and-whisker diagrams of the RNA levels for the HLA alleles of PBMC samples using datasets 2-4 that include 2,175 (763 class I + 1,260 class II + 152 HLA-DRB3/DRB4/DRB5) heterozygous alleles (Table  S4A ).
HLA Polymorphisms and RNA Expression Levels in Specific HLA Loci and Haplotypes of PBMC Samples Relationship Between HLA-DR Haplotypes and RNA Levels Since the correlation between HLA-DRB1-HLA-DRB3/DRB4/ DRB5 haplotypes and RNA expression levels was unknown, we examined 31 DRB3/DRB4, 18 DRB3/DRB5, and 23 DRB4/DRB5 heterozygous samples (a total of 144 DRB1-DRB3/DRB4/DRB5 haplotypes) from dataset 4 (Table  S4A ). In this dataset, there was a total of 28 DRB1-DRB3/DRB4/DRB5 haplotypes with 14 assigned as DRB1-DRB3, 11 as DRB1-DRB4, and 3 as DRB1-DRB5. These haplotypes were identified by estimating HLA-DRB1 and HLA-DRB3/DRB4/DRB5 alleles without observing any discrepancies to previously reported HLA-DR genomic structures  (53, 54). Figure  S3A  shows the comparative relationships of RNA levels expressed by the HLA-DRB1 and HLA-DRB3/DRB4/DRB5 loci using 17 DRB1-DRB3/DRB4/DRB5 haplotypes that were analyzed using at least three different samples (Table  S5 ).
RNA Expression Levels of HLA-DPB1 Alleles and Genotypes of rs9277534 The SNP marker rs9277534 is located within the 3 ′ UTR of HLA-DPB1, and the RNA levels expressed by the AA genotype were reportedly significantly (P < 0. 001) lower than those expressed by the GG genotype (Figure  S3C )  (25). In our analysis of the same genotypes by the capture RNA-Seq method, the read numbers for the AA genotype using 12 samples and the GG genotype using 24 samples that were selected from dataset 3 of PBMC samples (Table  S4A ) produced a box-and-whisker diagram (Figure  S3C ) that was similar to the results of the previous report  (25, 56)  with a significant difference (P = 0. 0019) of expression between the AA and GG genotypes. However, this result was not consistent with individual alleles shown in Figure  2E  because DPB1 * 04:01:01 (low) and DPB1 * 05:01:01 (high) are thought to be outliers, while DPB1 * 04:02:01, DPB1 * 02:01:02 and DPB1 * 02:02 that are supposed to be low expression levels have similar  RNA levels as those of DPB1 * 09:01:01 and DPB1 * 06:01:01 that are supposed to be high expression levels  (57).
RNA Expression Levels of Null or Low Expressed HLA Alleles Of over 25,000 HLA alleles released from the IPD-IMGT/HLA database (http://hla. alleles. org/), ∼1,000 alleles are characterized as null and low expressed alleles. We tested if the RNA-Seq method is able to discriminate those null alleles by analyzing read data corresponding to the HLA-A * 02:15N and A * 02:53N alleles, which have been categorized as null. Examination of the RNA levels expressed by the known HLA-A null alleles A * 02:15N and A * 02:53N (Figure  S3D ) revealed that they were at 34. 3% (41,242 reads) and 18. 2% (21,902 reads), respectively, of the average median of HLA-A allelic expression (120,366 reads in Table  2 ). This result suggests that the capture RNA-Seq can directly identify null and low expression allele in a quantitative manner.
Comparison of the HLA RNA Levels in PBMC and UCB A box-and-whisker diagram of the normalized read numbers (RNA levels) expressed by 12 HLA loci (Figure  S4A ) in UCB was constructed using the dataset 1 that includes 280 phased alleles (Table  S4B ). The ANOVA statistical difference between the expression levels of the 12 HLA loci of UCB was highly significant (ANOVA, P < 1. 0 × 10 -95 ) similarly to those of PBMC (Figure  1  and Figure  S4A ). The DAE was observed for all HLA class I and II genes, except for HLA-DRA and HLA-DRB5. Collectively weak statistical significances were also noted for RNA levels expressed by the HLA alleles of HLA-DPA1 (P = 1. 2 × 10 -2 ) to HLA-DQB1 (P = 1. 6 × 10 -31 ) (Table  S6 ). The observation of higher p values in UCB than in PBMC is thought to depend on the number of samples.
Although specific RNA capture probes are an important first step for accurate and reliable quantitation of allele expression by the capture RNA-Seq method, the NGS and analytical bioinformatic methods for obtaining correct read numbers for RNA (cDNA) sequences expressed by particular alleles are equally important steps in the overall accuracy and reliability of the protocol. In general, it is difficult to obtain the correct read numbers for each allele using the publicly available RNA-Seq analysis software because read mapping is not performed easily under 100% matching conditions, and in such cases of reduced stringency, there is a possibility that reads from other highly similar HLA genes or alleles may be mapped unexpectedly. Therefore, we focused only on coding regions (exons 2 and 3 of class I loci and exons 2 of class II loci) that can be divided easily into each polymorphic phase and the reads mapped to sequence references at 100% matching condition.
DATA AVAILABILITY STATEMENT The novel HLA allele sequence is available in GenBank/DDBJ/ENBL-EBI DNA databases under the Accession Number LC499658. This work described in the article was performed with permission from The Japanese Data Center for Hematopoietic Transplantation (JDCHCT: http://www. jdchct. or. jp/en/outline/). The NGS data will be stored and maintained on a data server at Tokai University School of Medicine for at least 5 years and will be made available to interested parties upon request for validating the findings described in the paper. However, if anybody wants to use the raw NGS data beyond evaluating the current work, it is considered to be secondary usage of the data at JDCHCT (office@jdchct. or. jp), and written permission will need to be obtained from JDCHCT for such usage.
FUNDING This work was supported by  MEXT KAKENHI  (No. 16H06502 ), and by the  Practical Research Project for Allergic Diseases and Immunology (Research on Technology of Medical Transplantation ) from the  Japan Agency for Medical Research and Development  ( 17ek0510022h0001 ,  18ek0510022h0002  and 19ek0510022h0003). Work in SB's laboratory is supported by grants from the  Agence Nationale de la Recherche (ANR)  ( ANR-11-LABX-0070_TRANSPLANTEX ) andMSD-Avenir (AUTOGEN).
For over a century, researchers have assumed that the plane of the lateral semicircular canal of the inner ear lies parallel to the horizon when the head is at rest, and used this assumption to reconstruct head posture in extinct species. Although this hypothesis has been repeatedly questioned, it has never been tested on a large sample size and at a broad taxonomic scale in mammals. This study presents a comprehensive test of this hypothesis in over one hundred "ungulate" species. Using CT scanning and manual segmentation, the orientation of the skull was reconstructed as if the lateral semicircular canal of the bony labyrinth was aligned horizontally. This reconstructed cranial orientation was statistically compared to the actual head posture of the corresponding species using a dataset of 10,000 photographs and phylogenetic regression analysis.
The saiga antelope pictures were kindly provided by K. H. Vogel. The dataset represents about 10,000 pictures documenting the head posture of 129 species and is available here: https ://osf. io/4vpnj /?view_only=3dc98 7012f cd44a 6a64a d7d89 49ec0 1f (https ://doi. org/10. 17605 /OSF. IO/4VPNJ ). The pictures were taken from outside the enclosures to avoid interaction with the animals. It was essential for this study that the animals remain calm and act naturally, so their environment was not disturbed, and the animals were not put on leash or isolated. As such, individual identification was not possible. Representatives of both sexes are mixed in the dataset as sexes could not always be determined. The typical photography set up is illustrated in Fig. 1. To ensure that the photographed head postures were comparable between individuals and species, all pictures were taken by one of the authors only (J.
2a ). An average neutral head posture was then calculated for each species (Table  1 ). The intraspecific standard deviation (measurement error) for neutral head posture is ± 1. 6°. The bony labyrinth is one of the first organs to completely ossify in mammals as its adult size and shape are reached at mid-gestation  50, 51. However, the orientation of the LSC seems to show age-related variations in some tetrapod species, including humans, which may impact their head posture  26, 52, 53. As such, juveniles were excluded from the dataset. S1  for details), were used.
Head The bony labyrinths of each skull were segmented manually and reconstructed in 3D using the software AVIZO 9 (FEI VSG, Hillsboro OR, USA) at the virtual imaging labs of the Evolutionary Studies Institute and the Natural History Museum of Basel. The skull was reconstructed using either the Isosurface or threshold functions under the same software. The angle between the plane of the LSC and the main axis of the skull was then measured in lateral view in 2D (Fig. 2b ). The plane of the LSC was determined visually in lateral view, following most previous authors  19, 20, 22, [24] [25] [26]. The main axis of the skull was traced as the axis running from just above the premaxilla (approximately at the level of the centre of the nasal opening) to the middle of the occiput (Fig. 2b ) in order to maximize the homology with the measurements taken on living animals.
This angle represents the anterior tilting of the head if the LSC is considered horizontal. This angle is hereafter referred to as "the reconstructed cranial orientation" or "reconstructed head posture". Measurements were taken bilaterally when both bony labyrinths were available and then averaged for each species (Table  1 ). For consistency, all measurements were taken by the same author (J. B. ). None of the samples expressed strong lateral tilting of the LSC or an undulating morphology that could impede taking this measurement or affect its accuracy. The intraspecific standard deviation (measurement error) for reconstructed head posture is ± 2. 1°. The complete dataset of reconstructed head postures is available in the Supplementary Table  S1. This dataset was complemented by measurements made on the published pictures from Girard and Schellhorn  5, 30  (see Supplementary Table  S1 ).
As for the picture dataset, only the individuals showing reasonable signs of maturity (e. g. cranial bone fusion, erupted molars) were considered. Data processing. The dataset was analyzed using phylogenetic comparative methods to control for the non-independence of observations  [54] [55] [56]. We used the time-calibrated phylogenetic tree of mammals of Bininda-Emonds et al. 57  because it encompasses all the species in our dataset and fossils can be easily added to it in future analyses. The tree was pruned to match the species in our dataset using function 'drop. tip' in R package ape  58. All subsequent analyses were performed in R v3. 6. 3 (R Core Team, 2020). The phylogenetic signal of individual variables was estimated using Pagel's lambda  59  for continuous features (reconstructed cranial orientation, neutral head posture, body mass) using function 'phylosig' in package phytools  60.
Lambda was chosen over the other commonly used estimator K 61 because of the latter's poor performance for trees with small sample sizes and polytomies  62, 63  , both of which can be found in our dataset. For binary traits (head-butting; see below), phylogenetic signal was estimated with the D-statistic 64 using function 'phylo. d' in package caper  65. To test whether the plane of the LSC can be used as a reliable proxy to reconstruct the neutral head posture, we regressed the neutral head posture of living animals on the reconstructed cranial orientation using data in Table  1 , and phylogenetic generalized least squares (PGLS) regressions  66, 67. PGLS were compiled using the 'gls' function in package nlme  68  , with correlation structures for each evolutionary model specified in ape  58.
A model selection procedure based on the corrected Akaike information criterion (AICc) was applied to the regressions using the package AICcmodavg  69. Five evolutionary models were considered for this selection procedure (see  70  ): Brownian Motion, Pagel's Lambda, Ornstein-Uhlenbeck, Early Burst, and White Noise -i. e. non-phylogenetic, ordinary least squares (OLS) regression. All regressions were performed using raw and log-transformed data (natural logarithm). Both variables in the models are in the same unit and order of magnitude, and the models  built with raw data showed a higher significance and met parametric assumptions better than models built with log-transformed data. For this reason, we used the former to assess the relationship between the two variables. Because of the high degree of body mass allometry in neuroanatomical features  [71] [72] [73]  , body mass measurements for all species in the sample were taken from the literature (Supplementary Table  S1 ) and included as a co-predictor to be tested against models built with only the reconstructed and neutral head postures as predictors in the AICc-based model selection procedures.
Results All the data in the dataset for which a phylogenetic signal could be measured (neutral head posture, reconstructed cranial orientation, body mass, and head-butting) carry a strong phylogenetic signal (lambda > 0. 8 for the first three variables; D = -0. 2841056 for head-butting) (See Supplementary Table  S1 ). Species with body mass under 100 kg have an average neutral head posture of 30° and reconstructed cranial orientation of 39°, whereas species larger than 100 kg have a neutral head posture averaging 37° and average cranial orientation of 40°. This suggests an effect of body mass on head posture as was hypothesized by Köhler  47  , but not on the orientation of the LSC (Fig. 3 ). This is consistent with statistical analyses, which identify a very weak effect of body mass on neutral head posture (R 2 = 0.
6 ), but a slight trend toward more downwardly tilted head postures seems to occur in species living in a more open habitat (Fig. 6 ); however, this trend is not significant (F = 1. 343; p-value = 0. 792). Semi-aquatic species seem to have a more posteriorly tilted LSC resulting in a higher reconstructed cranial orientation (23°) than fully terrestrial species, but this does not reflect on the neutral head posture (Fig. 6 ). Unfortunately, the sample size for this category was too low to effectively test if this difference was significant or simply the result of the scarcity of semi-aquatic species in the dataset. Head-butting is found to have a highly significant statistical effect on reconstructed head posture (F = 39. 467; p-value = 0. 002), with a difference of 13° between head-butting and non-head-butting species on average (Fig.
In both cases, the variance of the residuals is high, which might indicate a low predictive power of these models (R 2 equals 0. 26 and 0. 33, respectively). The misalignment between the plane of the LSC and the horizontal is consistent with the results obtained by Marugán-Lobón et al. 43  on birds using Duijm's dataset 8 , though their approach to the study of head posture was different from the one presented here, which limits comparisons. The reason why the LSC would not be aligned with the horizontal in the neutral posture is still unclear. It may be explained by the very function of the canals and ampullae, which are meant to record head movements and play crucial roles in the vestibulo-ocular and vestibulo-collic reflexes to compensate for the movements and accelerations of the head compared to the eyes and the rest of the body  6, 13, 14, 43.
The effect of phylogeny. Both the neutral and reconstructed head postures carry an important phylogenetic signal (Lambda equals 0. 97 and 0. 84, respectively). For paleontologists, this strong phylogenetic signal implies that the best way to predict the head posture of an extinct "ungulate" is to look at the neutral head posture of its modern relatives. In comparison, once the data are corrected for phylogeny, diet is found to have only a weak correlation with the reconstructed cranial orientation (F = 7. 723; p-value = 0. 046), and no significant effect on the neutral head posture (F = 2. 663; p-value = 0. 516). This reflects well in the dataset. The Tylopoda is the group in which the head is the most consistently tilted upward, with an average neutral head posture of 10°. This reflects on their reconstructed cranial orientation which averages 17°.
Tilting of the head was hypothesized to be correlated to body size in "ungulates"  47  , with small, forest-dwelling species holding their head higher than large species adapted to savannah. A similar trend is found here, with species above 100 kg having their head tilted 37° anteriorly on average whereas species below 100 kg hold their heads 30° below the horizontal on average (Fig. 3 ). Statistical tests on our dataset find a significant correlation between body mass and head posture (p-value = 0. 014), but this correlation is no longer significant once the data are corrected for the effect of phylogeny (p-value = 0. 060). This strongly suggests that the trend observed here and by Köhler  47  actually reflects the fact that large savannah herbivores belong to just a few clades (e. g. equids, alcelaphins, and hippotragins) whereas the small ones mostly belong to the Antilopinae.
A more significant effect of body mass might nevertheless be found while including very small-bodied species (e. g. rodents, shrews) because their head posture would be more constrained by its proximity to the substrate. Similarly, species with a sprawling posture would also have to keep their head higher, as already observed in many reptiles  12, [41] [42] [43]. The relationship between LSC orientation and phylogeny has been empirically anticipated as the way the LSC enters the vestibule (either directly above the posterior ampulla or at different levels within the ampulla) is distinctive between different clades of ruminant  50, 51, [86] [87] [88]. The selection of an Early Burst model as the best fit for the whole dataset suggests that the evolution of head posture might represent a classic example of adaptive radiation  61, 78.
This may be the effect of the abundance of bovids in our dataset, which originated in the early Neogene and rapidly adapted to a wide variety of ecological niches, diet, body mass, social behavior, and habitat  48, 89. However, the presence of a strong phylogenetic signal for both head posture variables cannot be directly interpreted as evidence for such a radiation in terms of evolutionary process, which would require further analyses of diversification rates  90. The increase of phenotypic divergence resulting in different niches for a given character in a clade does not always correspond to an adaptive radiation, even when it closely matches the underlying phylogeny. This is due to ecological interactions between distantly related species, which can result in a similar timing of evolutionary shifts for distinct clades, the detail of which is often very difficult to decipher without exhaustively sampling each of these clades  91.
As such, a gradually more anteriorly tilted neutral head posture is expected as moving from browsing species to mixed feeders, and finally grazers  20, 30. Schellhorn  30  was the first to compare the reconstructed cranial orientation of Rhinocerotidae to their actual head posture (using an open-access database of photographs) and found results consistent with such a gradient. Measuring the reconstructed cranial orientation from Schellhorn's published figures and adding our own observations of neutral head posture, we do find a more tilted reconstructed cranial orientation in the grazing Cerathotherium (average reconstructed cranial orientation = 38°), than in the mixed feeder Rhinoceros (average reconstructed cranial orientation = 34°), and the browsing Dicerorhinus and Diceros (average reconstructed cranial orientation = 31°) (Fig.
9 ); however, this gradient does not reflect on the neutral head posture that shows no particular trend among rhinocerotids (Fig. 9 ). Despite the large difference between the average head posture of browsers and grazers, the very low head posture of mixed feeder rhinocerotids casts some doubts on the validity of the correlation between head posture and diet (Fig. 9 ). The Cervidae constitutes a more striking example (Fig. 10 ). In cervids, the head is consistently kept within about 10° around the average neutral head posture (20°) regardless of diet, and browser and grazers are not distinguishable based on neutral head posture (average = 30° for browser; average = 28° for grazers) or reconstructed cranial orientation (average = 41° for browsers; average = 45° for grazers) (Table  1 ). The situation in rhinocerotids illustrates that for the whole dataset.
Semi-aquatic adaptation. No significant result indicative of a correlation between habitat and head posture or reconstructed cranial orientation was found; however, semi-aquatic species show a noticeably high reconstructed posture of the skull on average (23°) compared to other species (Fig. 6 ). The low number of semiaquatic species in the dataset (one rhinocerotid, three tapirids, and two hippopotamids, Table  1 ) likely prevents this trend to be identified as significant in our sample. A high head posture is not observed in semi-aquatic species (Fig. 6 ), even though it would be expected of species that have to keep breathing above water level most of the time while immersed  27, 30. Recently, a semi-aquatic habit for the Triassic archosaur Proterosuchus and the therapsid Lystrosaurus has been hypothesized as these two species would have their head tilted upward anteriorly when the plane of the LSC is horizontal  27, 94  (Fig.
11b ). Among fossil species, the likely terrestrial sauropod Ngwevu intloko (Fig. 11c ) would also have had its reconstructed cranial orientation tilted 17° above the horizontal (identified as Massospondylus carinatus in Sereno et al. 20  ; see Chapelle et al. 95  ). The peculiar orientation of the LSC in Lystrosaurus, Proterosuchus, and Massospondylus is remarkable as such a downward tilting of the LSC superior to 15° has never been found in any modern species to date, particularly not in the semi-aquatic species studied here which all have a posteriorly tilted LSC as all other "ungulates" (average reconstructed cranial orientation of semi-aquatic species = 23°) (Fig. 6 ; Table  1 ). The heron and razorbill mentioned above would have an anterior tilting of less than 4° (Supplementary Table  S1 ), and Duijm's 8 dataset includes mostly semi-aquatic species, which limits comparisons.