dataesr/scientific-paragraphs-categorization huggingface dataset:
The test data of Study 8 also included trials with physically (fingernails on chalkboard) and emotionally (screaming, crying, etc. ) aversive sounds with three pre-defined intensity levels of each stimulus type. Study 8 was designed to test specificity vs. generalizability to aversive sounds and matched in duration and approximate aversiveness ratings based on pilot studies; trials were randomly intermixed with heat pain trials. Application of the original PDMs on the sound data revealed no significant indirect effects (Figure  4B , Figure  4 -supplement 3) and only nine significant paths ( or ) in total. Thus, pain PDMs do not mediate the relationship between sound intensity and intensity ratings for ether type of sound. These results indicate specificity to somatic pain vs. sound.
45, indicating that the two maps reflect substantially different brain processes. Similarities between individual PDMs and the two univariate maps were ordered according to their order of estimation (and the variance explained in the training dataset), with the exception of PDM 3, which was negatively related to both maps. The NPS (black dot) was positioned between PDMs 2 and 4. However, the low overall similarity values for PDMs 3, 5-10, suggest that the space defined by univariate maps of temperature and pain rating related brain responses do not capture all components involved in pain processing. A higher dimensional representation may be more consistent with psychological theories of pain experience.
, 2017) , the present mediation approach yields higher predictive accuracy. Both approaches may yield whole brain maps that can be used as predictive models of acute pain that can be applied prospectively to new data. Application of the PDMs to new datasets can be used to (i) further evaluate the sensitivity and specificity of the model, and (ii) to evaluate the effects of psychological or medical interventions on the brain processes supporting pain. Testing the PDMs on a large, independent data set showed that the PDMs generalize to other pain data, but do not generalize to aversive sounds. This speaks against the notion that the brain mediators are completely driven by stimulus independent features, such as general feelings of aversiveness or unpleasantness. In summary, the new high-dimensional mediation analysis revealed a comprehensive picture of brain responses underlying the complex, multi-faceted pain experience.
Procedures In all studies, participants received a series of contact-heat stimuli and rated their experienced pain following or during each stimulus. The number of trials, stimulation sites, intertrial intervals, rating scales, and stimulus intensities and durations varied across studies, but were comparable; these variables are summarized in Tables  2  and 3. Each study also comprised a specific psychological manipulation (except Study 8), such as placebo treatment, which will be or has been reported elsewhere (Table  1 ). Study 8, which was used for validation purposes (see below), also presented aversive sounds to participants. Trials with aversive sounds were used to test the specificity of the pain PDMs. Sounds included were a physically aversive recording of nails on a chalkboard and a set of emotionally aversive sounds (attacks, screaming, and crying) from the International Affective Digital Sounds database (IADS)  (Bradley and Lang, 2007).
Preprocessing Structural T1-weighted images were co-registered to the mean functional image for each subject using the iterative mutual information-based algorithm implemented in SPM  (Ashburner and Friston, 2005) , and then normalized to MNI space using SPM. The version of SPM used varied across studies (Studies 1 and 6 used SPM5; while all other studies used SPM8; http://www. fil. ion. ucl. ac. uk/spm/). Following normalization, Studies 1 and 6 included an additional step of normalization to the group mean using a genetic algorithm-based normalization  (Wager and Nichols, 2003; Atlas et al. , 2010 Atlas et al. , , 2014)). For each functional dataset, initial volumes were removed to allow for image intensity stabilization (see  Lindquist et al. (2017)  for details). In addition, volumes with signal values that were outliers within the time series (i.
Data sets and PDM validation The high-dimensional brain mediators (PDMs, see below) were estimated on the training data comprised of Studies 1-7  (Lindquist et al. , 2017). Even though this data set is large (N=209) and diverse, the possibility of overfitting in the training data might reduce the generalizability of the PDMs. To test for the generalizability of the PDMs, we validated the PDMS on independent test data (Study 8, N=75). Computing the inner product of each PDM with each single-trial beta image from Study 8 resulted in 10 potential mediator variables. Each of these potential mediators was then subjected to a multi-level mediation analysis  (Wager et al. , 2009)  with p-values determined by a bootstrap procedure with 5,000 iterations each. If the PDMs generalize to the new dataset, paths a : , b : , and the indirect effect ab : should be significant for all A = 1, … ,10 PDMs.
We also tested whether the PDMs specifically mediate the relationship between temperature and pain intensity. To this end, we also tested the original PDMs on the aversive sound trials from Study 8. If the PDMs reflect specific patterns of brain activity involved in pain processing, they should not mediate the relationship between sound stimulation level and intensity ratings. We thus expect no significant indirect effect for the sound trials. A further test to validate the stability of PDM estimation was conducted by switching training and test data. That is, pain PDMs were estimated on Study 8 and tested on the original training data from Studies 1-7 as described above.
Dimension reduction The training data set consisted of a total of 13,372 single-trial beta images, each consisting of 229,519 voxels, from 209 participants. To reduce the dimensionality of the data to a computationally tractable size, a generalized version of population value decomposition (PVD)  (Caffo et al. , 2010; Crainiceanu et al. , 2011; Chén et al. , 2017)  was applied (using PVD. m as part of the M3 mediation toolbox available at https://github. com/canlab/MediationToolbox). This procedure is similar to singular value decomposition (SVD) but decomposes the data matrix into both participant specific and population specific components. We chose a dimensionality of D = 30 based on a tradeoff between variance explained and the number of trials available for each participant. The beta images were z-scored within each participant before PVD application.
This problem can be solved using a nonlinear programming solver such as the interior-point algorithm. Inference is performed using a bootstrap procedure with 5,000 iterations, as described in  Chén et al. (2017). We also test individual voxel weights for the joint PDM for significance using the bootstrap procedure above. All PDM maps are thresholded at a false discovery rate (FDR) of * < 0. 05. We present results of 10 PDMs accounting for more than 99% of the total indirect effect (Figure  2 ). The PDM implementation is available at https://github. com/canlab/MediationToolbox (multivariateMediation. m). In summary, we obtain scalar coefficients for paths ( : , ) : , and a′ : , as well as the indirect effect () : for each PDM as in a standard, univariate mediation analysis. In addition, we obtain the voxel weight vector ^: that maximizes the indirect effect () :.
Acknowledgements We are grateful for the funding support of the  DFG  ( GE 2774/1-1  to S. G. ) and the  NIH , which supported this work under grants  R01DA035484  (T. D. W. ),  2R01MH076136  (T. D. W. ),  R01DA027794  (T. D. W. ),  R01 EB016061  (M. A. L. ) and  P41 EB015909  (M. A. L. ).
A high number of fungal strains were isolated from roots of Brassicaceae species collected across western and southern Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of this helotialean genus. We provide phylogenetic placement of all of our isolates based on a four-gene dataset, analyze their phenotypic traits in relation to their phylogenetic relationships, and infer the potential distribution ranges of the species by sequence comparisons with available databases. We consider seven well supported phylogenetic lineages as species new to science. Six further lineages probably also represent new species but remain undescribed due to the lack of diagnostic morphological characters.
Soon after its creation, the genus was considered a synonym of Phialophora (Chaetothyriales, Eurotiomycetes) according to similar phialide morphology  (Conant 1937 ), but it was later reinstated as a valid taxon within the Helotiales based on teleomorph links and molecular data  (Gams 2000; Harrington and McNew 2003; Day et al. 2012)   (Day et al. 2012; Fehrer et al. 2019). Sequence data have also led to the recent inclusion of Cadophora in the newly established family Ploettnerulaceae  (Baral 2016; Johnston et al. 2019). Presently, the genus Cadophora comprises 22 accepted species (Index Fungorum, accessed on 19 May 2020) with diverse ecologies and modes of nutrition. The teleomorph stage is unknown for most Cadophora species, with the exception of several species producing mollisioid apothecia  (Harrington and McNew 2003; Day et al.
Fungal material The fungi used in this study were isolated as root endophytes from Microthlaspi spp. plant individuals collected across western and southern Europe  (Glynou et al. 2016). The only exception is isolate P6587, which was obtained from roots of Arabidopsis thaliana grown under laboratory conditions on a sterilized substrate containing a 1 g soil sample from a grassland in The Netherlands (Maciá-Vicente, unpublished). The isolates were selected for their relationship to Cadophora sensu lato, based on comparisons of their ITS sequences with the UNITE database of reference fungal sequences  (Kõljalg et al. 2005)  as described in  Glynou et al. (2016) , and by BLAST searches against NCBI GenBank. UNITE Species Hypothesis (SH) codes  (Kõljalg et al. 2013)  were assigned to each isolate using a similarity threshold of 0.
Phylogenetic analyses Sequences of reference strains from species related to our strains, including species types when available, were retrieved from NCBI GenBank and included in the datasets (Table  S2 ). The sequence datasets for each locus (ITS, LSU, tef1-α, and rpb2) were rst aligned using MAFFT v7. 271  (Katoh and Standley 2013)  using the G-INS-i parameters and manually edited and concatenated in the Geneious software package  (Kearse et al. 2012). Genealogical concordance between the ITS, LSU, tef1-α, and rpb2 datasets was assessed using R v3. 6. 1 (R Core Team 2019), by means of the partition homogeneity test (function CADM. global) available in package ape v5. 3  (Paradis et al. 2004). Because no signi cant support was found for incongruence among the tree topologies resulting from all four loci, a multilocus Maximum Likelihood (ML) phylogeny was obtained with RAxML v8.
correlog of R package vegan v2. 5-6  (Oksanen et al. 2015). Cophenetic distances among isolates were extracted from the phylogenetic tree and compared with Euclidean distances calculated from the coordinates of the morphology PCA (see above), or from the geographic coordinates of each location (geographic distance). To assess the relationships with soil physicochemical (soil distance) and climatic (climatic distance) conditions (Table  S1 ), partial Mantel tests were applied to account for covariation with geographic distance. The data and command line code to reproduce all these analyses is available at https://github. com/jgmv/helotialean_root_endophytes.
Estimation of species' distribution ranges The distribution ranges of the species in the isolates' selection were estimated by comparisons against publicly available geographical data on fungal isolations and sequence reads. The ITS sequences of all isolates were rst compared using standalone BLAST (blastn version 2. 2. 31+) searches against a local copy of the NCBI nucleotide (nt) database, containing all fungal ITS sequences in GenBank as of August 2019. A second set of BLAST searches were performed against a selection of NCBI sequence read archive (SRA) objects, representing a selection of high-throughput ITS amplicon sequencing studies of fungi from soils or root samples worldwide, using the function blastn_vdb version 2. 6. 1+ of the NCBI SRA Toolkit (https://trace. ncbi. nlm. nih. gov/Traces/sra/sra.
cgi?view=software). A summary of all databases used for these comparisons is provided in Table  S3. In both analyses, records from all BLAST matches with a minimum of 98 % identity, and with a minimum alignment length of 200 nt in the case of SRA objects, were retained. The geographical locations of the records, as latitude/longitude coordinates or countries, were obtained from the sequences' metadata, when available, using custom python scripts. When only data on country but no coordinates were available, the geographical coordinates for the country's centroid were obtained using the R package maps version 3. 3. 0  (Becker et al. 2018). The geographical distribution of records was visualized using functions in the R package ggplot2 version 2. 3. 2. 0  (Wickham et al. 2019 ) and maps of package rnaturalearth version 0.
Molecular phylogenetic analyses Ninety-three isolates originating as root endophytes from brassicaceous hosts were included in this study. A nities with members of the helotialean genus Cadophora were recognized based on BLAST comparisons of ITS sequences against the UNITE database (Table  S1 ). Sequences from a selection of 75 strains with reliable species-level identi cations were retrieved from NCBI GenBank and used as references for phylogenetic comparison (Table  S2 ). The alignment of partial sequences of ITS, LSU, rpb2, and tef1-α had 2,767 characters  (638, 885, 725, and 519, respectively). Both the ML and BI phylogenetic trees agreed in showing a clear paraphyly in the genus Cadophora, with representative species scattered across four main clades (Fig. 1  Bien & Damm; which were interspersed with species of the genera Collembolispora, Mycochaetophora, Oculimacula, Rhexocercosporidium, and Rhynchosporium.
cf. orchidicola, given the absence of sequence data for the type specimen of this species. These species-level clades were strongly supported by PP, whereas support was low or only moderately high (89 % in C. cf. orchidicola) based on BS. Other two isolates, P1381 and P2092, were classi ed as C. luteo-olivacea because of their grouping in a lineage including the ex-type sequence of this species (Fig. 1 ). The other 13 clades grouped separately from other known species (Fig. 1 ), and here we propose seven of them as new species (Fig. 1 ). The remaining six lineages (Cadophora sp. 1, Cadophora sp. 2, Cadophora sp. 3, Cadophora sp. 5, and Mycochaetophora sp. ) apparently represent new species but are not described as new due to the lack of discriminating morphological characters of many cultures which remained sterile even after prolonged cultivation on diverse media.
Species distribution ranges Comparison of ITS sequences from all isolates with GenBank records and sequences from highthroughput amplicon sequencing studies of fungal diversity worldwide (Table  S3 ) showed potential distribution ranges largely restricted to the northern hemisphere (Fig. 4 , Fig. S5 ). We evaluated BLAST results with a minimum of 97 % sequence similarity to account for unde ned ITS-based species delimitations, but only values above 99 % are likely to approximate actual species boundaries (Fig. S1 ), with 100 % values providing conservative assignments. At 100 % similarity, most species showed a restricted European distribution, with matches both in the nt and SRA databases spanning a maximum of 5,000 km (Fig. 4B , Fig. S5 ). Only C. obovata, C. cf. orchidicola, Cadophora sp.
1, Cadophora sp. 4, and C. variabilis surpassed that threshold, with reports in either North America and/or Asia, but never south from the equator (Fig. 4B , Fig. S5 ). In contrast to these species, C. fascicularis, C. ferruginea, Cadophora sp. 3, Cadophora sp. 5, and Mycochaetophora sp. showed very restricted ranges with respect to GenBank records, often even at low percent identities (Fig. 3B , Fig. S4 ). Note: The a nity of M. dextrinospora, distinct by dextrinoid reaction of its ascospores, to the genus Cadophora, and notably to C. fastigiata, was recognized already by  Greenleaf and Korf (1980)  and later con rmed by  Gams (2000). The combination into Cadophora is further supported by the current placement of Mollisia in a lineage distinct from Ploettnerulaceae  (Jaklitsch et al. 2016) , and its connection with Phialocephala  (Tanney and Seifert 2016).
5)10. 5-16(20) µm long and 2. 5-4 µm wide. Conidia hyaline, smooth, elongated lemon shaped to fusiform with slight constriction in the middle, forming short chains, (6. 5)8-11(15) µm long and 2-3 µm wide, the mean conidium length/width ratio 3. 5:1. Type. Germany, Darstadt, 49. 68 N, 010. 00 E, 278 m a. s. l. , endophytic in roots of M. erraticum, 6 June 2013, col. by K. Glynou and J. G. Maciá-Vicente, isol. by K. Glynou, FR 0255219 (ex-type culture: P2794 = CBS 146382; GenBank accessions: ITS = KT269992, LSU = MN339414, tef1-α = MN325918). Note: Cadophora fascicularis differs from most Cadophora species by a lack of phialidic conidiogenous cells. It is morphologically somehow comparable to C. antarctica that also produces chains of ramoconidia and conidia on holoblastic conidiogenous cells.
48 W, 1,630 m a. s. l. , endophytic in roots of M. perfoliatum, 2 May 2013, col. by J. G. Maciá-Vicente, isol. by J. G. Maciá-Vicente, FR 0255144 (ex-type culture: P1323 = CBS 146363; GenBank accessions: ITS = KT268618, LSU = MN339356, tef1α = MN325861). Note: Cadophora ferruginea belongs among other phialidic members of this genus, but produces phialides that are generally smaller and may be distinguished by reddish mycelium. Cadophora gamsii Koukol & Maciá-Vicente, sp. nov. -Figs. 1, 9.
5) µm long and 3. 5-5. 5 µm wide (1-septate up to 20 µm long), the mean conidium length/width ratio 3. 9:1, thick walled conidia 7-14. 5(18. 5) µm long and 5-9 µm wide, the mean conidium length/width ratio 1. 7:1. Type. France, Malbrans, 47. 11 N 006. 07 E, 543 m a. s. l. , endophytic in roots of M. erraticum, 4 May 2013, col. by A. K. Buch and X. Xia, isol. by K. Glynou, FR 0255184 (ex-type culture: P2437 = CBS 146379; GenBank accessions: ITS = KT269668, tef1-α = MN325899, rpb2 = MN367272). Additional material. France, Malbrans, 47. 11 N 006. 07 E, 543 m a. s. l. , endophytic in roots of M. erraticum, 4 May 2013, col. by A. K. Buch and X. Xia, isol. by K. Glynou (culture: P2440 = CBS 146379). Note: Cadophora gamsii produces long chains of conidia of variable shapes similarly to C. echinata, where these chains branch and may form large sclerotia-like bodies.
Thines, isol. by K. Glynou, FR 0255171 (ex-type culture: P1963 = CBS 146374; GenBank accessions: ITS = KT269230, LSU = MN339384, tef1-α = MN325888, rpb2 = MN367298). Additional material. France, Saint-Georges-Armont, 47. 41 N 006. 56 E, 285 m a. s. l. , endophytic in roots of M. erraticum, 19 April 2013, col. by J. G. Maciá-Vicente, isol. by J. G. Maciá-Vicente, FR 0255142 (culture: P1101 = CBS 146359). Germany, Ettringen, 50. 37 N 007. 22 E, 504 m a. s. l. , endophytic in roots of M. erraticum, 9 May 2013, col. by M. Thines, isol. by K. Glynou, FR 0255174 (culture: P1978). Germany, Ettringen, 50. 37 N 007. 22 E, 504 m a. s. l. , endophytic in roots of M. erraticum, 9 May 2013, col. by M. Thines, isol. by K. Glynou, FR 0255176 (culture: P1992). Note: The newly described species is distinct from other Cadophora species by having a putatively monoblastic conidiogenous cell.
Conidiogenous cells cylindrical, slightly conical or in ated in lower part, presumably enteroblastic, but without apparent collarette, 6-9. 5(  12 ) µm long and up to 2. 5-5 µm wide. Conidia produced sympodially, ellipsoid, hyaline, with smooth wall, 3-5 µm long and 1. 5-2. 5 µm wide, forming clusters of 2-4 on the top of the conidiogenous cell, the mean conidium length/width ratio 1. 9:1. Specimens examined. Bulgaria, Begunovtsi, 42. 70 N 022. 83 E, 770 m a. s. l. , endophytic in roots of M. erraticum, 14 May 2013, col. by T. Ali and S. Ploch, isol. by K. Glynou, FR 0255161 (culture: P1854 = CBS 146372). Note: The identi cation of this clade formed by 23 isolates sequenced in this study is only tentative due to ambiguous evidence from phenotypic and molecular data. Currently, C. orchidicola is not represented by any ex-type sequence, is neither epitypi ed, and the GenBank database contains more than 380 sequences of Cadophora/Leptodontidium orchidicola (search 11 January 2020).
5)11-21(27) µm long and 5. 5-9 µm wide, the mean conidium length/width ratio 2. 2:1. Type. Croatia, Jasenice, 44. 24 N, 015. 54 E, 760 m a. s. l. , endophytic in roots of M. perfoliatum, 4 May 2013, col. by T. Ali, isol. by K. Glynou, FR 0255203 (ex-type culture: P1176 = CBS 146360; GenBank accessions: ITS = KT268493, LSU = MK539845, tef1-α = MK550890, rpb2 = MN367276). Additional material. Spain, Puebla de Don Fadrique, 38. 04 N, 002. 48 W, 1630 m a. s. l. , endophytic in roots of M. perfoliatum, 2 May 2013, col. by J. G. Maciá-Vicente, isol. by K. Glynou, FR 0255145 (culture: P1331 = CBS 146364). Note: Cadophora variabilis is highly similar to C. antarctica, which also produces chains of ramoconidia and conidia on holoblastic conidiogenous cells. However, ramoconidia and conidia of C. variabilis are larger than those of C.
The nal dataset assembled in our study not only expands several times the clade C of  Day et al. (2012) , but also provides a clear support for the paraphyly of Cadophora. Species of the genera Collembolispora, Helgardia, Mycochaetophora, Oculimacula, Rhexocercosporidium, and Rhynchosporium, are interspersed between the clades formed by Cadophora species (Fig. 1 ). The ITS sequences alone are not enough to differentiate species within this group, and even single coding-gene phylogenies may result in misleading information. Interestingly, the same gene may have different taxonomic value for different Cadophora clades. Whilst  Walsh et al. (2018)  found clear differentiation of C. interclivum and C. meredithiae based on the β-tubulin gene,  Bien and Damm (2020)  suspected the same gene of having paralogues in C.
Distribution patterns Comparisons of ITS sequences with data available in public databases showed that many of the focal species in this study are related to fungi widely distributed across the northern hemisphere, although in most cases nearly identical sequences were exclusively found within Europe. This is in line with previous observations on the distribution of other helotialean DSE in the Phialocephala fortinii C. J. K. Wang & H. E. Wilcox and Acephala applanata Grünig & T. N. Sieber species complexes  (Grünig et al. 2001; Piercey et al. 2004; Queloz et al. 2011) , which show a widespread distribution in northern temperate zones. The absence of similar sequences in the southern hemisphere can be caused by biases in the geographic representation of fungal ITS sequence data in GenBank, with several southern-hemisphere countries being underrepresented as compared to countries in the North.