dataesr/scientific-paragraphs-categorization huggingface dataset:
MBE undergo massive HIM-mediated chromosomal integration in host tissues during parasitism. We thus sought to assess whether HT of PDV circles occurred from wasp to lepidopterans through HIM-mediated chromosomal integration in the germline of lepidopteran hosts, followed by vertical transmission in host populations. For this, we used HIM-containing HdIV and CtBV circles to perform blastn similarity searches on 775 lepidopteran genomes available in Genbank as of December 2021. Our search yielded 4,648 and 49,079 lepidopteran sequences longer than 300 bp that showed similarity to HIM-containing HdIV and CtBV circles, respectively, with an e-value lower than 0. 0001. We reasoned that if some of these sequences were integrated through double-strand breaks within HIM, then they were bordered by the J1 and J2 motifs (fig.
Twelve individuals of each species were collected from three different locations in France. We obtained specific bands by PCR amplification of the junctions between flanking and viral sequences for all individuals (fig. 11 ). Sequencing of the PCR products confirmed that J1 and J2 constituted actually the extremities of the four insertions identified from P. rapae and P. napi genomes, which thus appear to be fixed in the population and not a particular feature of the individuals used for genome sequencing. All sequences are provided in supplementary Dataset 2, Supplementary Material online. The P. napi HdIV 12 J2 sequence corresponds to the blastn hit number 167 in supplementary table S1, Supplementary Material online. The other five verified junctions were not recovered in the bioinformatic search because this experimental study was performed independently by three of us (G.
MBE the genome of two or more species. Our approach allowed us to identify five BV fragments and eight IV fragments shared by two or more species at the same genomic position (table  2 ). One IV orthologous fragment, found in Calephelis metalmarks may be as old as the monarch integration as it shows only 82. 1% nucleotide identity between C. nemesis and C. virginiensis and the split between the two species has been dated at 4. 9 Ma (table 2, supplementary Dataset 3, Supplementary Material online)  (Cong et al. 2017). By contrast, all other cases involve species for which divergence time is unknown but is likely recent because the species are congeneric and/or nucleotide identity between orthologous fragments is high (from 90. 9% to 99. 3%; mean = 96. 6%). Regarding IV orthologous fragments, two are shared between four very closely related species of metalmark butterflies (genus Apodemia, Riodiniidae)  (Zhang et al.
2019) , one of them is shared between the green-veined white (Pieris napi, Pieridae) and its close relative P. macdunnoughi  (Chew and Watt 2006)  and another one is shared between the European corn borer (Ostrinia nubilalis, Crambidae) and the Asian corn borer (O. furnacalis), which diverged recently (table 2; supplementary Dataset 3, Supplementary Material online)  (Bourguet et al. 2014). In terms of BV orthologous fragments, three are shared between C. nemesis and C. perditalis metalmark butterflies, one is shared between two species of firetips (Oxynetra hopfferi and O. stangelandi) and one is shared between Emesis lupina and E. tegula (table 2; supplementary Dataset 4, Supplementary Material online)  (Cong et al. 2017). In addition to orthologous fragments shared between species, we found several paralogous IV fragments sharing the same immediate flanking genome region (supplementary table S5 and supplementary Dataset 5, Supplementary Material online).
We also found that many of the PDV fragments integrated into lepidopteran genomes contained a single, recombined DRJ motif (supplementary tables S1 and S2; supplementary Dataset 1, Supplementary Material online; fig. 1 ), consistent with the transfer of wasp PDV circles that were then linearized and integrated into host genomes. Furthermore, we PCR-validated typical extremities of HIM-mediated junctions of two IV and two BV integrations in multiple individuals of two species of Pieris butterflies and uncovered multiple integrations shared at orthologous loci between two to four lepidopteran species. Altogether these results indicate that HIM-mediated germline infiltration of PDV circles is widespread in lepidopterans, the main hosts of braconid and ichneumonid parasitoid wasps. The number of J1-or J2-bordered PDV circle fragments we report here is necessarily underestimated because we only used HdIV and CtBV circles, for which HIM were annotated using the same approach  (Muller et al.
Reference Genomes Used to Characterize Somatic Insertions of H. didymator Ichnovirus The genome of S. frugiperda (corn strain) was sequenced by  Gimenez et al. (2020)   (Bolger et al. 2014 ) and the quality was evaluated with FastQC v. 0. 11. 8  (Wingett and Andrews 2018). To get statistics on sequencing depth, we aligned the four datasets of trimmed paired-end reads using Bowtie2 v. 2. 3. 4. 1  (Langmead and Salzberg 2012)  in end-to-end mode on both S. frugiperda and H. didymator reference genomes. We converted the output SAM files into sorted BAM files with samtools v. 1. 9. The sequencing depth for each of our samples was estimated with bedtools genomecov v2. 26. 0 (Quinlan and Hall 2010) on both reference genomes (-ibam and -d options). To get the sequencing depth of H. didymator proviral segments, we used bedtools coverage v2.
Characterizing Integrations of Wasp Ichnovirus DNA Circles in Somatic Host Genomes To identify integrations of HdIV DNA circles in the S. frugiperda somatic genomes, we searched for chimeric reads, that is reads for which a portion aligns exclusively on HdIV and another portion aligns exclusively on the S. frugiperda genome. Reverse and forward raw fastq files were converted into fasta files. The resulting fasta files were aligned on the wasp genome with blastn version 2. 6. 0 (-task megablast -max_target_seqs 1 -outfmt 6). Reads aligning on the wasp genome were extracted from the fasta file using seqtk subseq (https://github. com/lh3/seqtk) and aligned with blastn (same options as above) on the S. frugiperda genome. To further find chimeric reads most likely to result from the integration of HdIV into S.
frugiperda genome, we used the approach described in  Muller et al. (2021). Briefly, we used the tabulated outputs of the two successive blastn searches as entries of an R pipeline initially written to identify artificial chimeras generated during deep sequencing library preparation  (Peccoud et al. 2018). This script identifies reads as chimeric reads if 1) at least 90% of the read aligns on one or the other genome, 2) at least 16 bp align only on one of the two genomes, 3) with a maximal of 20 bp overlap between the two read portions aligning on Heisserer et al. • https://doi. org/10. 1093/molbev/msad050 MBE a different genome, and 4) a maximal of random 5 bp insert at the chimeric junction. Then, we estimated the number of independent IEs by counting as one event all reads with identical or nearly identical coordinates in the two genomes.
Searching for Polydnavirus DNA Circles in Lepidopteran Genomes To search for HIM-mediated HT of PDV circles in lepidopteran genomes available in Genbank, we used the seven HIM-containing HdIV circles and the 16 HIM-containing C. typhae BV (CtBV) circles previously described in  Muller et al. (2021)  as queries to perform similarity searches using blastn (-task blastn) on lepidopteran genomes. All HdIV and CtBV DNA circle sequences are provided in supplementary Dataset 6, Supplementary Material online and the HIM coordinates within these circles are provided in supplementary Dataset 7, Supplementary Material online. The sequences of each HIM motifs of HdIV and CtBV circles are also provided as a multiple alignment in supplementary Dataset 8, Supplementary Material online as well as in figure  4.
A total of 844 lepidopteran genomes were available in Genbank as of December 2021. When more than one genome per species was available, we only retained the largest one, resulting in 775 genomes that were submitted to our search. Accession numbers, size, and N50 of these genomes are provided in supplementary table S6, Supplementary Material online. Blastn outputs were filtered in R (R Core Team) based on hit size, e-value, and coordinates. Some PDV circles are similar to each other. For example, Hd12 and Hd16 are similar to each other over most of their length. To avoid counting multiple times the same lepidopteran genome region as resulting from HIM-mediated HT, alignment coordinates of blastn hits were thus merged using bedtools v2. 26. 0 merge (-s -c 4 -o distinct)  (Quinlan and Hall 2010).
Merging was performed independently for IV-like and BV-like sequences. The script written for this part of the study is available on GitHub: https://github. com/ HeloiseMuller/Chimera/tree/master/scriptsArticles/Heisserer 2022. DRJ, recombined DRJ (also called "DRJ circle") and HIM motifs were searched manually or by blastn in lepidopteran PDV insertions using DRJ and HIM motifs previously annotated in CcBV and HdIV as queries  (Legeai et al. 2020; Gauthier et al. 2021).
Sequencing Depth Surrounding Junctions Between PDV DNA Circles and Lepidopteran Genomes To compute sequencing depths on junctions between PDV DNA circles and lepidopteran genomes, raw Illumina reads were downloaded from Genbank for nine species in which more than four junctions were found. Accession numbers of these reads are provided in supplementary table S7, Supplementary Material online. Reads were mapped on the genome of the nine species using bowtie2 (default options)  (Langmead and Salzberg 2012). Read depth over 300 bp upstream and downstream of each junction was obtained using bedtools v2. 26. 0 coverage  (Quinlan and Hall 2010).
Characteristics of J1-or J2-bordered PDV Fragments Shared at Orthologous Loci Between Two or More Lepidopteran Species. orJ2-bordered PDV fragments are listed by pair of species, number refer to their number label in sequence alignments provided in supplementary Datasets 3 and 4, Supplementary Material online. Letters between brackets indicate pairs of species sharing the same orthologous fragment (e. g. , PDV fragments 1, 5, and 7 are shared at the same orthologous locus in Apodemia duryi,A. virgulti, A. mejicanus and A. mormo).
Legeai et al. (2020)PacBio RSII (Pacific Biosciences) technology and assembled with Platanus. It is available on the BIPAA platform (https:// bipaa. genouest. org/is/;Rennes,France)andunderaccession number PRJNA662887 in NCBI. This genome is 384. 46Mb, it has an N50 (i. e. , minimum contig length that covers 50% of the genome) of 13. 15 Mb and it is composed of 125 contigs. The genome of H. didymator was sequenced by Legeai et al. (2020) using the short-read Illumina HiSeq technology and assembled with Platanus. It is available in the NCBI database under accession number PRJNA 589497. The genome is 226. 9Mb, it has an N50 of 3. 3 Mb and it is composed of 131,161 sequences. HdIV regions were annotated byLegeai et al. (2020)using the genome annotation editor Apollo browser. Fifty-seven viral segments localized in 66 viral loci were annotated in 32 scaffolds.
Data Availability All data produced during this study are available in public repositories. Genbank accession numbers of raw reads produced from S. frugiperda larvae parasitized by H. didymator are provided in table 1. Scripts are provided in GitHub: https://github. com/HeloiseMuller/Chimera/tree/master/ scriptsArticles/Heisserer2022. All wasp PDV circles and all lepidopteran PDV fragments bordered by HIM are provided in supplementary Datasets 6, Supplementary Material online and supplementary tables S1 and S2, Supplementary Material online. Accession numbers of lepidopteran genomes surveyed in this study are provided in supplementary table S7, Supplementary Material online.
Measuring Sequencing Depth on H. didymator and S. frugiperda Genomes The four datasets of Illumina reads we obtained (two para- sitized caterpillar tissues at two timepoints post-parasitism; SRA accession numbers provided in table 1) were quality-trimmed with Trimmomatic v. 0. 38 (LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 options).
Statistical Analysis We used IBM SPSS Statistics 26 (https://www. ibm. com) for all statistical analyses. We expressed categorical variables as frequencies and percentages and SYNOPSIS continuous variables as medians with interquartile ranges (IQRs). To compare cytokine/chemokine levels between patient and control groups, we used the Mann-Whitney U test and set p <0. 05 as statistically significant. We performed Friedman 2-way analysis of variance of ranks to determine the changes in cytokine/ chemokine and laboratory parameter levels over the 3 time intervals. We calculated the time interval contributing to change using Pearson pairwise comparison with Bonferroni correction. Finally, we determined correlation between laboratory tests and cytokine/ chemokine levels with Pearson correlation analysis.
Here we observe that CEI strikingly follows such an adaptive behavior with the same frequency bandwidth dependence as traditional cochlear filters  46, 47. We tested this by fitting a linear filter bank equivalent to CEI when processing a large database of speech sounds. This allowed us to compute the equivalent center frequencies and bandwidths for each CEI's mode considered as the result of a band-pass filter on the input signal (see Fig. 3d ). Strikingly, the relationship between the center frequency and the bandwidth was compatible with psychoacoustics models based on the ERB. Such an adaptive behavior differs from current modeldriven constant-Q transforms that consider the cochlea as a fixed band-pass filter bank. This makes it potentially compatible with adaptive efficient coding  22, 23.
Adaptive filter bank Pure tones + pink noise. Tests signals composed either of pink noise, i. e. , a random signal with a spectrum defined by S(f) = 1/f 2 and a random phase, or two pure tones with frequencies at 100 and 1000 Hz. The CEI decomposition of each signal is first computed and the CEI power spectrum of each mode is then computed. The operation is repeated 100 times with 100 different pink noise excerpts. The power spectra of each mode are then averaged. Sound database. Speech and environmental sounds are 1500 excerpts from the Making Sense of Sounds (MSoS) challenge which are excerpts from the Freesound database  67  , the ESC-50 dataset  68. We chunked the 1500 excerpts in segments of 800 ms leading to 148,500 short sound excerpts. Equivalent linear filter bank. Each excerpt e(t) of the 148,500 segments was first decomposed with the CEI in 6 modes.
Data availability The sounds from the Making Sense of Sounds dataset can be accessed here: https://dcaserepo. github. io/dcase_datalist/datasets/sounds/msos. html or upon request. https://doi. org/10. 17866/rd. salford. 6901475. v4. The source data of all the figures are available here: https://doi. org/10. 6084/m9. figshare. 23264405. Please contact the corresponding author for any additional requests.
Code availability The custom codes to generate all the figures included in the paper can be accessed at the following repository: https://github. com/EtienneTho/hearing-as-cei/ and at this permanent link  70  : https://doi. org/10. 5281/zenodo. 8025054. The MATLAB scripts for computing the Cascaded Envelope Interpolation are provided here: https://github. com/ EtienneTho/cei/ and at this permanent link  70  : https://doi. org/10. 5281/zenodo. 8025054.
Method Preregistrations All surveys reported in this paper were implemented in Qualtrics. Power analyses conducted on initial pilot studies suggested required sample sizes of ∼320 to detect a small effect of d = 0. 2 at 80% power. Experiments 1 and 3 were preregistered at https:// aspredicted. org/blind. php?x=9bw9ww and Experiment 4 at https://osf. io/wrd5y. Experiment 2 was not preregistered, but its design and data analysis were identical to those of Experiments.
One partisan news story on each issue was typically congruent for liberals on the issue (e. g. gun control supporters), and the other was typically congruent for conservatives on the issue (e. g. gun rights supporters). More speci cally, a partisan news story was de ned as being politically congruent to a given political side or group when it reported on an event or societal fact that served its policy agenda, or pointed at a threat members of that political group would typically nd credible and relevant. To be retained in the stimuli database, the partisan news items, whether true or fake, had to clearly be identi ed by independent MTurk raters as favoring one political side on each issue in two pretest studies. The two pretest studies contained eight true and eight fake items, respectively.
Analyses Responses to the attitude questions were originally collected on axes ranging from [0] the most conservative position to [100], the most liberal position on each issue. To facilitate interpretation of the data during our analyses on an intuitive liberal (left)-conservative (right) axis on each issue, scores were reverse coded prior to statistical analyses, to arrive at [0] for the most liberal position and [100] for the most conservative position on each issue. From there, a political news story advancing a conservative narrative on an issue was considered as congruent with a participant (a dichotomous measure) if that participant's attitude on the issue was ≥50 and as incongruent if the participant's attitude on the issue was strictly <50. The reverse was true for news advancing a typically liberal narrative.
As to a participant's level of attitude extremity on each issue, it was de ned by taking the absolute distance between their attitude score on the issue and the middle of the scale, 50, and then by rescaling that distance score to a 0-1 continuous range (by dividing scores by 50). The goal of that rescaling to a 0-1 range was to make the attitude extremity measure more comparable to the issue moralization measure. In contrast with issue moralization (dichotomous) and news congruence (dichotomous), attitude extremity as used in the analyses was a continuous measure. (For data visualizations, moreover, a respondent was coded dichotomously as being attitudinally extreme ["Yes"] if her level of attitude extremity was strictly >0. 5 and not extreme ["No"] when this was not the case; see Fig. 2.
Participants and design We rst run a pilot study, Experiment 5a, for which we recruited 325 participants on MTurk. Thirty-eight participants were removed from the data in Experiment 5a because they failed the attention or the English uency checks, so 287 remained (M age = 37, SD age = 11, 47% women). The study was run in May 2019 and used the same eight true news as Experiments 1-3 (abortion, gun control, racial equality, and gender equality) and measured willingness to share on a dichotomous scale. Experiment 5b, the nal experiment, used six fake news (gun control, racial equality, and gender equality), a four-point measure of willingness to share, and was run in October 2021. The study was preregistered at https://osf. io/3jgea (see online supplementary material, B). Experiment 5b and its preregistration did not include the hostile fake items touching on abortion found to be less subject to myside sharing in Experiment 4.
We reasoned that the best test of the ef cacy of a possible intervention would be to assess its in uence over the items that showed the relevant effects most strongly. A power analysis suggested 800 participants were needed to detect a small effect at 80% power. We recruited 905 US citizens, representative of the US population on age, ethnicity, and sex, on Proli c. However, we excluded 99 participants who failed either the attention check or the manipulation check, such that 806 participants remained in the data set, our target sample size (M age = 43. 8, SD age = 16. 4, 53% women).
Participants and design We began by running a pilot study in August 2019, Experiment 6a, for which we recruited 290 participants on MTurk. Eleven participants were removed from Experiment 6a because they failed the attention or English uency checks, leaving 279 in the data set (M age = 36, SD age = 11, 45% female). We used the same eight true partisan news as in Experiments 1-3 (abortion, gun control, racial equality, and gender equality). Experiment 6a manipulated whether participants were asked to imagine sharing the news to people they agree with vs. disagree with on each issue. Experiment 6b, the nal experiment, was preregistered at https://osf. io/tjeh4 (see online supplementary material, B) and run in October 2021. It asked participants to imagine sharing news to people that have the same vs.
an opposite position from them on each issue. Our power analysis suggested 800 participants were needed to detect a small effect of audience type at 80% power. We recruited a sample of 955 people on Proli c, representative of the US population on age, ethnicity, and sex. One-hundred and thirty-six participants were removed from the data because they failed the attention or the manipulation checks, leaving 819 participants, our preregistered target sample size (M age = 40, SD age = 16, 53% female). Experiment 6b used six fake partisan news stories exposed in a random order (gun control, racial equality, and gender equality).
Participants and design A power analysis recommended 800 participants per study to detect a small effect at 80% power. A total of 1,166 participants were recruited on MTurk in February 2020 for Experiment 7, which comprised eight true partisan news items (abortion, gun control, racial equality, and gender equality). One-hundred and seventyve participants were removed from the data because they failed either the attention check or the English pro ciency check. Eight-hundred and eighty-nine participants remained in the data set (M age = 39, SD age = 12, 45% women). Participants in the control condition merely reported their willingness to share each item, whereas in the intervention condition, the headlines were preceded by a message about our inclination to process political information in ways partial to our political agenda (the "myside bias").
Experiment 8, which recruited 937 participants in December 2019 on MTurk, followed the same design as Experiment 7 (with an intervention message) and used the same eight fake political news items as in Experiment 4 (abortion, gun control, racial equality, and gender equality). One-hundred and ninety-three participants were removed because they either did not pass the attention check or failed the English pro ciency test. Seven-hundred and forty-four participants remained in the data set (M age = 37, SD age = 12, 41% women).
Participants and design Experiment 9 was preregistered at https://osf. io/vyu7f (see online supplementary material, B) and run in November 2021. Our power analysis suggested 800 participants were needed to detect a small effect at 80% power. Eight-hundred and sixteen respondents, representative of the US population on age, ethnicity, and sex, were recruited on Proli c, and none were removed from the data (M age = 35, SD age = 14, 74% women). Experiment 9 randomly exposed participants to the same six fake political news items as Experiments 5b and 6b (gun control, racial equality, and gender equality). In contrast, and in order to gauge the robustness of our ndings, Experiment 10 employed 22 entirely novel items: 10 fake partisan, 10 true partisan, and 2 true neutral items (see online supplementary material, O-R).