cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4751302.v1
title: File S2: All Luc Like (fasta format) from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751305.v1
title: File S1: A. filiformis RLuc-like sequences (cDNA/DNA) (fasta format) from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751320.v1
title: Electroencephalogram-based Decoding Cognitive States usingConvolutional Neural Network and Likelihood Ratio Based Score Fusion

description: This EEG data is for an event related design which is made for a simple visual task.
DOI: 10.6084/m9.figshare.4751299
title: Table S3: Reciprocal BLAST results of A. filiformis RLuc-like sequences in NR database (Genbank) from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751287
title: Table S2: Similarity/identity matrix of RLuc-like predicted proteins from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751293
title: Table S1: BLAST searches of known luciferase-like in the arm transcriptome of A. filiformis from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751293.v1
title: Table S1: BLAST searches of known luciferase-like in the arm transcriptome of A. filiformis from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751299.v1
title: Table S3: Reciprocal BLAST results of A. filiformis RLuc-like sequences in NR database (Genbank) from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.6084/m9.figshare.4751287.v1
title: Table S2: Similarity/identity matrix of RLuc-like predicted proteins from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

description: Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
DOI: 10.7910/dvn/pkjufn/lpw3ne
title: FCC2001.294.ran

description: :unav
DOI: 10.6084/m9.figshare.4751281
title: Data Set S1 from Seasonal body size reductions with warming covary with major body size gradients in arthropod species

description: Seasonal temperature-body size data used in this study.
DOI: 10.6084/m9.figshare.4751149
title: Tamil Data for Royal Society

description: These data include pregnancy diet cravings, anthropometrics, and predictors of
DOI: 10.7910/dvn/pkjufn/pbdikq
title: FCC2003.300.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/yq9kxh
title: FCC2002.014.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/fty1qo
title: FCC2003.327.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/uimupp
title: FCC2001.365.ran

description: :unav
DOI: 10.6084/m9.figshare.4751095
title: Supplementary material from "Visual comparison of two data sets: Do people use the means and the variability?"

description: In our everyday lives, we are required to make decisions based upon our statistical intuitions. Often, these involve the comparison of two groups, such as luxury versus family cars and their suitability. Research has shown that the mean difference affects judgements where two sets of data are compared, but the variability of the data has only a minor influence, if any at all. However, prior research has tended to present raw data as simple lists of values. Here, we investigated whether displaying data visually, in the form of parallel dot plots, would lead viewers to incorporate variability information. In Experiment 1, we asked a large sample of people to compare two fictional groups (children who drank ‘Brain Juice’ versus water) in a one-shot design, where only a single comparison was made. Our results confirmed that only the mean difference between the groups predicted subsequent judgements of how much they differed, in line with previous work using lists of numbers. In Experiment 2, we asked each participant to make multiple comparisons, with both the mean difference and the pooled standard deviation varying across data sets they were shown. Here, we found that both sources of information were correctly incorporated when making responses. Taken together, we suggest that increasing the salience of variability information, through manipulating this factor across items seen, encourages viewers to consider this in their judgements. Such findings may have useful applications for best practices when teaching difficult concepts like sampling variation.
DOI: 10.6084/m9.figshare.4751149.v1
title: Tamil Data for Royal Society

description: These data include pregnancy diet cravings, anthropometrics, and predictors of
DOI: 10.7910/dvn/pkjufn/p9kreo
title: FCC2003.003.ran

description: :unav
DOI: 10.6084/m9.figshare.4751050
title: Supplementary Material for: At the Edge of Intonation: The Interplay of Utterance-Final F0 Movements and Voiceless Fricative Sounds

description: The paper is concerned with the ‘edge of intonation’ in a twofold sense. It focuses on utterance-final F0 movements and crosses the traditional segment-prosody divide by investigating the interplay of F0 and voiceless fricatives in speech production. An experiment was performed for German with four types of voiceless fricatives: /f/, /s/, /ʃ/ and /x/. They were elicited with scripted dialogues in the contexts of terminal falling statement and high rising question intonations. Acoustic analyses show that fricatives concluding the high rising question intonations had higher mean centres of gravity (CoGs), larger CoG ranges and higher noise energy levels than fricatives concluding the terminal falling statement intonations. The different spectral-energy patterns are suitable to induce percepts of a high ‘aperiodic pitch’ at the end of the questions and of a low ‘aperiodic pitch’ at the end of the statements. The results are discussed with regard to the possible existence of ‘segmental intonation’ and its implication for F0 truncation and the segment-prosody dichotomy, in which segments are the alleged troublemakers for the production and perception of intonation.
DOI: 10.7910/dvn/pkjufn/fn3jk6
title: FCC2001.231.ran

description: :unav
DOI: 10.6084/m9.figshare.4751065
title: Supplementary Material for: The Impact of Ovarian Stimulation on the Expression of Candidate Reprogramming Genes in Mouse Preimplantation Embryos

description: Ovarian stimulation with gonadotrophins is an integral part of assisted reproductive technologies in human subfertility/infertility treatment. Recent findings have associated ovarian stimulation with the increased incidence of imprinting disorders in humans as well as defects in genome-wide methylation reprogramming and, in particular, imprinting in mice. Here, we present the first study that determined the impact of ovarian stimulation on the expression of developmentally important reprogramming genes <i>(Apex1, Lig1, Lig3, Mbd2, Mbd3, Mbd4, </i>and<i> Polb)</i> in single early mouse morula embryos (16-cell stage). Using absolute quantification of mRNA by quantitative real-time PCR, we observed an association of ovarian stimulation with a downregulation of mRNAs encoding the base excision repair proteins APEX1 and POLB as well as the 5-methyl-CpG-binding domain protein MBD3 in individual morula embryos. Whole mount immunofluorescence staining of early and late morula embryos with an antibody against APEX1 revealed individual embryos with lower protein expression levels after ovarian stimulation and a correlation of mRNA expression with protein abundance. Our data argue for a negative impact of ovarian stimulation during female gametogenesis and/or early embryo development affecting the expression of candidate reprogramming factors.
DOI: 10.6084/m9.figshare.4751026
title: Supplementary Material for: Intonation Adapts to Lexical Tone: The Case of Kammu

description: In this paper, we investigate how lexical tones interact with intonation, using data from the Austroasiatic language Kammu, one of few languages with two dialects whose only major phonological difference is the presence or absence of lexical tones. Northern (and Western) Kammu have developed tones in connection with the merger of voiceless and voiced initial consonants, while the non-tonal Eastern dialect kept the segmental opposition with no tones. We found the following prosodic hierarchy: (1) lexical tones, (2) phrase-final boundary tone, (3) focus marking. The results strongly suggest that the intonational systems of the two Kammu dialects are basically identical, and that the main differences between the dialects are adaptations of intonation patterns to the lexical tones when the identities of the tones are jeopardized.
DOI: 10.6084/m9.figshare.4751050.v1
title: Supplementary Material for: At the Edge of Intonation: The Interplay of Utterance-Final F0 Movements and Voiceless Fricative Sounds

description: The paper is concerned with the ‘edge of intonation’ in a twofold sense. It focuses on utterance-final F0 movements and crosses the traditional segment-prosody divide by investigating the interplay of F0 and voiceless fricatives in speech production. An experiment was performed for German with four types of voiceless fricatives: /f/, /s/, /ʃ/ and /x/. They were elicited with scripted dialogues in the contexts of terminal falling statement and high rising question intonations. Acoustic analyses show that fricatives concluding the high rising question intonations had higher mean centres of gravity (CoGs), larger CoG ranges and higher noise energy levels than fricatives concluding the terminal falling statement intonations. The different spectral-energy patterns are suitable to induce percepts of a high ‘aperiodic pitch’ at the end of the questions and of a low ‘aperiodic pitch’ at the end of the statements. The results are discussed with regard to the possible existence of ‘segmental intonation’ and its implication for F0 truncation and the segment-prosody dichotomy, in which segments are the alleged troublemakers for the production and perception of intonation.