cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5729761
title: Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations

description: This dataset collects the unprocessed (= outputs from calculations) and processed (= plots, average values for orbital and ionization energies) results discussed in the paper titled "Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations" by Richard Asamoah Opoku, Céline Toubin, and André Severo Pereira Gomes.
description: We acknowledge support by the French government through the Program "Investissement d'avenir" through the Labex CaPPA (contract ANR-11-LABX-0005-01), the I-SITE ULNE project OVERSEE and MESONM International Associated Laboratory (LAI) (contract ANR-16-IDEX-0004), the Franco-German project CompRIXS (Agence nationale de la recherche ANR-19-CE29-0019, Deutsche Forschungsgemeinschaft JA 2329/6-1), CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research) and French national supercomputing facilities (grants DARI A0050801859, A0070801859, and A0090801859 ).
DOI: 10.18112/openneuro.ds003850.v1.0.1
title: Next Gen VASO data at 0.1 micro liter voxels for ISMRM 2022
DOI: 10.5281/zenodo.5729760
title: Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations

description: This dataset collects the unprocessed (= outputs from calculations) and processed (= plots, average values for orbital and ionization energies) results discussed in the paper titled "Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations" by Richard Asamoah Opoku, Céline Toubin, and André Severo Pereira Gomes.
description: We acknowledge support by the French government through the Program "Investissement d'avenir" through the Labex CaPPA (contract ANR-11-LABX-0005-01), the I-SITE ULNE project OVERSEE and MESONM International Associated Laboratory (LAI) (contract ANR-16-IDEX-0004), the Franco-German project CompRIXS (Agence nationale de la recherche ANR-19-CE29-0019, Deutsche Forschungsgemeinschaft JA 2329/6-1), CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research) and French national supercomputing facilities (grants DARI A0050801859, A0070801859, and A0090801859 ).
DOI: 10.6084/m9.figshare.16750393
title: Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk

description: Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant macrofaunal groups in the deep sea. Tanaidacea is one of the most thread-dependent taxa in the Crustacea, constructing tubes, spun with their silk, for shelter. In this work, we sequenced and assembled the comprehensive transcriptome of 23 tanaidaceans encompassing 14 families and 4 superfamilies of Tanaidacea, and performed silk proteomics of <i>Zeuxo ezoensis </i>to search for its silk genes. As a result, we identified two families of silk proteins, that are conserved across the four superfamilies. The long and repetitive nature of these silk genes resembles that of other silk-producing organisms, and the two families of proteins are similar in composition to silkworm and caddisworm fibroins, respectively. Moreover, the amino acid composition of the repetitive motifs of tanaidacean silk tends to be more hydrophilic, and therefore could be a useful resource to study their unique adaptation of silk use in a marine environment. The availability of comprehensive transcriptome data in these taxa, coupled with proteomic evidence of their silk genes, will facilitate evolutionary and ecological studies. <b></b><br>This supplementary data includes the raw alignment and tree files used for the phylogenetic analysis.
DOI: 10.6084/m9.figshare.16750393.v1
title: Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk

description: Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant macrofaunal groups in the deep sea. Tanaidacea is one of the most thread-dependent taxa in the Crustacea, constructing tubes, spun with their silk, for shelter. In this work, we sequenced and assembled the comprehensive transcriptome of 23 tanaidaceans encompassing 14 families and 4 superfamilies of Tanaidacea, and performed silk proteomics of <i>Zeuxo ezoensis </i>to search for its silk genes. As a result, we identified two families of silk proteins, that are conserved across the four superfamilies. The long and repetitive nature of these silk genes resembles that of other silk-producing organisms, and the two families of proteins are similar in composition to silkworm and caddisworm fibroins, respectively. Moreover, the amino acid composition of the repetitive motifs of tanaidacean silk tends to be more hydrophilic, and therefore could be a useful resource to study their unique adaptation of silk use in a marine environment. The availability of comprehensive transcriptome data in these taxa, coupled with proteomic evidence of their silk genes, will facilitate evolutionary and ecological studies. <b></b><br>This supplementary data includes the raw alignment and tree files used for the phylogenetic analysis.
DOI: 10.6084/m9.figshare.13372325
title: Proteomic evidence for the silk fibroin genes of spider mites (order Trombidiformes: family Tetranychidae)

description: Spider mites are a group of arachnids belonging in the family Tetranychidae, known to produce nano-scale silk fibers characterized by high Young’s modulus. Silk fibroin gene of spider mites has been computationally suggested through genomic analysis of <i>Tetranychus urticae</i>, but it is yet to be confirmed by proteomic evidences. In this work, we sequenced and assembled the transcriptome from two genera of spider mites, <i>Tetranychus kanzawai</i>and <i>Panonychus citri</i>, and combined with the silk proteomics of <i>T. urticae </i>and <i>P. citri</i>to characterize the fibroin genes through comparative genomics and multi-omics analysis. As a result, two fibroins were identified, that are different genes from the previous computational prediction. Amino acid composition and secondary structure suggests similarity to aciniform or cylindrical spidroins of spider silk, which partly mirrors their mechanical property exhibiting high Young’s modulus. Availability of full-length fibroin sequences of spider mites facilitates the study of the evolution of silk genes that emerged in multiple lineages sometimes in convergent manner, and in the industrial application of artificial protein fibers through the study of the amino acid sequence and the resulting mechanical properties of these silks. <br>Sample preservation, RNA extraction, sequencing and assembly have been conducted for <i>T. kanzawai</i>, and <i>P. citri</i>based on methods previously described for spiders [18], with some modification. Briefly, a single specimen of each of the spider mite was preserved in RNAlater stored at -80 ˚C, and RNA was extracted using Direct-zol RNA Microprep Kit (Zymo Research). Illumina library was prepared using KAPA HyperPlus Kit (KAPA Biosystems) targeting 300bp fragments. Sequence library was then sequenced on NextSeq 500 (Illumina) with High Output Mode 300 cycles as paired-end reads. Sequences were basecalled, demultiplexed, and adaptors sequences were removed with bcls2fastq v.2 software (Illumina). Transcriptome assembly was performed using Bridger software with default parameters [19]. Expression levels of transcripts were quantified using kallisto v.0.44 [20]using the assembled transcriptome as well as previously published predicted coding sequences from the genome of <i>T. urticae</i>[16]. Assembly completeness was assessed using BUSCO v.3 [21]with Arthropoda dataset through gVolante server [22].
DOI: 10.6084/m9.figshare.13372325.v1
title: Proteomic evidence for the silk fibroin genes of spider mites (order Trombidiformes: family Tetranychidae)

description: Spider mites are a group of arachnids belonging in the family Tetranychidae, known to produce nano-scale silk fibers characterized by high Young’s modulus. Silk fibroin gene of spider mites has been computationally suggested through genomic analysis of <i>Tetranychus urticae</i>, but it is yet to be confirmed by proteomic evidences. In this work, we sequenced and assembled the transcriptome from two genera of spider mites, <i>Tetranychus kanzawai</i>and <i>Panonychus citri</i>, and combined with the silk proteomics of <i>T. urticae </i>and <i>P. citri</i>to characterize the fibroin genes through comparative genomics and multi-omics analysis. As a result, two fibroins were identified, that are different genes from the previous computational prediction. Amino acid composition and secondary structure suggests similarity to aciniform or cylindrical spidroins of spider silk, which partly mirrors their mechanical property exhibiting high Young’s modulus. Availability of full-length fibroin sequences of spider mites facilitates the study of the evolution of silk genes that emerged in multiple lineages sometimes in convergent manner, and in the industrial application of artificial protein fibers through the study of the amino acid sequence and the resulting mechanical properties of these silks. <br>Sample preservation, RNA extraction, sequencing and assembly have been conducted for <i>T. kanzawai</i>, and <i>P. citri</i>based on methods previously described for spiders [18], with some modification. Briefly, a single specimen of each of the spider mite was preserved in RNAlater stored at -80 ˚C, and RNA was extracted using Direct-zol RNA Microprep Kit (Zymo Research). Illumina library was prepared using KAPA HyperPlus Kit (KAPA Biosystems) targeting 300bp fragments. Sequence library was then sequenced on NextSeq 500 (Illumina) with High Output Mode 300 cycles as paired-end reads. Sequences were basecalled, demultiplexed, and adaptors sequences were removed with bcls2fastq v.2 software (Illumina). Transcriptome assembly was performed using Bridger software with default parameters [19]. Expression levels of transcripts were quantified using kallisto v.0.44 [20]using the assembled transcriptome as well as previously published predicted coding sequences from the genome of <i>T. urticae</i>[16]. Assembly completeness was assessed using BUSCO v.3 [21]with Arthropoda dataset through gVolante server [22].
DOI: 10.5281/zenodo.5730007
title: Improved genome annotation of Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions

description: Improved genome annotation of the <em>Rhynchosporium commune</em> isolate UK7 using Illumina short reads of <em>in vitro</em> and <em>in plantae</em> conditions. The short reads used for the annotation are available at https://doi.org/10.5281/zenodo.5729968 and https://doi.org/10.5281/zenodo.5729863.To create the gene models, we used tophat v. 2.0.14 to align short reads to the UK7 reference genome (Trapnell et al., 2009). The Intron splice site hints were generated using bam2hints, included in the AUGUSTUS v. 3.2.1 software (Stanke et al., 2006). Due to the very high RNA-sequencing depth available, intron splice hints were filtered for a minimum coverage of 20 reads to avoid an impact of spurious splice signals on gene prediction. To produce <em>ab initio </em>gene models, the BRAKER v. 1.0 pipeline (Hoff et al., 2016) combining GeneMark-ET <em>ab initio </em>gene model predictions and AUGUSTUS v. 3.2.1. GeneMark-ET was trained using the RNA-seq-based splice information as hints. AUGUSTUS was automatically trained using <em>ab initio </em>gene models that were fully supported by splice information. Finally, AUGUSTUS was used to predict gene models using both RNA-seq splice information and coding sequence hints based on exonerate protein alignments as extrinsic evidence.
DOI: 10.5281/zenodo.5730006
title: Improved genome annotation of Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions

description: Improved genome annotation of the <em>Rhynchosporium commune</em> isolate UK7 using Illumina short reads of <em>in vitro</em> and <em>in plantae</em> conditions. The short reads used for the annotation are available at https://doi.org/10.5281/zenodo.5729968 and https://doi.org/10.5281/zenodo.5729863.To create the gene models, we used tophat v. 2.0.14 to align short reads to the UK7 reference genome (Trapnell et al., 2009). The Intron splice site hints were generated using bam2hints, included in the AUGUSTUS v. 3.2.1 software (Stanke et al., 2006). Due to the very high RNA-sequencing depth available, intron splice hints were filtered for a minimum coverage of 20 reads to avoid an impact of spurious splice signals on gene prediction. To produce <em>ab initio </em>gene models, the BRAKER v. 1.0 pipeline (Hoff et al., 2016) combining GeneMark-ET <em>ab initio </em>gene model predictions and AUGUSTUS v. 3.2.1. GeneMark-ET was trained using the RNA-seq-based splice information as hints. AUGUSTUS was automatically trained using <em>ab initio </em>gene models that were fully supported by splice information. Finally, AUGUSTUS was used to predict gene models using both RNA-seq splice information and coding sequence hints based on exonerate protein alignments as extrinsic evidence.
DOI: 10.15468/b3x32e
title: A new tiger beetle from the Gulf Coast of Texas (Coleoptera, Cicindelidae, Cicindelini)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Duran, Daniel P., Roman, Stephen J., Huber, Ronald L. (2021): A new tiger beetle from the Gulf Coast of Texas (Coleoptera, Cicindelidae, Cicindelini). Zootaxa 5072 (1): 73-80, DOI: https://doi.org/10.11646/zootaxa.5072.1.8
DOI: 10.25449/ruspsydata.16669276
title: Research database: Psychosemiotic Analysis of Non-Complete Sentences of Mothers Suffering from Schizophrenia

description: With the aim to investigate the attitude of mothers suffering from schizophrenia towards their children we used psychosemiotic analysis and the procedure of biclustering of the semi-structured parental essay in the incomplete-sentence form (test «Рarental composition») of 30 mothers of the clinical group and 30 mentally health mothers. Statistical analysis confirmed the relevance of psychosemiotic parameters. The procedure of biclustering showed that three of the lists of binary parameters show regular combinations that differ in healthy and ill mothers. One of the combinations is found only in the texts of ill mothers and describes a weak parent who cannot withstand ambivalence and sees his child in the perspective of an abstract future. Another combination occurs in the texts of only healthy mothers and describes a parent who is able to withstand ambivalence and perceives the child as a person with his own feelings in the present time.
DOI: 10.25449/ruspsydata.16669276.v1
title: Research database: Psychosemiotic Analysis of Non-Complete Sentences of Mothers Suffering from Schizophrenia

description: With the aim to investigate the attitude of mothers suffering from schizophrenia towards their children we used psychosemiotic analysis and the procedure of biclustering of the semi-structured parental essay in the incomplete-sentence form (test «Рarental composition») of 30 mothers of the clinical group and 30 mentally health mothers. Statistical analysis confirmed the relevance of psychosemiotic parameters. The procedure of biclustering showed that three of the lists of binary parameters show regular combinations that differ in healthy and ill mothers. One of the combinations is found only in the texts of ill mothers and describes a weak parent who cannot withstand ambivalence and sees his child in the perspective of an abstract future. Another combination occurs in the texts of only healthy mothers and describes a parent who is able to withstand ambivalence and perceives the child as a person with his own feelings in the present time.
DOI: 10.5281/zenodo.5730017
title: Nothomitra cinnamomea SPAdes preassembly

description: .
DOI: 10.5281/zenodo.5730016
title: Nothomitra cinnamomea SPAdes preassembly

description: .
DOI: 10.15468/phrnza
title: A new species of Psyllipsocus (Psocodea: Trogiomorpha: Psyllipsocidae) from the mid-Cretaceous amber of Myanmar

description: This dataset contains the digitized treatments in Plazi based on the original journal article Liang, Feiyang, Liu, Xingyue (2021): A new species of Psyllipsocus (Psocodea: Trogiomorpha: Psyllipsocidae) from the mid-Cretaceous amber of Myanmar. Zootaxa 5072 (1): 81-87, DOI: https://doi.org/10.11646/zootaxa.5072.1.9
DOI: 10.3886/e116327v1-102560
title: Replication data for: Incentives and Services for College Achievement: Evidence from a Randomized Trial

description: This paper reports on an experimental evaluation of strategies designed to improve academic performance among college freshmen. One treatment group was offered academic support services. Another was offered financial incentives for good grades. A third group combined both interventions. Service use was highest for women and for subjects in the combined group. The combined treatment also raised the grades and improved the academic standing of women. These differentials persisted through the end of second year, though incentives were given in the first year only. This suggests study skills among some treated women increased. In contrast, the program had no effect on men. (JEL I21, I28)
DOI: 10.15468/t93typ
title: Variation in Fukienogomphus prometheus (Lieftinck, 1939) reveals Stylurus takashii (Asahina, 1966) as a junior synonym, with discussion on the status of F. choifongae Wilson & Tam, 2006 (Odonata: Gomphidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Hu, Fang-Shuo, Chen, Szu-Lung, Song, Rui-Bin, Yeh, Wen-Chi (2021): Variation in Fukienogomphus prometheus (Lieftinck, 1939) reveals Stylurus takashii (Asahina, 1966) as a junior synonym, with discussion on the status of F. choifongae Wilson & Tam, 2006 (Odonata: Gomphidae). Zootaxa 5072 (1): 23-33, DOI: https://doi.org/10.11646/zootaxa.5072.1.3
DOI: 10.6084/m9.figshare.12752648
title: The sources of sex differences in aging in annual fishes

description: Original dataset used for analyses presented in Reichard et al. (sex differences in lifespan in Nothobranchius) for Journal of Animal Ecology paper (2021/2022)<br>It includes readme file, R scripts and basic data.<br><br>
DOI: 10.6084/m9.figshare.12752648.v3
title: The sources of sex differences in aging in annual fishes

description: Original dataset used for analyses presented in Reichard et al. (sex differences in lifespan in Nothobranchius) for Journal of Animal Ecology paper (2021/2022)<br>It includes readme file, R scripts and basic data.<br><br>
DOI: 10.6084/m9.figshare.12752648.v2
title: Sex differences in lifespan - Nothobranchius

description: Original dataset used for analyses presented in Reichard et al. (sex differences in lifespan in Nothobranchius)<br>
DOI: 10.6084/m9.figshare.11297489
title: Data from: Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci

description: <b>1) Immune gene locus annotations (gff format)</b> IGH.gff, IGK.gff, IGL.gff, TRA_TRD.gff, TRB.gff, TRG.gff, MHC.gff<b>2) Immune gene sequences (fasta format)</b> V_sequence.fasta, D_sequence.fasta, J_sequence.fasta, C_sequence.fasta<b>3) Assemblied genome sequence (fasta format, gzip)</b> scaffold.fasta.gz, contig_FALCON_Unzip.fasta.gz
DOI: 10.6084/m9.figshare.11297489.v2
title: Data from: Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci

description: <b>1) Immune gene locus annotations (gff format)</b> IGH.gff, IGK.gff, IGL.gff, TRA_TRD.gff, TRB.gff, TRG.gff, MHC.gff<b>2) Immune gene sequences (fasta format)</b> V_sequence.fasta, D_sequence.fasta, J_sequence.fasta, C_sequence.fasta<b>3) Assemblied genome sequence (fasta format, gzip)</b> scaffold.fasta.gz, contig_FALCON_Unzip.fasta.gz
DOI: 10.6084/m9.figshare.11297489.v1
title: Data from: Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci

description: <b>1) Immune gene locus annotations (gff format)</b> IGH.gff, IGK.gff, IGL.gff, TRA_TRD.gff, TRB.gff, TRG.gff, MHC.gff<b>2) Immune gene sequences (fasta format)</b> V_sequence.fasta, D_sequence.fasta, J_sequence.fasta, C_sequence.fasta<b>3) Assemblied genome sequence (fasta format, gzip)</b> scaffold.fasta.gz, contig_FALCON_Unzip.fasta.gz
DOI: 10.6084/m9.figshare.17086403
title: Microbiome taxonomic and functional profiles of two domestic sewage treatment systems

description: Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like <i>Methanobacterium</i>, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to <i>Methanosaeta</i> genus. Also, important syntrophic microorganisms (<i>Smithella, Syntrophus, Syntrophobacter</i>) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2–30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60–83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.