cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17032691
title: Data_and_scripts_Notelaea

description: Tackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complex <i>Nestegis</i>, <i>Notelaea</i>, <i>Osmanthus</i>, <i>Phillyrea</i>, and <i>Picconia</i> within the subtribe Oleinae, we aim to elucidate their boundaries and relationships and to evaluate their biogeographic history in light of their peculiar disjunct distribution in Macaronesia, the Mediterranean Region, and the Pacific. Based on phylogenomic data from plastid and nuclear DNA and extensive sampling, the results show six subclades within this generic complex, which are also geographic segregates found in Australia (<i>Notelaea</i>), Hawaiian Islands (<i>Nestegis sandwicensis</i>), Macaronesia (<i>Picconia</i>), Mediterranean Region (<i>Phillyrea</i>), New Caledonia (<i>Osmanthus</i> section <i>Notosmanthus</i>), and New Zealand (<i>Nestegis s.s.</i>). Accounting for broad morphological overlaps within this clade, we recognize three genera (<i>Phillyrea</i>, <i>Picconia</i>, and <i>Notelaea s.l.</i>), subsuming all Pacific taxa under <i>Notelaea s.l.</i> Molecular dating and biogeographic analyses indicate that this clade originated in Eurasia during the Early Miocene (ca. 23 Mya) and that dispersal only can be favored to explain its global disjunct distribution. Although the colonization route to the Hawaiian Islands is unclear, island-hopping and local extinction seem to be the hallmark of the evolutionary history of this group.
DOI: 10.6084/m9.figshare.17032691.v2
title: Data_and_scripts_Notelaea

description: Tackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complex <i>Nestegis</i>, <i>Notelaea</i>, <i>Osmanthus</i>, <i>Phillyrea</i>, and <i>Picconia</i> within the subtribe Oleinae, we aim to elucidate their boundaries and relationships and to evaluate their biogeographic history in light of their peculiar disjunct distribution in Macaronesia, the Mediterranean Region, and the Pacific. Based on phylogenomic data from plastid and nuclear DNA and extensive sampling, the results show six subclades within this generic complex, which are also geographic segregates found in Australia (<i>Notelaea</i>), Hawaiian Islands (<i>Nestegis sandwicensis</i>), Macaronesia (<i>Picconia</i>), Mediterranean Region (<i>Phillyrea</i>), New Caledonia (<i>Osmanthus</i> section <i>Notosmanthus</i>), and New Zealand (<i>Nestegis s.s.</i>). Accounting for broad morphological overlaps within this clade, we recognize three genera (<i>Phillyrea</i>, <i>Picconia</i>, and <i>Notelaea s.l.</i>), subsuming all Pacific taxa under <i>Notelaea s.l.</i> Molecular dating and biogeographic analyses indicate that this clade originated in Eurasia during the Early Miocene (ca. 23 Mya) and that dispersal only can be favored to explain its global disjunct distribution. Although the colonization route to the Hawaiian Islands is unclear, island-hopping and local extinction seem to be the hallmark of the evolutionary history of this group.
DOI: 10.6084/m9.figshare.17032691.v1
title: Data_and_scripts

description: Tackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complex <i>Nestegis</i>, <i>Notelaea</i>, <i>Osmanthus</i>, <i>Phillyrea</i>, and <i>Picconia</i> within the subtribe Oleinae, we aim to elucidate their boundaries and relationships and to evaluate their biogeographic history in light of their peculiar disjunct distribution in Macaronesia, the Mediterranean Region, and the Pacific. Based on phylogenomic data from plastid and nuclear DNA and extensive sampling, the results show six subclades within this generic complex, which are also geographic segregates found in Australia (<i>Notelaea</i>), Hawaiian Islands (<i>Nestegis sandwicensis</i>), Macaronesia (<i>Picconia</i>), Mediterranean Region (<i>Phillyrea</i>), New Caledonia (<i>Osmanthus</i> section <i>Notosmanthus</i>), and New Zealand (<i>Nestegis s.s.</i>). Accounting for broad morphological overlaps within this clade, we recognize three genera (<i>Phillyrea</i>, <i>Picconia</i>, and <i>Notelaea s.l.</i>), subsuming all Pacific taxa under <i>Notelaea s.l.</i> Molecular dating and biogeographic analyses indicate that this clade originated in Eurasia during the Early Miocene (ca. 23 Mya) and that dispersal only can be favored to explain its global disjunct distribution. Although the colonization route to the Hawaiian Islands is unclear, island-hopping and local extinction seem to be the hallmark of the evolutionary history of this group.
DOI: 10.5281/zenodo.6553424
title: flatJACS 3.0

description: A CSV dataset representing JACS 3.0 subject areas, principal subjects, and detailed subject codes in a unified dataset.
description: {"references": ["Higher Education Statistics Agency (2012/2013). Joint Academic Coding System 3.0 (JACS 3.0). CC BY 4.0. https://www.hesa.ac.uk/support/documentation/jacs"]}
DOI: 10.5519/qd.q2tmgl25
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (12 records)
DOI: 10.48786/edbt.2022.56
title: Learned Query Optimizer: At the Forefront of AI-Driven Databases
DOI: 10.48786/edbt.2022.57
title: Conceptual models and databases for searching the genome
DOI: 10.48786/edbt.2022.58
title: From Cloud to Serverless: MOO in the new Cloud epoch
DOI: 10.6084/m9.figshare.19551601
title: Supplementary Material for: Welfare assessment on healthy and tumor-bearing mice after repeated ultrasound imaging

description: Introduction: Ultrasound (US) imaging enables tissue visualization in high spatial resolution with short examination times. Thus, it is often applied in preclinical research. Diagnostic US, including contrast-enhanced ultrasound (CEUS), are considered to be well tolerated by laboratory animals although no systematic study has been performed to confirm this claim. Therefore, the aim of this study was to screen for possible effects of US and CEUS examinations on welfare of healthy mice. Additionally, the potential influence of CEUS and molecular CEUS on well-being and therapy response to regorafenib was investigated in breast cancer-bearing mice. Material and Methods: 40 healthy Balb/c mice were randomly assigned for examination with US or CEUS (3x/week) for four weeks. Untreated healthy mice and mice receiving only isoflurane anesthesia served as controls (n= 10/group). Ninety-four 4T1 tumor-bearing Balb/c mice were allocated randomly to the following groups: no imaging, isoflurane anesthesia, CEUS and molecular CEUS. They either received 10 mg/kg regorafenib or vehicle solution daily by oral gavage. Animals were examined three times within two weeks. CEUS measurements were performed using phospholipid-microbubbles and phospholipid-microbubbles targeting the vascular endothelial growth factor receptor-2 were applied for molecular CEUS. Welfare evaluation was performed by daily observational score sheets, measuring the heart rate, Rotarod performance and fecal corticosterone metabolites twice per week. On the last day, pathological changes of serum corticosterone concentrations, hemograms, and organ weights were obtained. Moreover, a potential influence of isoflurane anesthesia, CEUS and molecular CEUS on regorafenib response in tumor-bearing mice was examined. Analysis of variance and Dunnett post hoc test were performed as statistical analyses. Results: Severity parameters were not altered after repeated US and CEUS examinations of healthy mice, but spleen sizes were significantly lower after isoflurane anesthesia. In tumor-bearing mice, no effect on animal-welfare after repeated CEUS and molecular CEUS could be observed. However, leukocyte counts and spleen weights of tumor-bearing mice were significantly lower in animals examined with CEUS and molecular CEUS compared to the control groups. This effect was not visible in regorafenib-treated animals. Conclusions: Repeated US and (molecular) CEUS have no detectable impact on animal welfare in healthy and tumor-bearing mice. However, CEUS and molecular CEUS in combination with isoflurane anesthesia might attenuate immunological processes in tumor-bearing animals and may consequently affect responses to anti-tumor therapy.
DOI: 10.6084/m9.figshare.19772059
title: Survey and Grammar Test

description: The study employs descriptive and inferential statistics to analyze the data. Study sample comprises 80 Saudi EFL students out of the population of 120 students enrolled in EFL programs at Qassim University, Saudi Arabia with sample size being determined using online sampling calculator Raosoft. The results of the present study show that the Saudi EFL learners manifest a favorable level of awareness in developing grammatical forms while they still not having attained mastery of English grammar. Results also indicate that grammatical competence and level of awareness are more advanced among the Saudi EFL female learners compared to their male counterparts. The outcomes of this research imply that Saudi EFL learners have sufficient performance in grammar learning but need further nurturance. Implications of this study will serve as a basis for English language learning development interventions in the benefit of the students. <br> Data were analyzed through quantitative research data interpretation. For descriptive statistics, the frequency and parentages were used, while for inferential statistics, the use of independent sample t-test was used to assess the difference of students' attributes when grouped according to their gender. It is common to use the Independent Samples T-Test to determine the following: Disparities in the mean values between two groups in this study sex was taken. Before the use of the t-test, the following were the assumptions followed: (1) the measurement scale of the study, (2) the utilization of random sampling, (3) the normality of data distribution, and (4) the adequacy of the sampling size of the study.
DOI: 10.5281/zenodo.6552725
title: Data Set used in "Full backward and forward dependencies through regional hypothetical extraction method"

description: This set of data was obtained from EUREGIO database, developed by the Tinbergen Institute, which is a set of global IO tables with regional and sectoral disaggregation. The EUREGIO database collects the productive structure and commercial relations of the WIOD in the period 2000-2010. The table is broken down into 249 administrative regions at the NUTS2 level, from 24 EU countries, 16 non-EU countries, and a block that brings together countries from the rest of the world, making a total of 266 regions. The statistical information is organised in 11 IO tables, one for each year. The data base that we provid in this repository is used in our study with the aim to determine the key regions of the Spanish economy. In order to address this objective, IO tables of smaller dimensions are built, through an aggregation and disaggregation procedure. First, the 14 industries are grouped, then the 4 sectors of final demand and, lastly, the 4 components of value added. Below, the 266 EUREGIO regions are grouped into 21 regions. Of these, 19 regions correspond to Spain [1], one region includes the rest of the NUTS2 in the EU and another region covers the rest of the world. [1] The 17 Spanish regions and the two autonomous cities of Ceuta and Melilla.
DOI: 10.5281/zenodo.6552724
title: Data Set used in "Full backward and forward dependencies through regional hypothetical extraction method"

description: This set of data was obtained from EUREGIO database, developed by the Tinbergen Institute, which is a set of global IO tables with regional and sectoral disaggregation. The EUREGIO database collects the productive structure and commercial relations of the WIOD in the period 2000-2010. The table is broken down into 249 administrative regions at the NUTS2 level, from 24 EU countries, 16 non-EU countries, and a block that brings together countries from the rest of the world, making a total of 266 regions. The statistical information is organised in 11 IO tables, one for each year. The data base that we provid in this repository is used in our study with the aim to determine the key regions of the Spanish economy. In order to address this objective, IO tables of smaller dimensions are built, through an aggregation and disaggregation procedure. First, the 14 industries are grouped, then the 4 sectors of final demand and, lastly, the 4 components of value added. Below, the 266 EUREGIO regions are grouped into 21 regions. Of these, 19 regions correspond to Spain [1], one region includes the rest of the NUTS2 in the EU and another region covers the rest of the world. [1] The 17 Spanish regions and the two autonomous cities of Ceuta and Melilla.
DOI: 10.5281/zenodo.6553492
title: Input files and data for sensitivity analysis of ParFlow-CLM

description: This zip file includes all the input files and forcing data for the sensitivity analysis of ParFlow-CLM. The file of "Stettbach_SA" includes all the information for the sensitivity analysis of Stettbach catchment. The file of "high_slope_SA" includes all the information for the sensitivity analysis of high slope effect in section 2.5.1 Topography effects. The file of "low_slope_SA" includes all the information for the sensitivity analysis of low slope effect in section 2.5.1 Topography effects. The file of "Barcelona_SA" includes all the information for the sensitivity analysis of Barcelona in section 2.5.2 Climate effects. The file of "LK_SA" includes all the information for the sensitivity analysis of Lemmenjoke national park in Finland in section 2.5.2 Climate effects. The file of "Stettbach_2020_2021" includes all the information for the runoff comparison between simulation and observation in 2020 and 2021 in section 3.1 (Model performance in Stettbach catchment). The file of "results_process_code" includes all the scripts used for the analysis of this study.
DOI: 10.5281/zenodo.6553491
title: Input files and data for sensitivity analysis of ParFlow-CLM

description: This zip file includes all the input files and forcing data for the sensitivity analysis of ParFlow-CLM. The file of "Stettbach_SA" includes all the information for the sensitivity analysis of Stettbach catchment. The file of "high_slope_SA" includes all the information for the sensitivity analysis of high slope effect in section 2.5.1 Topography effects. The file of "low_slope_SA" includes all the information for the sensitivity analysis of low slope effect in section 2.5.1 Topography effects. The file of "Barcelona_SA" includes all the information for the sensitivity analysis of Barcelona in section 2.5.2 Climate effects. The file of "LK_SA" includes all the information for the sensitivity analysis of Lemmenjoke national park in Finland in section 2.5.2 Climate effects. The file of "Stettbach_2020_2021" includes all the information for the runoff comparison between simulation and observation in 2020 and 2021 in section 3.1 (Model performance in Stettbach catchment). The file of "results_process_code" includes all the scripts used for the analysis of this study.
DOI: 10.6084/m9.figshare.17695559
title: SentiCode datasets

description: SentiCode generated from raw text
DOI: 10.6084/m9.figshare.19771453
title: one-to-one orthologs

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19771453.v1
title: one-to-one orthologs

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19771999
title: Supplementary Material for: Low-Dose Alcohol-Induced Inhibition of Mouse Orthotopically Transplanted Tumors Is Associated with T-Cell Response

description: <b><i>Introduction:</i></b> The effects of low-dose alcohol consumption on colorectal cancer development are not well understood. Epidemiological studies have reported that people who consume small amounts of alcohol have lower mortality rates than both nondrinkers and heavy drinkers. This phenomenon has been labeled the “J-curve effect” of alcohol. This study examined the effects of low-dose alcohol (0.5%, 1%, and 2%) on tumor growth in a transplant colon cancer model. <b><i>Methods:</i></b> BALB/c and BALB/c nude mice were used to analyze T-cell immunity. Syngeneic CT26 murine colon cancer cells were implanted into the cecal wall, and the resulting T-cell immune effects were monitored. <b><i>Results:</i></b> The growth of orthotopic tumors was markedly inhibited upon ingestion of low-dose (0.5%) alcohol compared with that in the control mice. In contrast, cells from the same line were injected into the cecal wall of nude mice, and tumor growth inhibition was not observed. Histopathological and RNA sequence analyses were performed to elucidate the mechanisms underlying tumor growth inhibition. An increase in tumor CD8<sup>+</sup> T lymphocytes and changes in cytokine levels were observed. Microbiome analysis using 16S rRNA gene sequencing of cecal contents was performed and revealed <i>Mucispirillum schaedleri</i> and <i>Clostridium cocleatum</i> showed decreased and increased abundance, respectively, in the alcohol group. <b><i>Discussion/Conclusion:</i></b> Ingesting a threshold amount of alcohol results in the infiltration of T lymphocytes, which may enhance immune responsiveness in mouse colorectal cancer models.
DOI: 10.6084/m9.figshare.19772128
title: Projection of asymmetric boundary shifts along latitude gradient for Chinese trees under climate change

description: Climate change is causing widespread boundary shifts of terrestrial plants. However, current works mainly focus on leading edges, but seldom takes a comparative study of trailing and leading edge shifts. Here, the shifts of Chinese trees were simulated along the leading and trailing edges under the maximum representative concentration path (RCP8.5). The results show that Chinese trees likely exhibit a variety of asymmetric boundary shift pattern. Synchronous northward (62.7%) dominant the trade off shift between leading and trailing edge and temperature factors have a significant positive correlation with the boundary shift distance. The other 37.3% species show a southward shift for one or two edges and this pattern could be mainly the comprehensive interaction of heat, low temperature, available water and topographic factors. The study suggest that simple view of polarward shift for leading and trailing edges is not suitable for the explanation of tree migration in China.
DOI: 10.6084/m9.figshare.19772128.v1
title: Projection of asymmetric boundary shifts along latitude gradient for Chinese trees under climate change

description: Climate change is causing widespread boundary shifts of terrestrial plants. However, current works mainly focus on leading edges, but seldom takes a comparative study of trailing and leading edge shifts. Here, the shifts of Chinese trees were simulated along the leading and trailing edges under the maximum representative concentration path (RCP8.5). The results show that Chinese trees likely exhibit a variety of asymmetric boundary shift pattern. Synchronous northward (62.7%) dominant the trade off shift between leading and trailing edge and temperature factors have a significant positive correlation with the boundary shift distance. The other 37.3% species show a southward shift for one or two edges and this pattern could be mainly the comprehensive interaction of heat, low temperature, available water and topographic factors. The study suggest that simple view of polarward shift for leading and trailing edges is not suitable for the explanation of tree migration in China.
DOI: 10.6084/m9.figshare.16980592
title: GWAS treefile and nexus alignment for network analysis in SplitsTree

description: treefile and nexus alignment for network analysis in SplitsTree
DOI: 10.6084/m9.figshare.16980610.v1
title: Alignment files of intergenic regions containing SNP/indels indicated by GWAS

description: MAFFT aligned intergenic regions containing SNP/indels indicated by GWAS
DOI: 10.6084/m9.figshare.16980610
title: Alignment files of intergenic regions containing SNP/indels indicated by GWAS

description: MAFFT aligned intergenic regions containing SNP/indels indicated by GWAS
DOI: 10.25345/c5wh2dj6j
title: MassIVE MSV000089480 - Native metabolomics of E.coli CutA with cell extracts of E.coli and S.elongatus WT and deltaCutA
title: E.coli CutA was flow injected against cell extracts (cell pellets - of exponential growing cultures- have been extracted with 20% or 80% MeOH) of E.coli BW24113 and Synechococcus elongatus sp. PCC 7942 WT or deltacutA
DOI: 10.5281/zenodo.6553448
title: Telemeeting Profile Template

description: This data set contains a Telemeeting Profile Template, a tool that has been developed for a holistic characterization of telemeetings from a Quality of Experience (QoE) perspective. For more information, see our survey paper on telemeeting QoE, which will be published shortly: Janto Skowronek et al,<br> Quality of Experience in Telemeetings and Videoconferencing: A Comprehensive Survey<br> accepted for publication on May 5, 2022<br> IEEE Access<br> 2022
description: The upload contains data sheets with the Profile Template and a list of corresponding references used in the Profile Template. The two data sheets can be found in the Excel file and in the respective CVS exports.