cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5844404
title: Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies

description: Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (https://www.ebi.ac.uk/ena/browser/view/PRJEB50024). Transposable Element annotations: we used RepeatMasker 4.1.0 (http://repeatmasker.org/) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters. Gene annotations: We retrieved gtf files from FlyBase : ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-r2,02.gtf.gz. The corresponding fasta files were also downloaded from FlyBase: ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/fasta/dmel-all-chromosome-r6.46.fasta.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/fasta/dsim-all-chromosome-r2,02.fasta.gz. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.
DOI: 10.5281/zenodo.5844405
title: Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies

description: Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (https://www.ebi.ac.uk/ena/browser/view/PRJEB50024). Transposable Element annotations: we used RepeatMasker 4.1.0 (http://repeatmasker.org/) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters. Gene annotations: For <em>D. melanogaster</em>, <em> </em>we retrieved dmel-all-exon-r6.16.fasta, dmel-all-intron-r6.16.fasta, dmel-all-five_prime_UTR-r6.16.fasta, dmel-all-five_prime_UTR-r6.16.fasta, and dmel-all-gene-r6.16.fasta, which are available at ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.16_FB2017_03/fasta/. For <em>D. simulans</em>, we retrieved dsim-all-exon-r2.02.fasta, dsim-all-intron-r2.02.fasta, dsim-all-five_prime_UTR-r2.02.fasta, dsim-all-three_prime_UTR-r2.02.fasta, and dsim-all-gene-r2.02.fasta, which are available at ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2.02_FB2017_04/fasta/. These different sequence sets were aligned to our assemblies using BLAT (Kent 2002) and pslReps from the BLAT suite, in order to keep the best hit (-singleHit). We filtered out genes with 0 hit and genes with multiple hits. For each gene, we also checked that the positions of the hits for each of the internal regions (<em>i.e.</em> exon, intron, 5’ UTR, and 3’ UTR) were included in the positions of the complete gene hit. We excluded regions that did not fulfill these criteria. We also excluded hits that were not on the same chromosome as the corresponding gene on the reference genome.
DOI: 10.5281/zenodo.7189887
title: Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies

description: Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (https://www.ebi.ac.uk/ena/browser/view/PRJEB50024). Transposable Element annotations: we used RepeatMasker 4.1.0 (http://repeatmasker.org/) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters. Gene annotations: We retrieved gtf files from FlyBase : ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-r2,02.gtf.gz. The corresponding fasta files were also downloaded from FlyBase: ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/fasta/dmel-all-chromosome-r6.46.fasta.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/fasta/dsim-all-chromosome-r2,02.fasta.gz. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.
DOI: 10.25502/0bg3-a967/d
title: Tracking storage root bulking of cassava under NPK application

description: Until now, the root architecture of cassava has been less studied, yet cassava is the sixth most important crop in the world and the third largest carbohydrate source, feeding more than 200 million people in sub-Saharan Africa. Furthermore, it is resilient to climate change and is a major source of food and raw material especially for many countries in Africa. In the previous studies, we established fertigation concentrations at which maximum storage root yields were achieved in the field for three cassava varieties: Mweru, Nalumino, and Kampolombo (Omondi et al., 2018). This work laid the basis of fertigation in cassava and showed increase in root yield using that method of fertilizer application. Additionally, other studies have observed increase in cassava root yield by the application of fertilizers through banding. Therefore, it is necessary to provide accurate recommendations for banding of fertilizer – the most popular method of fertilizer application – and test the efficacy of controlled-release fertilizers in the field. Consequently, tracking the bulking process at Murriaze and Namialo in Mozambique enabled staggering of fertilizer application in split doses, synchronizing nutrients uptake and cassava growth.
DOI: 10.6084/m9.figshare.21317835
title: Bird species in Xuzhou

description: The dataset is comprised of field recordings of five bird species, consisting of 300 bird acoustic events.
DOI: 10.5517/ccdc.csd.cc2764l6
title: CCDC 2061487: Experimental Crystal Structure Determination

description: Related Article: Yan Fan, Zhiming Zeng, Hui Shu, Mingbo Zhou, Ling Xu, Yutao Rao, Tingting Gu, Xu Liang, Weihua Zhu, Jianxin Song|2021|Org.Chem.Front.|8|6080|doi:10.1039/D1QO01161H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27zcg2
title: CCDC 2084764: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Constantin G. Daniliuc, Klaus Bergander, Gerald Kehr, Gerhard Erker|2021|J.Am.Chem.Soc.|143|14992|doi:10.1021/jacs.1c07465
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28kcw3
title: CCDC 2102075: Experimental Crystal Structure Determination

description: Related Article: Yan-E Zhang, Shuo Tong, Mei-Xiang Wang|2021|Org.Lett.|23|7259|doi:10.1021/acs.orglett.1c02643
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28kcx4
title: CCDC 2102076: Experimental Crystal Structure Determination

description: Related Article: Yan-E Zhang, Shuo Tong, Mei-Xiang Wang|2021|Org.Lett.|23|7259|doi:10.1021/acs.orglett.1c02643
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7189907
title: Imperial Robotics Lab- Lake Vrana Freshwater Dataset

description: Raw bird diversity data and soundscape index data extracted from acoustic data and used for the analysis of acoustic diversity and bird diversity. R scripts are included for PCA , bird composition and soundscape analysis.
DOI: 10.5281/zenodo.7189906
title: Imperial Robotics Lab- Lake Vrana Freshwater Dataset

description: Raw bird diversity data and soundscape index data extracted from acoustic data and used for the analysis of acoustic diversity and bird diversity. R scripts are included for PCA , bird composition and soundscape analysis.
DOI: 10.6073/pasta/200b9c492419ec14c43a68d4411ad076
title: Data for Avolio et al. Making sense of multivariate community responses in global change experiments

description: Ecological communities are being impacted by global change worldwide. Experiments are a powerful tool to understand how global change will impact communities by comparing control and treatment replicates. Communities consist of multiple species and their associated abundances making multivariate methods a powerful approach to studying community compositional differences between control and treated replicates. Dissimilarity metrics are a commonly employed multivariate measure of compositional differences; however, while highly informative, dissimilarity metrics do not elucidate the specific ways in which communities differ. Integrating two multivariate methods, dissimilarity metrics and rank abundance curves has the potential to detect complex differences based on dissimilarity metrics and detail the how these differences came about through differences in richness, evenness, species ranks, or species identity. Here we use a database of 106 global change experiments located in herbaceous ecosystems and explore how patterns of ordinations based on dissimilarity metrics relate to rank abundance-curve based differences. We find that combining dissimilarity metrics alongside rank abundance curve-based measures clarify how global change treatments are altering communities. We find that when there is no difference in community composition (no distance between centroids of control and treated replicates), there are rarely differences in species ranks or species identities and more often differences in richness or evenness alone. In contrast, when there are differences between centroids of control and treated replicates, this is most often associated with differences in ranks either alone or co-occurring with differences in richness, evenness, or species identities. We suggest that integrating these two multivariate measures of community composition results in a deeper understanding of how global change impacts communities.
DOI: 10.6084/m9.figshare.21311748
title: Black Phosphorous-based Human-Machine Communication Interface

description: Dataset related to Figures 3, 4, and Supplementary Figures 3, 5, and 6.
DOI: 10.5281/zenodo.7189963
title: Aureobasidium pullulans strain CRUB 1823 mtDNA annotation

description: <em>Aureobasidium pullulans</em> strain CRUB 1823 mtDNA annotation
DOI: 10.5281/zenodo.7189962
title: Aureobasidium pullulans strain CRUB 1823 mtDNA annotation

description: <em>Aureobasidium pullulans</em> strain CRUB 1823 mtDNA annotation
DOI: 10.25387/g3.21200395.v1
title: Supplemental Material for Macdonald and Long, 2022

description: <strong>Analysis</strong> The "malathion_analysis.zip" zipped file resolves to a series of R/shellscripts and required files enabling the reproduction of the analysis in the study. <br> <strong>Supplementary Text/Figures</strong> The "supp_2022_09_20.pdf" includes supplementary figures S1 and S2, supplementary text S1, and the legend for supplementary table S1 (available for separate download). <br> <strong>Supplementary Table S1</strong> This text file ("Supplementary_Table_S1.txt") contains all details on the genes within the mapped QTL intervals. Its legend is presented in "supp_2022_09_20.pdf". <br> <strong>Haplotypes</strong> The "malathion_haps_genetic_1p5cM.txt.gz" gunzipped text file holds the founder haplotype calls at a series of genetic positions along the genome for several mixed, sequenced populations. Along with the scripts (see "malathion_analysis.zip"), these data can be used to recreate the figures from the study without starting from scratch (i.e., with raw reads from the SRA). <br>
DOI: 10.25387/g3.21200395
title: Supplemental Material for Macdonald and Long, 2022

description: <strong>Analysis</strong> The "malathion_analysis.zip" zipped file resolves to a series of R/shellscripts and required files enabling the reproduction of the analysis in the study. <br> <strong>Supplementary Text/Figures</strong> The "supp_2022_09_20.pdf" includes supplementary figures S1 and S2, supplementary text S1, and the legend for supplementary table S1 (available for separate download). <br> <strong>Supplementary Table S1</strong> This text file ("Supplementary_Table_S1.txt") contains all details on the genes within the mapped QTL intervals. Its legend is presented in "supp_2022_09_20.pdf". <br> <strong>Haplotypes</strong> The "malathion_haps_genetic_1p5cM.txt.gz" gunzipped text file holds the founder haplotype calls at a series of genetic positions along the genome for several mixed, sequenced populations. Along with the scripts (see "malathion_analysis.zip"), these data can be used to recreate the figures from the study without starting from scratch (i.e., with raw reads from the SRA). <br>
DOI: 10.5519/qd.4hdwoklc
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.7189944
title: Metabolite identification dataset: "Magnitude-Preserving Ranking for Structured Outputs" Brouard et al. (2017)

description: Metabolite identification dataset used to for the IOKR and MP-IOKR experiments in the publication: "Magnitude-Preserving Ranking for Structured Outputs" by Brouard et al. (2017) The code to run the experiments can be found on Github: https://github.com/aalto-ics-kepaco/iokr_for_metabolite_identification (mp-iokr/application/ACML17). The tar-files need to be unpacked.
DOI: 10.5281/zenodo.7189943
title: Metabolite identification dataset: "Magnitude-Preserving Ranking for Structured Outputs" Brouard et al. (2017)

description: Metabolite identification dataset used to for the IOKR and MP-IOKR experiments in the publication: "Magnitude-Preserving Ranking for Structured Outputs" by Brouard et al. (2017) The code to run the experiments can be found on Github: https://github.com/aalto-ics-kepaco/iokr_for_metabolite_identification (mp-iokr/application/ACML17). The tar-files need to be unpacked.
DOI: 10.21227/h9rd-pm63
title: Embedded electrode micro-LEDs with high modulation bandwidth for visible light communication

description: GaN-based light emitting diodes (LEDs) are the ideal light sources for visible light communication (VLC). However, both the low modulation bandwidth (MB) and unstable lighting output power (LOP) of LEDs at high current density that restrict the further development of VLC. In this work, micro-LEDs (μLEDs) with embedded N electrodes have been proposed, possessing high MB and remarkable stability. The as-prepared μLEDs show a high MB of 240 MHz @ 8.5 kA/cm2 and a small LOP aging rate of 6% under high temperature and humidity conditions thanks to the embedded electrode structure, which can effectively improve the uniformity of current spreading and increase the injection saturation current density, thereby effectively broadening the -3 dB MB and improving the LOP stability of μLEDs in harsh environments with high temperature and high humidity. Such high MB and reliable μLEDs shed light on a promising solution for industrial fabrication and chip arrays in underwater VLC system
DOI: 10.34740/kaggle/dsv/4318319
title: Mahanagar Yatayat Dataset
DOI: 10.5281/zenodo.7190210
title: lithophaga_antillarum_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.7190209
title: lithophaga_antillarum_zanfona_1.fasta.gz

description: .
DOI: 10.7910/dvn/oywuhl
title: Replication Data for: Valuation of Rice Postharvest Losses in Sub-Saharan Africa and Its Mitigation Strategies

description: Data on rice harvest and postharvest loss in Sub-Sahara Africa (SSA) is scanty making it difficult for stakeholders to appreciate the loss and set priority areas for loss reduction along the value chain. To address this problem, a protocol was developed and validated for postharvest loss (PHL) quantification in SSA. Quantitative losses at each segment were determined by field measurements. Interactive effect of origin of rice (domestic versus imported) and type of processing (white versus parboiled milled) on rice price in 33 markets in Africa was used to estimate qualitative loss for both white and parboiled milled rice. Total PHL for rice in SSA in 2018 is estimated at about US$ 10.24 billion, representing 47.63% of the expected total production. The highest loss recorded was quantitative loss before and during harvesting, followed by qualitative loss along the entire value chain, quantitative loss during milling, parboiling, threshing in that order, with the lowest being quantitative loss during drying. Priority areas to be targeted for PHL reduction in SSA and some loss mitigation tools and technologies piloted or suitable for SSA are proposed.
DOI: 10.34740/kaggle/dsv/4317682
title: Top 100 Bollywood IMDb movies by genres
DOI: 10.17909/z315-s081
title: Tess lc 112 Her
DOI: 10.7910/dvn/zhgkcl
title: Replication Data for: History and progress in genetic improvement for enhancing rice yield in sub-Saharan Africa

description: Genetic improvement has been given high priority in rice research for development in sub-Saharan Africa (SSA). This paper provides an overview of historical efforts of genetic improvement in SSA focused on improving rice productivity. It further describes yield gain of new rice varieties evaluated in recent field experiments in four selected breeding target domains, and summarizes adoption studies on rice varieties. Efforts to develop rice varieties adapted to diverse rice production systems in SSA have been made by several research organizations, including national agricultural research institutes, bilateral organizations, and three CGIAR centers. The efforts have resulted in the release of around 570 rice varieties in 10 major rice-producing SSA countries by 2020. Among these varieties, the most well-known are interspecfic upland rice varieties “New Rice for Africa (NERICA)” that were developed from crosses between improved Oryza sativa tropical japonica and Oryza glaberrima varieties. However, recent field assessements demonstrated that upland rice yield can be further improved through introduction of upland indica materials from Asia. In contrast, lowland interspecific rice varieties out-yielded the previously released improved O. sativa varieties in selected SSA countries. Field assessments in Senegal and Madagascar did not demonstrate the yield advantage of the recently-developed varieties including hybrids over best performing ones released before. The adoption level of improved varieties in terms of share of area occupied by improved varieties in 18 SSA countries was 40 % in 2008 with old varieties that were released before 2000 being dominant and 7% of the total rice area occupied by NERICA varieties. Especially in irrigated and rainfed lowland rice systems, the majority of dominant varieties were still those introduced from Asia. Panel data between 2002 and 2019 from the Senegal River Valley also confirmed this, and Sahel 108, which was introduced from Asia and released in Senegal in 1994, accounted for &gt;70 % of the total rice area in both the wet and dry seasons in 2019. The implications of this review for future rice genetic improvement and varietal replacement in SSA are discussed.
DOI: 10.23641/asha.21291384
title: Evaluation of BCI, EyeLink, and eye-tracking camera (Elliott et al., 2022)

description: <strong>Purpose: </strong>Augmentative and alternative communication (AAC) systems are important to support communication for individuals with complex communication needs. A recent addition to AAC system options is the brain–computer interface (BCI). This study aimed to compare the clinical application of the P300 speller BCI with two more common AAC systems, the EyeLink board, and an eye-tracking camera. <strong>Method:</strong> Ten participants without communication impairment (18–35 years of age) used each of the three AAC systems to spell three-letter words in one session. Accuracy and speed of letter selection were measured, and questionnaires were administered to evaluate usability, cognitive workload, and user preferences. <strong>Results: </strong>The results showed that the BCI was significantly less accurate, slower, and with lower usability and higher cognitive workload compared to the eye-tracking camera and EyeLink board. Participants rated the eye-tracking camera as the most favorable AAC system on all measures. <strong>Conclusions: </strong>The results demonstrated that while the P300 speller BCI was usable by most participants, it did not function as well as the eye-tracking camera and EyeLink board. The clinical use of the BCI is, therefore, currently difficult to justify for most individuals, particularly when considering the substantial cost and setup resourcing needed. <strong>Supplemental Material S1. </strong>Range in accuracy and speed for words spelled per participant and system. Elliott, C., Sutherland, D., Gerhard, D., & Theys, C. (2022). An evaluation of the P300 brain–computer interface, EyeLink board, and eye-tracking camera as augmentative and alternative communication devices. <em>Journal of Speech, Language, and Hearing Research</em>. Advance online publication. https://doi.org/10.1044/2022_JSLHR-21-00572