cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16305741.v1
title: Additional file 5 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 5: Table S2. Functional transcriptome annotation using groups of orthologs (eggNOG), gene ontology terms (GO), conserved domains (CDs) and analyses of gene expression with DeSeq2. Differentially Expressed Genes (DEG) were identified with a threshold of pvalue ≤ 0.05 and with a log2 Fold Change (log2|FC|) of at least 1.5 at different times of the dissociation/reaggregation process. (A) List of transcripts with orthologs. (B) List of transcripts with GO terms. (C) List of transcripts with CDs. (D) List of transcripts without any annotations. Related to Figs. 6, 7 and Additional file 14: Figure S4.
DOI: 10.6084/m9.figshare.16305750
title: Additional file 8 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 8: Table S5. Completeness of conserved domain arrangements (CDAs) estimated by the proportion of the CDAs found among the expected conserved CDAs in different metazoan species using DOGMA. Related to Fig. 6E.
DOI: 10.6084/m9.figshare.16305750.v1
title: Additional file 8 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 8: Table S5. Completeness of conserved domain arrangements (CDAs) estimated by the proportion of the CDAs found among the expected conserved CDAs in different metazoan species using DOGMA. Related to Fig. 6E.
DOI: 10.6084/m9.figshare.16305747.v1
title: Additional file 7 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 7: Table S4. General information about available sponge transcriptomes (according to Riesgo et. al, 2014; [47, 134], This study).
DOI: 10.6084/m9.figshare.16305753
title: Additional file 9 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 9: Table S6. Differential Expressed Genes (DEG) during (A) Dissociation process (B) dissociation and reaggregation processes and (C) reaggregation process. DEG extracted from DeSeq2 analysis with a threshold of pvalue ≤ 0.05 and log2 |Fold Change| of at least 1.5 at different times of dissociation (1hD, 4hD) and reaggregation (1hR, 3hR). Related to Fig. 7.
DOI: 10.6084/m9.figshare.16305747
title: Additional file 7 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 7: Table S4. General information about available sponge transcriptomes (according to Riesgo et. al, 2014; [47, 134], This study).
DOI: 10.6084/m9.figshare.16305753.v1
title: Additional file 9 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

description: Additional file 9: Table S6. Differential Expressed Genes (DEG) during (A) Dissociation process (B) dissociation and reaggregation processes and (C) reaggregation process. DEG extracted from DeSeq2 analysis with a threshold of pvalue ≤ 0.05 and log2 |Fold Change| of at least 1.5 at different times of dissociation (1hD, 4hD) and reaggregation (1hR, 3hR). Related to Fig. 7.
DOI: 10.6084/m9.figshare.16614581
title: Additional file 2 of Caenorhabditis elegans exhibits positive gravitaxis

description: Additional file 2: Raw Data.
DOI: 10.6084/m9.figshare.16614581.v1
title: Additional file 2 of Caenorhabditis elegans exhibits positive gravitaxis

description: Additional file 2: Raw Data.
DOI: 10.6084/m9.figshare.16614593
title: Additional file 2 of A novel Penicillium sumatraense isolate reveals an arsenal of degrading enzymes exploitable in algal bio-refinery processes

description: Additional file 2: Data S1–S3. Sequences of predicted genes (Data S1), CDSs (Data S2) and proteins (Data S3) as obtained from the annotated genome of the unknown fungal isolate (FASTA format). Data S4. GTF (Gene Transfer format) obtained by BRAKER annotation with gene structure and coordinates. Data S5. Functional annotations of predicted proteins (TXT format). Data S6. Phylogenetic markers used for the classification of the unknown fungal isolate.
DOI: 10.6084/m9.figshare.16614593.v1
title: Additional file 2 of A novel Penicillium sumatraense isolate reveals an arsenal of degrading enzymes exploitable in algal bio-refinery processes

description: Additional file 2: Data S1–S3. Sequences of predicted genes (Data S1), CDSs (Data S2) and proteins (Data S3) as obtained from the annotated genome of the unknown fungal isolate (FASTA format). Data S4. GTF (Gene Transfer format) obtained by BRAKER annotation with gene structure and coordinates. Data S5. Functional annotations of predicted proteins (TXT format). Data S6. Phylogenetic markers used for the classification of the unknown fungal isolate.
DOI: 10.6084/m9.figshare.16539135.v1
title: TIPs

description: TE insertions in 524 <i>Brassica rapa</i> genomes.The haplotypes of candidate genes with TIPs in gene regions<br>
DOI: 10.6084/m9.figshare.16614277
title: Considerable uncertainties in simulating land carbon sinks induced by different precipitation products

description: Precipitation, a key determinant of soil moisture variations, plays an important role in regulating terrestrial carbon fluxes on multiple time-scales. It is a critical meteorological forcing to drive terrestrial biosphere model (TBM), however, with a large uncertainty itself. We here investigated to what extent precipitation alone can cause uncertainties of model-simulated carbon flux from terrestrial ecosystems to atmosphere (F<sub>TA</sub>), based on 8 precipitation products and a TBM, VEGAS. We find that the pattern of uncertainties in simulated F<sub>TA</sub> obviously differs from the pattern of discrepancies in precipitation, owing to divergent water sensitivities of vegetation over different regions. Globally, the uncertainty in F<sub>TA</sub> can be up to approximately 40.73% of the uncertainty in TRENDYv6 multi-model simulated F<sub>TA</sub> which is caused by model structural and parameter uncertainty. A good linear relationship emerges between global area-averaged land climatological annual precipitation and simulated total F<sub>TA</sub> with the slope of −0.0040 PgC yr<sup>−1</sup> per mm yr<sup>−1</sup> ( = 0.03; negative for carbon sink), where 70% is explained by the sensitivity over extra-tropical northern hemisphere (NH). For seasonal cycle, compared to nearly constant inter-precipitation spreads over tropics plus extra-tropical southern hemisphere (Trop+SH), uncertainties in corresponding simulated F<sub>TA</sub> show obvious seasonal differences with the relatively larger uncertainties in March-April-May (MAM) and August-September-October (ASO). For interannual variability, uncertainties in simulated total F<sub>TA</sub> are, albeit smaller, nonnegligible, which are 40.61% (global), 38.17% (Trop+SH), and 29.63% (NH) of the TRENDYv6 inter-model uncertainty, respectively. Therefore, generating better global precipitation product is important for reducing the uncertainty in simulating terrestrial carbon sinks.
DOI: 10.6084/m9.figshare.16614277.v1
title: Considerable uncertainties in simulating land carbon sinks induced by different precipitation products

description: Precipitation, a key determinant of soil moisture variations, plays an important role in regulating terrestrial carbon fluxes on multiple time-scales. It is a critical meteorological forcing to drive terrestrial biosphere model (TBM), however, with a large uncertainty itself. We here investigated to what extent precipitation alone can cause uncertainties of model-simulated carbon flux from terrestrial ecosystems to atmosphere (F<sub>TA</sub>), based on 8 precipitation products and a TBM, VEGAS. We find that the pattern of uncertainties in simulated F<sub>TA</sub> obviously differs from the pattern of discrepancies in precipitation, owing to divergent water sensitivities of vegetation over different regions. Globally, the uncertainty in F<sub>TA</sub> can be up to approximately 40.73% of the uncertainty in TRENDYv6 multi-model simulated F<sub>TA</sub> which is caused by model structural and parameter uncertainty. A good linear relationship emerges between global area-averaged land climatological annual precipitation and simulated total F<sub>TA</sub> with the slope of −0.0040 PgC yr<sup>−1</sup> per mm yr<sup>−1</sup> ( = 0.03; negative for carbon sink), where 70% is explained by the sensitivity over extra-tropical northern hemisphere (NH). For seasonal cycle, compared to nearly constant inter-precipitation spreads over tropics plus extra-tropical southern hemisphere (Trop+SH), uncertainties in corresponding simulated F<sub>TA</sub> show obvious seasonal differences with the relatively larger uncertainties in March-April-May (MAM) and August-September-October (ASO). For interannual variability, uncertainties in simulated total F<sub>TA</sub> are, albeit smaller, nonnegligible, which are 40.61% (global), 38.17% (Trop+SH), and 29.63% (NH) of the TRENDYv6 inter-model uncertainty, respectively. Therefore, generating better global precipitation product is important for reducing the uncertainty in simulating terrestrial carbon sinks.
DOI: 10.25919/bg98-wj10
title: Updated Australian bathymetry: merged 250m bathyTopo

description: Accurate coastal wave and hydrodynamic modelling relies on quality bathymetric input. Many national scale modelling studies, hindcast and forecast products, have, or are currently using a 2009 digital elevation model (DEM), which does not include recently available bathymetric surveys and is now out of date. There are immediate needs for an updated national product, preceding the delivery of the AusSeabed program’s Global Multi-Resolution Topography for Australian coastal and ocean models. There are also challenges in stitching coarse resolution DEMs, which are often too shallow where they meet high-resolution information (e.g. LiDAR surveys) and require supervised/manual modifications (e.g. NSW, Perth, and Portland VIC bathymetries). This report updates the 2009 topography and bathymetry with a selection of nearshore surveys and demonstrates where the 2009 dataset and nearshore bathymetries do not matchup.
DOI: 10.25919/x8hh-5528
title: Parkes observations for project P1066 semester 2021APRS_12

description: We propose 36 hrs of Parkes observations to continue our successful Deeper, Wider, Faster (DWF) program to detect fast transients and fast radio burst (FRB) counterparts and help resolve their nature. DWF coordinates over 80 observatories worldwide at all wavelengths, from radio to gamma-ray to detect and follow-up FRBs and other elusive fast (millisecond-to-hours duration) transients. Crucially, we coordinate simultaneous deep, fast-cadenced, wide-field observations at all wavelengths to observe the same field at the same time as Parkes, enabling multi-wavelength detection before, during, and after the radio detection. Little to no multi-wavelength observations to any significant depth have been done on these timescales, leaving this parameter space underexplored. DWF coordinates major facilities to observe with Parkes, such as South Pole Telescope (mm/sub-mm), GROND (infrared), CTIO Dark Energy Camera (optical), Astrosat (UV/X-ray), HXMT (X-ray), HESS (gamma-ray), and Pierre Auger (high-energy). We perform realtime data processing and transient identification at all wavelengths that enables triggering our deep, rapid-response (within minutes) follow up programs for deep spectroscopy and imaging using the world's largest telescopes (e.g., Keck, VLT, Gemini, SALT, ATCA).
DOI: 10.6084/m9.figshare.16614679
title: Raw data for analyses shown in Fig 2 to Fig 4 of the manuscript (Goya et al.)

description: Raw data for analyses shown in Fig 2 to Fig 4 of the manuscript
DOI: 10.6084/m9.figshare.16614679.v1
title: Raw data for analyses shown in Fig 2 to Fig 4 of the manuscript (Goya et al.)

description: Raw data for analyses shown in Fig 2 to Fig 4 of the manuscript
DOI: 10.5281/zenodo.5504651
title: Torus-stable zone above starspots

description: This entry contains interactive figures and public data sets for Sun, Török, & DeRosa (2021), "Torus-stable zone above starspots". See README for details.
DOI: 10.5281/zenodo.5500723
title: Multiplexed imaging reveals an IFN-γ-driven inflammatory state in Nivolumab-associated gastritis (data)

description: MIBI-TOF images, segmentation output, cell phenotype maps, and extracted cell tables for Ferrian et al.
DOI: 10.5281/zenodo.5500722
title: Multiplexed imaging reveals an IFN-γ-driven inflammatory state in Nivolumab-associated gastritis (data)

description: MIBI-TOF images, segmentation output, cell phenotype maps, and extracted cell tables for Ferrian et al.
DOI: 10.6084/m9.figshare.16614413.v1
title: Additional file 1 of Morphology of lentic and lotic tadpoles from Madagascar

description: Additional file 1. Quantification of categories.
DOI: 10.6084/m9.figshare.16614410.v1
title: Additional file 1 of Gene co-expression network analysis in zebrafish reveals chemical class specific modules

description: Additional file 1.
DOI: 10.6084/m9.figshare.16614422
title: Additional file 3 of Morphology of lentic and lotic tadpoles from Madagascar

description: Additional file 3. PC scores of examined species.
DOI: 10.6084/m9.figshare.16614413
title: Additional file 1 of Morphology of lentic and lotic tadpoles from Madagascar

description: Additional file 1. Quantification of categories.
DOI: 10.6084/m9.figshare.16614410
title: Additional file 1 of Gene co-expression network analysis in zebrafish reveals chemical class specific modules

description: Additional file 1.
DOI: 10.6084/m9.figshare.16539135
title: TIPs

description: TE insertions in 524 <i>Brassica rapa</i> genomes.The haplotypes of candidate genes with TIPs in gene regions<br>
DOI: 10.6084/m9.figshare.16614967
title: Telops_IR_stabilized

description: Infrared image time series for experiment EE1 and EE3netcdf file format
DOI: 10.6084/m9.figshare.16615066
title: Sonic Anemometer Data

description: This is a 20 Hz time series of 3D sonic anemometer data measured at two vertical level over a spreading experimental fire burn
DOI: 10.6084/m9.figshare.16615174.v2
title: Flame thermocouple data

description: In-fire thermocouple data for two experimental burns
DOI: 10.6084/m9.figshare.16615174
title: Flame thermocouple data

description: In-fire thermocouple data for two experimental burns
DOI: 10.6084/m9.figshare.16615174.v1
title: Untitled Item

description: In-fire thermocouple data for two experimental burns
DOI: 10.5281/zenodo.5348595
title: ADAPTASI MAHASISWA DALAM PEMBELAJARAN DARING DI TENGAH PANDEMI COVID 19 DALAM PERSPEKTIF SOSIOLOGI PENDIDIKAN

description: Penelitian bertujuan untuk mengetahui upaya yang dilakukan mahasiswa dalam pembelajaran daring ditengah Pandemi Covid-19 yang dianalisis melalui perspektif Sosiologi Pendidikan. Metode yang digunakan dalam penelitian ini yaitu kualitatif dengan pendekatan fenomenologi, peneliti melakukan wawancara kepada partisipan, dan dianalisis menggunakan pendekatan dari Miles and Huberman. Hasil penelitian menunjukkan upaya yang dilakukan mahasiswa dalam pelaksanaan pembelajaran daring di tengah pandemic Covid-19 dengan menggunakan teori Parson (AGIL). Adaptasi (Adaptation): mahasiswa berupaya untuk dapat beradaptasi dengan memecahkan masalah yang dihadapinya dalam pembelajaran daring; Pencapaian Tujuan (Goal attainment): mahasiswa berupaya untuk memotivasi diri belajar daring dengan baik sesuai dengan tujuannya untuk menggapai citacita; Integrasi (Integration): mahasiswa berupaya untuk dapat mengintegrasikan pembelajaran daring dengan daya dukung pembelajaran daring baik dari sisi teknologi maupun sumber daya manusia, dan Pola Pemeliharaan (Latent pattern maintenance): mahasiswa berupaya untuk melakukan perbaikan dalam penggunaan teknologi pendukung pembelajaran, melakukan manajerial waktu maupun strategi belajar mahasiswa; komunikasi dengan dosen tetap dipelihara dengan baik. Dengan menjalankan keempat syarat tersebut maka pembelajaran daring dapat berjalan dengan baik. Perlu adanya kerjasama semua pihak baik dari dosen, mahasiswa, peguruan tinggi, bahkan pemerintah untuk mewujudkan pendidikan yang berkualitas di Indonesia ditengah pandemic Covid-19.
DOI: 10.5281/zenodo.5348594
title: ADAPTASI MAHASISWA DALAM PEMBELAJARAN DARING DI TENGAH PANDEMI COVID 19 DALAM PERSPEKTIF SOSIOLOGI PENDIDIKAN

description: Penelitian bertujuan untuk mengetahui upaya yang dilakukan mahasiswa dalam pembelajaran daring ditengah Pandemi Covid-19 yang dianalisis melalui perspektif Sosiologi Pendidikan. Metode yang digunakan dalam penelitian ini yaitu kualitatif dengan pendekatan fenomenologi, peneliti melakukan wawancara kepada partisipan, dan dianalisis menggunakan pendekatan dari Miles and Huberman. Hasil penelitian menunjukkan upaya yang dilakukan mahasiswa dalam pelaksanaan pembelajaran daring di tengah pandemic Covid-19 dengan menggunakan teori Parson (AGIL). Adaptasi (Adaptation): mahasiswa berupaya untuk dapat beradaptasi dengan memecahkan masalah yang dihadapinya dalam pembelajaran daring; Pencapaian Tujuan (Goal attainment): mahasiswa berupaya untuk memotivasi diri belajar daring dengan baik sesuai dengan tujuannya untuk menggapai citacita; Integrasi (Integration): mahasiswa berupaya untuk dapat mengintegrasikan pembelajaran daring dengan daya dukung pembelajaran daring baik dari sisi teknologi maupun sumber daya manusia, dan Pola Pemeliharaan (Latent pattern maintenance): mahasiswa berupaya untuk melakukan perbaikan dalam penggunaan teknologi pendukung pembelajaran, melakukan manajerial waktu maupun strategi belajar mahasiswa; komunikasi dengan dosen tetap dipelihara dengan baik. Dengan menjalankan keempat syarat tersebut maka pembelajaran daring dapat berjalan dengan baik. Perlu adanya kerjasama semua pihak baik dari dosen, mahasiswa, peguruan tinggi, bahkan pemerintah untuk mewujudkan pendidikan yang berkualitas di Indonesia ditengah pandemic Covid-19.
DOI: 10.5281/zenodo.5504649
title: Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth

description: Modified nucleosides in tRNAs are critical for protein translation. N<sup>1</sup>-methylguanosine-37 and N<sup>1</sup>-methylinosine-37 in tRNAs, both located at the 3’-adjacent to the anticodon, are formed by Trm5. Here we describe <em>Arabidopsis thaliana AtTRM5</em> (At3g56120) as a Trm5 ortholog. <em>Attrm5</em> mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In <em>Attrm5</em> mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. We show that <em>AtTRM5</em> complements the yeast <em>trm5</em> mutant, and <em>in vitro</em> methylates tRNA guanosine-37 to produce N<sup>1</sup>-methylguanosine (m<sup>1</sup>G). We also show <em>in vitro</em> that AtTRM5 methylates tRNA inosine-37 to produce N<sup>1</sup>-methylinosine (m<sup>1</sup>I) and in <em>Attrm5</em> mutant plants, we show a reduction of both N<sup>1</sup>-methylguanosine and N<sup>1</sup>-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Proteomics data showed that photosynthetic protein abundance is affected in <em>Attrm5</em> mutant plants. Finally, we show tRNA-Ala aminoacylation is not affected in <em>Attrm5</em> mutants. However the abundance of tRNA-Ala and tRNA-Asp 5’ half cleavage products are deduced. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m<sup>1</sup>G and m<sup>1</sup>I at tRNA position 37 in general plant growth and development.
description: This is the source code used to analyse datasets generated for the research publication titled "Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth" (https://doi.org/10.1371/journal.pone.0225064). The dataset analysed using this code can be found at NCBI with the GEO accession number GSE114898. Proteomics raw data has been deposited on iProX, with under accession number IPX0001222000 and is available at https://www.iprox.org//page/project.html?id=IPX0001222000.
DOI: 10.5281/zenodo.5504648
title: Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth

description: Modified nucleosides in tRNAs are critical for protein translation. N<sup>1</sup>-methylguanosine-37 and N<sup>1</sup>-methylinosine-37 in tRNAs, both located at the 3’-adjacent to the anticodon, are formed by Trm5. Here we describe <em>Arabidopsis thaliana AtTRM5</em> (At3g56120) as a Trm5 ortholog. <em>Attrm5</em> mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In <em>Attrm5</em> mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. We show that <em>AtTRM5</em> complements the yeast <em>trm5</em> mutant, and <em>in vitro</em> methylates tRNA guanosine-37 to produce N<sup>1</sup>-methylguanosine (m<sup>1</sup>G). We also show <em>in vitro</em> that AtTRM5 methylates tRNA inosine-37 to produce N<sup>1</sup>-methylinosine (m<sup>1</sup>I) and in <em>Attrm5</em> mutant plants, we show a reduction of both N<sup>1</sup>-methylguanosine and N<sup>1</sup>-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Proteomics data showed that photosynthetic protein abundance is affected in <em>Attrm5</em> mutant plants. Finally, we show tRNA-Ala aminoacylation is not affected in <em>Attrm5</em> mutants. However the abundance of tRNA-Ala and tRNA-Asp 5’ half cleavage products are deduced. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m<sup>1</sup>G and m<sup>1</sup>I at tRNA position 37 in general plant growth and development.
description: This is the source code used to analyse datasets generated for the research publication titled "Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth" (https://doi.org/10.1371/journal.pone.0225064). The dataset analysed using this code can be found at NCBI with the GEO accession number GSE114898. Proteomics raw data has been deposited on iProX, with under accession number IPX0001222000 and is available at https://www.iprox.org//page/project.html?id=IPX0001222000.
DOI: 10.21227/5tgs-4d28
title: The BIM and point cloud of DATA 1

description: 教学楼的BIM与点云