cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.18982874.v1
title: Supplementary Material for: Vocal communication in hummingbirds

description: Hummingbirds exhibit complex vocal repertoires that they use in their social interactions. Furthermore, they are capable of vocal production learning, an ability they share with songbirds, parrots, some non-oscine birds, and some mammals including humans. Despite these characteristics, hummingbirds have not received the same attention as other birds, especially songbirds and parrots in the study of vocal communication. Recent studies are advancing our knowledge of vocal communication in hummingbirds showing that these birds exhibit complex social learning and extraordinary abilities for vocal production. Moreover, vocal production learning in hummingbirds provides opportunities to study the evolution and diversification of vocal signals because of the presence of dialects in some species. In addition, the presence of high-frequency vocalizations in some hummingbirds underscores the relevance of these birds to study the evolution of communication signals and sensory adaptations. Not only do some species vocalize at unusually high frequencies compared to other birds, but evidence shows that at least one hummingbird species can hear these sounds, defying what we knew about avian hearing capabilities. Detailed descriptions of the hummingbird syrinx have shown that this organ exhibits homologous structures to those found in the syrinx of oscines, showing that vocal complexity in hummingbirds requires complex syringeal musculature. However, more research is needed to determine whether hummingbirds have unique adaptations that confer exceptional vocal and hearing abilities that exceed those found in other groups of birds.
DOI: 10.20363/heterobranchia-bunaken-prj-2.1
title: Marine Heterobranchia (Gastropoda, Mollusca) in Bunaken National Park, North Sulawesi, Indonesia—A Follow-Up Diversity Study

description: Bunaken National Park has been surveyed for a fourth time in 14 years, in an attempt to establish the species composition of heterobranch sea slugs in a baseline study for monitoring programs and protection of this special park. These molluscs are potentially good indicators of the health of an ecosystem, as many are species-specific predators on a huge variety of marine benthic and sessile invertebrates from almost every taxonomic group. Additionally, they are known to contain bio-compounds of significance in the pharmaceutical industry. It is therefore of paramount importance not only to document the species composition from a zoogeographic point of view, but to assist in their protection for the future, both in terms of economics and aesthetics. These four surveys have documented more than 200 species, with an approximate 50% of each collection found only on that survey and not re-collected. Many species new to science have also been documented, highlighting the lack of knowledge in this field.
DOI: 10.21227/6bzw-5571
title: Shahmukhi Database SMDB- SMHaroof V2

description: Punjabi Shahmukhi Alphabet dataset for machine learning projects SMDB V2
DOI: 10.6084/m9.figshare.19375259
title: Cs Data

description: Spectra collected for caesium nitrate, chloride and sulfate.<br>
DOI: 10.6084/m9.figshare.19375265
title: Sr Data

description: Spectral data for CG with Sr nitrate, chloride and carbonate<br>
DOI: 10.6084/m9.figshare.19375265.v1
title: Sr Data

description: Spectral data for CG with Sr nitrate, chloride and carbonate<br>
DOI: 10.6084/m9.figshare.19375256
title: Minimal Data Set. xlsx

description: During the artificial wheat-seed aging process, the activity levels of antioxidant enzymes and the contents of non-enzyme antioxidants decreased, leading to the accumulation of ROS and an increase in the carbonyl protein content, which ultimately led to a decrease in seed vigor, and there was a significant negative correlation between seed vigor and carbonyl protein content.
DOI: 10.6084/m9.figshare.19375256.v1
title: Minimal Data Set. xlsx

description: During the artificial wheat-seed aging process, the activity levels of antioxidant enzymes and the contents of non-enzyme antioxidants decreased, leading to the accumulation of ROS and an increase in the carbonyl protein content, which ultimately led to a decrease in seed vigor, and there was a significant negative correlation between seed vigor and carbonyl protein content.
DOI: 10.5281/zenodo.6364964
title: FCC-ee lattice

description: Repository containing the FCC-ee lattices.
DOI: 10.5281/zenodo.6364960
title: Dataset of the determination of the topographic spatial resolution of a confocal point sensor with a type ASG material measure

description: These original measurement data relate to the publication: J. Schaude, A. C. Gröschl, T. Hausotte: Effect of a Misidentified Centre of a Type ASG Material Measure on the Determined Topographic Spatial Resolution of an Optical Point Sensor, Metrology 2(1), p. 19-32, 2022, https://doi.org/10.3390/metrology2010002. Please refer to this open access publication for a detailed description of the measurement setup and procedure. All data are in ASCII-format. Each file contains four columns, where column one to three are the <em>x</em>, <em>y</em>, and <em>z</em>-coordinates of the positioning system and column four is the signal of the photodetector. <strong>Content of the folders</strong> 10_Plane: Axial probings on 18 points just outside the grooves. 20_Edges: Lateral probings from each point just outside the grooves in the direction of the roughly determined centre of the material measure. 30_PlaneArea: Repeated axial probing on a plane area near the material measure. 40_RadialMeasurement: Radial measurement of the material measure by lateral (radial) probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), and radii (referring to the centre of the circle fitted to the edges determined in 20_Edges). Each radial probing has its own data file, with the name of the data file being “radial_probing {radius in m} {height in m} {data and time of probing}.txt”. 50_LineMeasurement: Lateral probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), different lateral offsets (referring to the centre of the circle fitted to the edges determined in 20_Edges) and on two angles (on the groove (0°) and the adjacent top level (10°)). Please refer to sec. 5.2 of the aforementioned publication for a detailed description. Each lateral probing has its own data file, with the name of the file being “lateral probing {angle in °} {offset in m} {height in m} {data and time of probing}.txt”. <strong>Acknowledgement</strong> This project 20IND07 TracOptic has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. Funder name: European Metrology Programme for Innovation and Research (EMPIR); Funder ID: 10.13039/10001413
DOI: 10.5281/zenodo.6364959
title: Dataset of the determination of the topographic spatial resolution of a confocal point sensor with a type ASG material measure

description: These original measurement data relate to the publication: J. Schaude, A. C. Gröschl, T. Hausotte: Effect of a Misidentified Centre of a Type ASG Material Measure on the Determined Topographic Spatial Resolution of an Optical Point Sensor, Metrology 2(1), p. 19-32, 2022, https://doi.org/10.3390/metrology2010002. Please refer to this open access publication for a detailed description of the measurement setup and procedure. All data are in ASCII-format. Each file contains four columns, where column one to three are the <em>x</em>, <em>y</em>, and <em>z</em>-coordinates of the positioning system and column four is the signal of the photodetector. <strong>Content of the folders</strong> 10_Plane: Axial probings on 18 points just outside the grooves. 20_Edges: Lateral probings from each point just outside the grooves in the direction of the roughly determined centre of the material measure. 30_PlaneArea: Repeated axial probing on a plane area near the material measure. 40_RadialMeasurement: Radial measurement of the material measure by lateral (radial) probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), and radii (referring to the centre of the circle fitted to the edges determined in 20_Edges). Each radial probing has its own data file, with the name of the data file being “radial_probing {radius in m} {height in m} {data and time of probing}.txt”. 50_LineMeasurement: Lateral probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), different lateral offsets (referring to the centre of the circle fitted to the edges determined in 20_Edges) and on two angles (on the groove (0°) and the adjacent top level (10°)). Please refer to sec. 5.2 of the aforementioned publication for a detailed description. Each lateral probing has its own data file, with the name of the file being “lateral probing {angle in °} {offset in m} {height in m} {data and time of probing}.txt”. <strong>Acknowledgement</strong> This project 20IND07 TracOptic has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. Funder name: European Metrology Programme for Innovation and Research (EMPIR); Funder ID: 10.13039/10001413
DOI: 10.26165/juelich-data/yxlfkj
title: Replication Data for: HOPS: high-performance library for (non-)uniform sampling of convex-constrained models

description: This collection contains showcased models and pre-processing results (determining an independent flux space and rounding) that are used as basis for benchmarking the uniform sampling performance of the CHHR implementations of the HOPS library [10.1093/bioinformatics/btaa872] (https://github.com/modsim/hops) and the COBRA toolbox [doi.org/10.1038/s41596-018-0098-2]. Here, the pre-processing was performed with the COBRA toolbox for all benchmarks to guarantee fair comparability. The models are split in two classes: 1) simplices with 64, 256, 512, 1024, and 2048 dimensions; 2) metabolic network models (e_coli_core, iAT_PLT_256, iJO1366, RECON1, Recon2, Recon3D_301) [http://bigg.ucsd.edu/], [doi.org/10.1038/nbt.2488] formulated in SBML format [doi.org/10.1093/bioinformatics/btg015]. For each of these models, the left hand side of the constraint system (called A), the right hand side (called b), a shift of the transformation from sampling space, meaning the null space, to parameter space, meaning the full space of the model (called p_shift), the linear transformation from sampling space to parameter space (called N) and the Chebyshev center (called start) are provided. These files come in rounded and unrounded types, indicating if the rounding algorithm has been applied. For convenience, sometimes the rounding transformation is also given (indicated by T). The rounding transformation is only given in the rounded form, because it is identity otherwise. Additionally, the dataset contains an E. coli WT model with carbon atom transitions and isotope labelling measurements [10.1038/nprot.2009.58] used in the Bayesian inference non-uniform sampling example. The E. coli WT model is contained in a single FluxML file [doi.org/10.3389/fmicb.2019.01022]. To reproduce the data generated with the E. coli WT model, the rounding was calculated using the HOPS library and independent fluxes were provided by the high-performance simulator 13CFLUX2 [doi.org/10.1093/bioinformatics/bts646].
DOI: 10.5281/zenodo.5903334
title: Paired Sentinel-1 and Sentinel-2 Images for 2 Locations in Scotland and India for 2019 and 2020

description: The dataset contains two years of coverage (2019 and 2020) for two distant geographical areas in India and in Scotland. If using this dataset, please cite the paper where it has been introduced: <pre><code>@article{rs14061342, author = {Czerkawski, Mikolaj and Upadhyay, Priti and Davison, Christopher and Werkmeister, Astrid and Cardona, Javier and Atkinson, Robert and Michie, Craig and Andonovic, Ivan and Macdonald, Malcolm and Tachtatzis, Christos}, title = {Deep Internal Learning for Inpainting of Cloud-Affected Regions in Satellite Imagery}, journal = {Remote Sensing}, volume = {14}, year = {2022}, number = {6}, article-number = {1342}, url = {https://www.mdpi.com/2072-4292/14/6/1342}, ISSN = {2072-4292}, DOI = {10.3390/rs14061342} }</code></pre>
description: Cloud masks are now added separately in a cloud_masks directory. A PyTorch dataset class attached for potential use.
DOI: 10.5281/zenodo.5897694
title: Paired Sentinel-1 and Sentinel-2 Images for 2 Locations in Scotland and India for 2019 and 2020

description: The dataset contains two years of coverage (2019 and 2020) for two distant geographical areas in India and in Scotland. If using this dataset, please cite the paper where it has been introduced: <pre><code>@article{rs14061342, author = {Czerkawski, Mikolaj and Upadhyay, Priti and Davison, Christopher and Werkmeister, Astrid and Cardona, Javier and Atkinson, Robert and Michie, Craig and Andonovic, Ivan and Macdonald, Malcolm and Tachtatzis, Christos}, title = {Deep Internal Learning for Inpainting of Cloud-Affected Regions in Satellite Imagery}, journal = {Remote Sensing}, volume = {14}, year = {2022}, number = {6}, article-number = {1342}, url = {https://www.mdpi.com/2072-4292/14/6/1342}, ISSN = {2072-4292}, DOI = {10.3390/rs14061342} }</code></pre>
description: Cloud masks are now added separately in a cloud_masks directory. A PyTorch dataset class attached for potential use.
DOI: 10.5281/zenodo.6365015
title: Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - 3lambda SeMAD dataset

description: bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) for 3 wavelength Se MAD experiment (infl, inflection point, peak, peak, rem, high energy remote) and the associated data processing files (xds_inf, xds_peak, xds_rem)
DOI: 10.5281/zenodo.6365014
title: Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - 3lambda SeMAD dataset

description: bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) for 3 wavelength Se MAD experiment (infl, inflection point, peak, peak, rem, high energy remote) and the associated data processing files (xds_inf, xds_peak, xds_rem)
DOI: 10.5281/zenodo.6363832
title: Research Artifacts - A Learning-based Approach for Detecting Modularity Violations on Method Placement

description: This record contains research artifacts of our paper. The description of each file is as follows. case_study.xlsx: a spreadsheet that contains a list of our detected cases and results of our manual inspection java-large+.tar.gz: a preprocessed dataset used for training our detection model model_parameters.ckpt.gz: trained parameters and a word dictionary of our neural network model src.tar.gz: source code of our neural network model written in Python and a dataset preprocessor written in Java
DOI: 10.5281/zenodo.6365041
title: Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with an adenosine nucleotide analog.

description: bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds)
DOI: 10.5281/zenodo.6365040
title: Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with an adenosine nucleotide analog.

description: bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds)
DOI: 10.6084/m9.figshare.11093087
title: Downregulation of lumican enhanced mitotic defects and aneuploidy in lung cancer cells

description: Lumican is overexpressed in lung cancer cells and has been implicated in the pathogenesis of tumorigenesis and regulation of cancer cell invasion. Lumican is robustly associated with the binding of p120-catenin protein to modulate cell metastasis. However, its role in cancer cell proliferation is still unclear. This study investigated the effect of lumican on the cell division including mitosis and cytokinesis in non-small lung cancer cells. We found that the downregulation of lumican prolonged the doubling time of cells and retarded the cell growth in H460 and A549 cells. Along with tubulin, lumican localized to the mitotic spindle and centrosome during the metaphase-anaphase stage. The cell cycle was retained in the G2/M phase after the downregulation of lumican. Interestingly, lumican was found to play important roles in central spindle and midbody formation during cytokinesis. Lumican interacted with the midbody-associated proteins such as MKLP1, Aurora B, and ECT2. Notably, the downregulation of lumican decreased the level of MKLP1 accompanied by the retention of midbody-residual that resulted in multi-nucleated cells. Downregulation of lumican promoted the chromosome missegregation and the increment of the bi-/multinucleated cells. The results of this study indicated that lumican associated with tubulin is crucial for spindle fiber formation and midbody assembly in cell division. Downregulation of lumican displayed the defects in mitotic spindle assembly/dynamics and improper kinetochore-microtubules attachment that led to increase aneuploidy. This emerging property of lumican is suggested to tightly control chromosome segregation during cell division in lung cancer cells. <b>Abbreviations:</b> ESCRT: endosomal sorting complex required for transport; PRC1: protein regulator of cytokinesis 1; Nci: negative control siRNA; Lumi: lumican siRNAs; MKLP1: mitotic kinesin-like protein 1; H460LD and A549LD: H460 and A549 cell lines with less expressed lumican
DOI: 10.6084/m9.figshare.11093087.v1
title: Downregulation of lumican enhanced mitotic defects and aneuploidy in lung cancer cells

description: Lumican is overexpressed in lung cancer cells and has been implicated in the pathogenesis of tumorigenesis and regulation of cancer cell invasion. Lumican is robustly associated with the binding of p120-catenin protein to modulate cell metastasis. However, its role in cancer cell proliferation is still unclear. This study investigated the effect of lumican on the cell division including mitosis and cytokinesis in non-small lung cancer cells. We found that the downregulation of lumican prolonged the doubling time of cells and retarded the cell growth in H460 and A549 cells. Along with tubulin, lumican localized to the mitotic spindle and centrosome during the metaphase-anaphase stage. The cell cycle was retained in the G2/M phase after the downregulation of lumican. Interestingly, lumican was found to play important roles in central spindle and midbody formation during cytokinesis. Lumican interacted with the midbody-associated proteins such as MKLP1, Aurora B, and ECT2. Notably, the downregulation of lumican decreased the level of MKLP1 accompanied by the retention of midbody-residual that resulted in multi-nucleated cells. Downregulation of lumican promoted the chromosome missegregation and the increment of the bi-/multinucleated cells. The results of this study indicated that lumican associated with tubulin is crucial for spindle fiber formation and midbody assembly in cell division. Downregulation of lumican displayed the defects in mitotic spindle assembly/dynamics and improper kinetochore-microtubules attachment that led to increase aneuploidy. This emerging property of lumican is suggested to tightly control chromosome segregation during cell division in lung cancer cells. <b>Abbreviations:</b> ESCRT: endosomal sorting complex required for transport; PRC1: protein regulator of cytokinesis 1; Nci: negative control siRNA; Lumi: lumican siRNAs; MKLP1: mitotic kinesin-like protein 1; H460LD and A549LD: H460 and A549 cell lines with less expressed lumican
DOI: 10.6084/m9.figshare.10921601.v1
title: DNA damage responses in murine Pre-B cells with genetic deficiencies in damage response genes

description: DNA damage can be generated in multiple ways from genotoxic and physiologic sources. Genotoxic damage is known to disrupt cellular functions and is lethal if not repaired properly. We compare the transcriptional programs activated in response to genotoxic DNA damage induced by ionizing radiation (IR) in abl pre-B cells from mice deficient in DNA damage response (DDR) genes <i>Atm, Mre11, Mdc1, H2ax, 53bp1</i>, and <i>DNA-PKcs</i>. We identified a core IR-specific transcriptional response that occurs in abl pre-B cells from WT mice and compared the response of the other genotypes to the WT response. We also identified genotype specific responses and compared those to each other. The WT response includes many processes involved in lymphocyte development and immune response, as well as responses associated with the molecular mechanisms of cancer, such as TP53 signaling. As expected, there is a range of similarity in transcriptional profiles in comparison to WT cells, with <i>Atm</i>-/- cells being the most different from the core WT DDR and <i>Mre11</i> hypomorph (<i>Mre11<sup>A/A</sup></i>) cells also very dissimilar to WT and other genotypes. For example, NF-kB-related signaling and CD40 signaling are deficient in both <i>Atm</i>-/- and <i>Mre11<sup>A/A</sup></i> cells, but present in all other genotypes. In contrast, IR-induced TP53 signaling is seen in the <i>Mre11<sup>A/A</sup></i> cells, while these responses are not seen in the <i>Atm</i>-/- cells. By examining the similarities and differences in the signaling pathways in response to IR when specific genes are absent, our results further illustrate the contribution of each gene to the DDR. The microarray gene expression data discussed in this paper have been deposited in NCBI’s Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) and are accessible under accession number GSE116388.