cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21592829
title: Additional file 3 of Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration

description: Additional file 3.
DOI: 10.6084/m9.figshare.21592826
title: Additional file 2 of Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration

description: Additional file 2.
DOI: 10.5281/zenodo.10636792
title: Subsampled RBFOX2 eCLIP fastq files

description: RBFOX2 eCLIP fastq files, subsampled to 10% (about 2M reads) to be used for demo purposes.

2 replicates, each with IP and size-matched input control (4 files total).

Adapter sequence to trim ("RiL19"): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
DOI: 10.5281/zenodo.10636793
title: Subsampled RBFOX2 eCLIP fastq files

description: RBFOX2 eCLIP fastq files, subsampled to 10% (about 2M reads) to be used for demo purposes.

2 replicates, each with IP and size-matched input control (4 files total).

Adapter sequence to trim ("RiL19"): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
DOI: 10.5281/zenodo.7741571
title: Spin-polarizing electron beam splitter from crossed graphene nanoribbons

description: OPEN DATA related to the research publication:

S. Sanz, N. Papior, G. Giedke, D. Sánchez-Portal, M. Brandbyge, and T. Frederiksen, Spin-polarizing electron beam splitter from crossed graphene nanoribbons,Phys. Rev. Lett. 129, 037701 (2022) [arXiv:2201.07147]

Abstract: Junctions composed of two crossed graphene nanoribbons (GNRs) have been theoretically proposed as electron beam splitters where incoming electron waves in one GNR can be split coherently into propagating waves in two outgoing terminals with nearly equal amplitude and zero back-scattering. Here we scrutinize this effect for devices composed of narrow zigzag GNRs taking explicitly into account the role of Coulomb repulsion that leads to spin-polarized edge states within mean-field theory. We show that the beam-splitting effect survives the opening of the well-known correlation gap and, more strikingly, that a spin-dependent scattering potential emerges which spin polarizes the transmitted electrons in the two outputs. By studying different ribbons and intersection angles we provide evidence that this is a general feature with edge-polarized nanoribbons. A near-perfect polarization can be achieved by joining several junctions in series. Our findings suggest that GNRs are interesting building blocks in spintronics and quantum technologies with applications for interferometry and entanglement.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.5281/zenodo.7741572
title: Spin-polarizing electron beam splitter from crossed graphene nanoribbons

description: OPEN DATA related to the research publication:

S. Sanz, N. Papior, G. Giedke, D. Sánchez-Portal, M. Brandbyge, and T. Frederiksen, Spin-polarizing electron beam splitter from crossed graphene nanoribbons,Phys. Rev. Lett. 129, 037701 (2022) [arXiv:2201.07147]

Abstract: Junctions composed of two crossed graphene nanoribbons (GNRs) have been theoretically proposed as electron beam splitters where incoming electron waves in one GNR can be split coherently into propagating waves in two outgoing terminals with nearly equal amplitude and zero back-scattering. Here we scrutinize this effect for devices composed of narrow zigzag GNRs taking explicitly into account the role of Coulomb repulsion that leads to spin-polarized edge states within mean-field theory. We show that the beam-splitting effect survives the opening of the well-known correlation gap and, more strikingly, that a spin-dependent scattering potential emerges which spin polarizes the transmitted electrons in the two outputs. By studying different ribbons and intersection angles we provide evidence that this is a general feature with edge-polarized nanoribbons. A near-perfect polarization can be achieved by joining several junctions in series. Our findings suggest that GNRs are interesting building blocks in spintronics and quantum technologies with applications for interferometry and entanglement.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.6084/m9.figshare.13566101
title: Additional file 3 of Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness

description: Additional file 3.
DOI: 10.6084/m9.figshare.14920793.v1
title: Additional file 2 of Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex

description: Additional file 2: Table S1. Characteristics of sampled populations and ploidy levels of the A. chinensis complex. Table S2. List of ploidy level and haplotype for 608 individuals in cpDNA analysis. Table S3. Description of haplotypes in the A. chinensis complex from three combined chloroplast DNA fragments. Table S4. Genetic characteristics of cpDNA for 31 var. chinensis populations and 25 var. deliciosa populations. Table S5. Results of AMOVA testing of the A. chinensis complex. Table S6. List of primers for the eight cpDNA loci. Table S7 The six environmental variables used for ecological niche modeling.
DOI: 10.6084/m9.figshare.21069380
title: Additional file 1 of Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species

description: Additional file 1.
DOI: 10.5281/zenodo.7957719
title: Mach-Zehnder-like interferometry with graphene nanoribbon networks

description: S. Sanz, N. Papior, G. Giedke, D. Sanchez-Portal, M. Brandbyge, and T. FrederiksenMach–Zehnder-like interferometry with graphene nanoribbon networksJ. Phys.: Condens. Matter 35, 374001 (2023)

We study theoretically electron interference in a Mach–Zehnder-like geometry formed by four zigzag graphene nanoribbons (ZGNRs) arranged in parallel pairs, one on top of the other, such that they form intersection angles of 60˚ Depending on the interribbon separation, each intersection can be tuned to act either as an electron beam splitter or as a mirror, enabling tuneable circuitry with interfering pathways. Based on the mean-field Hubbard model and Green's function techniques, we evaluate the electron transport properties of such 8-terminal devices and identify pairs of terminals that are subject to self-interference. We further show that the scattering matrix formalism in the approximation of independent scattering at the four individual junctions provides accurate results as compared with the Green's function description, allowing for a simple interpretation of the interference process between two dominant pathways. This enables us to characterize the device sensitivity to phase shifts from an external magnetic flux according to the Aharonov–Bohm effect as well as from small geometric variations in the two path lengths. The proposed devices could find applications as magnetic field sensors and as detectors of phase shifts induced by local scatterers on the different segments, such as adsorbates, impurities or defects. The setup could also be used to create and study quantum entanglement.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.5281/zenodo.7957720
title: Mach-Zehnder-like interferometry with graphene nanoribbon networks

description: S. Sanz, N. Papior, G. Giedke, D. Sanchez-Portal, M. Brandbyge, and T. FrederiksenMach–Zehnder-like interferometry with graphene nanoribbon networksJ. Phys.: Condens. Matter 35, 374001 (2023)

We study theoretically electron interference in a Mach–Zehnder-like geometry formed by four zigzag graphene nanoribbons (ZGNRs) arranged in parallel pairs, one on top of the other, such that they form intersection angles of 60˚ Depending on the interribbon separation, each intersection can be tuned to act either as an electron beam splitter or as a mirror, enabling tuneable circuitry with interfering pathways. Based on the mean-field Hubbard model and Green's function techniques, we evaluate the electron transport properties of such 8-terminal devices and identify pairs of terminals that are subject to self-interference. We further show that the scattering matrix formalism in the approximation of independent scattering at the four individual junctions provides accurate results as compared with the Green's function description, allowing for a simple interpretation of the interference process between two dominant pathways. This enables us to characterize the device sensitivity to phase shifts from an external magnetic flux according to the Aharonov–Bohm effect as well as from small geometric variations in the two path lengths. The proposed devices could find applications as magnetic field sensors and as detectors of phase shifts induced by local scatterers on the different segments, such as adsorbates, impurities or defects. The setup could also be used to create and study quantum entanglement.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.6084/m9.figshare.13566101.v1
title: Additional file 3 of Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness

description: Additional file 3.
DOI: 10.6084/m9.figshare.21069392.v1
title: Additional file 3 of Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L

description: Additional file 3: Table S3. Distribution of repeat sequences in the 14 studied Ferula plastomes.
DOI: 10.5281/zenodo.7994060
title: Hyperfine interactions in open-shell planar sp2-carbon nanostructures

description: ORCA data files for the publication:

S. Sengupta, T. Frederiksen, and G. GiedkeHyperfine interactions in open-shell planar sp2-carbon nanostructuresPhys. Rev. B 107, 224433 (2023) [arXiv:2303.11422]

We investigate hyperfine interaction (HFI) using density-functional theory for several open-shell planar sp2-carbon nanostructures displaying π magnetism. Our prototype structures include both benzenoid ([n]triangulenes and a graphene nanoribbon) as well as nonbenzenoid (indene, fluorene, and indene[2,1-b]fluorene) molecules. Our results obtained with orca indicate that isotropic Fermi contact and anisotropic dipolar terms contribute in comparable strength, rendering the HFI markedly anisotropic. We find that the magnitude of HFI in these molecules can reach more than 100 MHz, thereby opening up the possibility of experimental detection via methods such as electron spin resonance-scanning tunneling microscopy (ESR-STM). Using these results, we obtain empirical models based on π-spin polarizations at carbon sites. These are defined by generic sp2 HFI fit parameters which are derived by matching the computed HFI couplings to π-spin polarizations computed with methods such as Orca, Siesta, or mean-field Hubbard (MFH) models. This approach successfully describes the Fermi contact and dipolar contributions for 13C and 1H nuclei. These fit parameters allow to obtain hyperfine tensors for large systems where existing methodology is not suitable or computationally too expensive. As an example, we show how HFI scales with system size in [n]triangulenes for large n using MFH. We also discuss some implications of HFI for electron-spin decoherence and for coherent nuclear dynamics.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.5281/zenodo.7994061
title: Hyperfine interactions in open-shell planar sp2-carbon nanostructures

description: ORCA data files for the publication:

S. Sengupta, T. Frederiksen, and G. GiedkeHyperfine interactions in open-shell planar sp2-carbon nanostructuresPhys. Rev. B 107, 224433 (2023) [arXiv:2303.11422]

We investigate hyperfine interaction (HFI) using density-functional theory for several open-shell planar sp2-carbon nanostructures displaying π magnetism. Our prototype structures include both benzenoid ([n]triangulenes and a graphene nanoribbon) as well as nonbenzenoid (indene, fluorene, and indene[2,1-b]fluorene) molecules. Our results obtained with orca indicate that isotropic Fermi contact and anisotropic dipolar terms contribute in comparable strength, rendering the HFI markedly anisotropic. We find that the magnitude of HFI in these molecules can reach more than 100 MHz, thereby opening up the possibility of experimental detection via methods such as electron spin resonance-scanning tunneling microscopy (ESR-STM). Using these results, we obtain empirical models based on π-spin polarizations at carbon sites. These are defined by generic sp2 HFI fit parameters which are derived by matching the computed HFI couplings to π-spin polarizations computed with methods such as Orca, Siesta, or mean-field Hubbard (MFH) models. This approach successfully describes the Fermi contact and dipolar contributions for 13C and 1H nuclei. These fit parameters allow to obtain hyperfine tensors for large systems where existing methodology is not suitable or computationally too expensive. As an example, we show how HFI scales with system size in [n]triangulenes for large n using MFH. We also discuss some implications of HFI for electron-spin decoherence and for coherent nuclear dynamics.
description: We acknowledge funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 863098 (FET-Open project "SPRING")
DOI: 10.6084/m9.figshare.14253638
title: Additional file 1 of A network pharmacology-based investigation on the bioactive ingredients and molecular mechanisms of Gelsemium elegans Benth against colorectal cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.21069680.v1
title: Additional file 3 of THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

description: Additional file 2. The different expression gene set of GIST-T1 cells after THZ1 treatment by RNA-sequencing analysis.
DOI: 10.6084/m9.figshare.21069660
title: Additional file 2 of Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

description: Additional file 2: Table S1. Patient information.
DOI: 10.6084/m9.figshare.21069680
title: Additional file 3 of THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

description: Additional file 2. The different expression gene set of GIST-T1 cells after THZ1 treatment by RNA-sequencing analysis.
DOI: 10.6084/m9.figshare.14253456
title: Additional file 2 of Women’s cancers in China: a spatio-temporal epidemiology analysis

description: Additional file 2: Table S2. The incidence and mortality of breast, cervical and ovarian cancer in each provincial unit from 2010 to 2015 (unit:1/100,000).
DOI: 10.5519/qd.yjejvchd
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4993245 records)
DOI: 10.6084/m9.figshare.14253459.v1
title: Additional file 3 of Women’s cancers in China: a spatio-temporal epidemiology analysis

description: Additional file 3: Table S3. The number of cases and deaths of breast, cervical and ovarian cancer in each provincial unit from 2010 to 2015.
DOI: 10.6084/m9.figshare.21069666.v1
title: Additional file 4 of Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

description: Additional file 4: Table S2. Top 100 marker genes of fibroblast, T cell, monocytes and blood vessel endothelium.
DOI: 10.5281/zenodo.10637044
title: CLINICAL CASE OF SECONDARY ANTIPHOSPHOLIPID SYNDROME IN A NEPHROLOGICAL PATIENT
DOI: 10.5281/zenodo.10637045
title: CLINICAL CASE OF SECONDARY ANTIPHOSPHOLIPID SYNDROME IN A NEPHROLOGICAL PATIENT
DOI: 10.6084/m9.figshare.23691114.v1
title: Additional file 1 of Independent flavonoid and anthocyanin biosynthesis in the flesh of a red-fleshed table grape revealed by metabolome and transcriptome co-analysis

description: Supplementary Material 1: Table S1: Primer sequences for genes used in assays in this study. Table S2: List of metabolites detected and quantified in the skin and flesh of ‘Mio Red’ grape. Table S3: List of metabolites differentially accumulated in the skin and flesh of ‘Mio red’ grape. Table S4: Relative contents of the 6 anthocyanin derivatives identified in the skin and flesh of ‘Mio Red’ grape. Table S5: Quality check of the raw data from the RNA-seq. Table S6: Overview of transcriptome sequencing dataset and mapping statistics of ‘Mio Red’ grape. Table S7: Expression profile (FPKM values) of the 23,786 genes detected in the skin and flesh of ‘Mio Red’ grape. Table S8: Identification of structural genes in flavonoid-biosynthesis pathway of ‘Mio Red’ grape. Table S9: GenBank accession numbers of the transcription factors in the phylogenetic tree analysis.
DOI: 10.34943/0b381b7b-cca5-4258-812a-42be38f09e64
title: Burrard Inlet Hydrophone Deployed 2023-07-25

description: The Ocean Sonics icListen HF Hydrophone 1354 was deployed on 2023-07-25 at Burrard Inlet. Burrard Inlet is a coastal fjord in southwestern British Columbia. This device is a Hydrophone. Hydrophones are devices containing transducers that convert underwater sound waves into electrical signals. They are acoustic instruments that can process data while they are being collected to produce calibrated waveform data. Hydrophones are typically used to study vocalizations of marine mammals, ship traffic and ambient noise. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6084/m9.figshare.21069663.v1
title: Additional file 3 of Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

description: Additional file 3: Table S2. Cell numbers and percentages of each major cell type.
DOI: 10.6084/m9.figshare.21069669
title: Additional file 5 of Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

description: Additional file 5: Table S4. IHC staining results of SFRP4 and DCN.
DOI: 10.6084/m9.figshare.23691217
title: Additional file 1 of Lung cancer-derived exosomal miR-132-3p contributed to interstitial lung disease development

description: Additional file 1. Supplementary figures and information.
DOI: 10.6084/m9.figshare.21069669.v1
title: Additional file 5 of Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

description: Additional file 5: Table S4. IHC staining results of SFRP4 and DCN.
DOI: 10.5281/zenodo.8261814
title: Energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces

description: Computational dataset for our research papers on energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces:

N. Okabayashi, T. Frederiksen, A. Liebig, and F. J. GiessiblDynamic friction unraveled by observing an unexpected intermediate state in controlled molecular manipulationPhys. Rev. Lett. 131, 148001 (2023)

N. Okabayashi, T. Frederiksen, A. Liebig, and F. J. GiessiblEnergy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfacesPhys. Rev. B 108, 165401 (2023)
DOI: 10.5281/zenodo.8250811
title: Energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces

description: Computational dataset for our research papers on energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces:

N. Okabayashi, T. Frederiksen, A. Liebig, and F. J. GiessiblDynamic friction unraveled by observing an unexpected intermediate state in controlled molecular manipulationPhys. Rev. Lett. 131, 148001 (2023)

N. Okabayashi, T. Frederiksen, A. Liebig, and F. J. GiessiblEnergy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfacesPhys. Rev. B 108, 165401 (2023)
DOI: 10.5281/zenodo.8250812
title: Energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces

description: Computational dataset for our research papers on energy dissipation of a carbon monoxide molecule manipulated using a metallic tip on copper surfaces.
DOI: 10.6084/m9.figshare.20545693
title: Additional file 1 of Effect of AKT silence on malignant biological behavior of renal cell carcinoma cells

description: Additional file 1. Data and analysis of this study.
DOI: 10.6084/m9.figshare.21594113.v1
title: Additional file 3 of Exploring the pharmacological mechanism of Shengjing capsule on male infertility by a network pharmacology approach

description: Additional file 3:
DOI: 10.5281/zenodo.5639643
title: Simulated responses of big sagebrush ecosystems to increased precipitation intensity in the western United States

description: Simulated responses of big sagebrush ecosystems to increased precipitation intensity. Here we use an individual plant-based ecohydrological model (STEPWAT2) to simulate water cycling and shrub, grass, and forb growth for 200 sites across the western United States, and test the effects of simulations conducted with 25%, 50% and 100% increases in precipitation event sizes without changing annual precipitation amounts. Simulations were also performed for 3 °C and 5 °C warming, and four soil textures. The files included in this repository are summarized output from model simulations. The include mean biomass responses for each sites (and treatment combination). Additionally, for each site and treatment values of numerous ecohydrological values are provided (e.g. transpiration, drainage, evaporation). Where relevant these include values for each of 8 soil layers. In the case of transpiration, values for are also provided for each plant functional type. 


Analyses using these data show that: Precipitation intensification generally increased shrub growth in arid and semi-arid sites, but not mesic sites, by decreasing evaporation and ‘pushing’ water deeper into the soil. This effect partially counteracted the mostly negative effects of warming on shrub growth. In contrast, forbs and grasses did not exhibit consistent responses to precipitation intensification. Overall precipitation intensification provided a competitive advantage to shrub growth under a wide range of aridity, soil textures, and temperatures and can be expected to contribute to the woody plant encroachment that has been observed around the world in the past 50 years.