cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/mj5xs54nbh.1
title: Crystallization and refluidization in very-narrow fluidized beds

description: These files contain an example of processing and post-processing of experimental image results. The processing and post-processing are carried out using image processing techniques. The macroscopic and microscopic measurements can be obtained by executing the provided MATLAB scripts. The parameter indicating crystallization can be obtained by running the 'phi_float' folder in Fortran90. The dataset contains segmented frames of each mono and bidisperse experiment, along with the scripts required to obtain them and calculate the macroscopic crystallization indicator. To perform these tasks, please follow the steps below. We also provide spatiotemporal diagrams of selected experiments, a summary of metric data from all the experiments, and videos showcasing samples of each type of bed.
DOI: 10.17632/scnp36wvgr.1
title: Cryo-electron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination

description: Fig. 1 A
Agarose gel shows DNA of native chromatin isolated from K562 cells and fractionated by ultracentrifugation of sucrose gradients (lanes 1-13), DNA size markers (lane 14 (M)), and total soluble chromatin (lane S2). 

Fig. 1 C
DNP agarose gel showing native electrophoresis of the K562 chromatin crosslinked by glutaraldehyde at the indicated concentration of Mg2+ (lanes 2 – 8). Lane 1 (M): DNA size markers.

Fig. 1 D (0 mM)
TEM of the K562 chromatin crosslinked by glutaraldehyde at 0 mM Mg2+
Fig. 1
D (0.75 mM)
TEM of the K562 chromatin crosslinked by glutaraldehyde at 0.75 mM Mg2+ 

Fig. 1 D (1.25 mM)
TEM of the K562 chromatin crosslinked by glutaraldehyde at 1.25 mM Mg2+. 

Fig. 1 D (2.0 mM)
TEM of the K562 chromatin crosslinked by glutaraldehyde at 2.0 mM Mg2+. 

Fig. 5 A (1-4)
18% SDS-PAGE gel stained by Coomassie R250 shows histones of control (lanes 1) and PAD4-treated (lanes 2, 3) nucleosome arrays from K562 cells. Lane 4: molecular mass markers. 

Fig. 5 A (5-7)
SDS-PAGE and Western blotting of histones from control (lane 5) and PAD4-treated (lanes 2, 3) nucleosome arrays detected by antibodies against histone H3 citrullinated at Arginine 2, 8, and 17

Fig. 5 A (8-9)
Triton-Acetate-Urea gel stained by Coomassie R250 shows histones extracted from control (lane 8) and PAD4-treated (lanes 9) nucleosome arrays from K562 cells.

Fig. 5 B
DNP agarose gel showing DNA size markers (lane 1) and native electrophoresis of the control (lanes 2-8) and PAD4-treated (lanes 9-15) nucleosome arrays from K562 cells.

Fig. 6 A (1-5)
18% SDS-PAGE gel stained by Coomassie R250 shows histones of control (lanes 1, 3) and PAD4-treated (lanes 2, 4) reconstituted nucleosome core arrays. M – m.w. markers (lane 5). 

Fig. 6 A (6-10)
Lanes 6-10: 18% SDS-PAGE gel stained by Coomassie R250 shows histones of control (lanes 7, 9) and PAD4-treated (lanes 8, 10) reconstituted nucleosome arrays additionally reconstituted with linker histone H1o after PAD4 treatment. 

Fig. 6 B (1-3)
DNP agarose gels showing DNA size markers (lane 1) and native electrophoresis of the control (lane 2) and PAD4-treated (lanes 3) reconstituted nucleosome core arrays crosslinked with glutaraldehyde at 1 mM Mg2+

Fig. 6 B (4-10)
DNP agarose gels showing DNA size markers (lane 4) and control (lanes 5, 7, 9) and PAD4-treated (lanes 6, 8, 10) reconstituted 183x12+H1 arrays after PAD4 treatment crosslinked at 0 to 1 mM Mg2+ as indicated.

Supp. Fig. S1 A
18% SDS-PAGE gel stained by Coomassie R250 shows molecular mass markers (1) and histones of K562 fraction #10 chromatin incubated at the indicated concentration of Mg2+ together with 10 nm fiduciary gold particles for 48 hrs. at +4oC (2 – 9). 

Supp. Fig. S3 A
Lanes 1-6 (S3 A) correspond to lanes 5-11: DNA size markers (lanes 5, 7, 9, 11), DNA of native MNase-digested chromatin isolated from K562 cells (6), HeLa cells (8) and PN21 mouse retina cells (10).
DOI: 10.17632/m2jny6sns3.1
title: LINF_210012800

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/z92nw4n73t.1
title: A simultaneous EEG-fNIRS dataset of the visual cognitive motivation study in healthy adults

description: Motivation has various positive influences on human activity and has been the topic of interest in the educational psychology field. To gain an in-depth understanding and insights into motivation, we must learn from the related brain activity during motivation events. Brain activity signals can be acquired with various methods. Each modality has its own strengths and weaknesses. We simultaneously measured Electroencephalogram (EEG) and functional near-infrared spectroscopy (fNIRS) at shared locations. Using simultaneous EEG (high temporal resolution but low spatial resolution) and fNIRS (high spatial resolution but relatively low temporal resolution compared to EEG), we can obtain both electrophysiological and hemodynamical brain activity data with high temporal and spatial resolution at the same time and locations. Hence, the motivation can be studied in a more complete picture than either of the individual modalities can offer. This dataset includes the simultaneous EEG-fNIRS data of 16 healthy participants measured while performing the cognitive motivation task. The cognitive motivation task is separated into two parts: attention and decision. Each visual stimulus, which is a randomly selected indoor/outdoor scene, was shown to the participant for 3 seconds during the attention period and then disappeared. The participants are required to decide whether or not they want to remember the scene stimulus they have seen within 9 seconds. There was no constraint or influence on their decisions. The EEG-fNIRS data were acquired during this whole cognitive experiment for 250 scene stimuli of each participant. The effect of their motivation was confirmed by the recognition test; the participants were tested with 500 mixed stimuli between 250 previously seen stimuli in the cognitive experiment and the new additional stimuli to test whether they could recognize the scene in the cognitive experiment or not. This dataset provides an opportunity for understanding and analyzing the process of attention and decision during the motivated brain state as well as the motivation and its effect on the recognition result afterward.
DOI: 10.17632/syyhczyn8n.1
title: LINF_210013300

description: Nucleolar protein 91 | NOP91; Leishmania infantum (strain JPCM5)
DOI: 10.17632/2sbbjm382b.1
title: LINF_210013400

description: proteasome regulatory non-ATP-ase subunit 5 | RPN5; Leishmania infantum (strain JPCM5)
DOI: 10.17632/hn223z96jy.1
title: LINF_210012900

description: hypothetical protein - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.pe2ruu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "ScientificName" : [
 "is one of (Barbastella barbastellus, Eptesicus isabellinus, Eptesicus serotinus, Hypsugo savii, Miniopterus schreibersii, Myotis alcathoe, Myotis bechsteinii, Myotis blythii, Myotis capaccinii, Myotis daubentonii, Myotis emarginatus, Myotis myotis, Myotis mystacinus, Myotis nattereri, Nyctalus lasiopterus, Nyctalus leisleri, Nyctalus noctula, Pipistrellus kuhlii, Pipistrellus maderensis, Pipistrellus nathusii, Pipistrellus pipistrellus, Pipistrellus pygmaeus, Plecotus auritus, Plecotus austriacus, Plecotus macrobullaris, Plecotus teneriffae, Rhinolophus euryale, Rhinolophus ferrumequinum, Rhinolophus hipposideros, Rhinolophus mehelyi, Tadarida teniotis)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004239-250117142028555/datasets/export for details.
DOI: 10.17632/bd958y27yb.1
title: Mendaley data for "Phase separation mediated transcriptional activity of FOXK1 triggers glycolysis and facilitates renal fibrosis"

description: Metabolic reprogram featured with enhanced glycolysis in tubular cells facilitates the renal fibrosis, but the mechanism underlying this dysregulation remain elusive. Forkhead box protein K1 (FOXK1), serving as a transcriptional factor involved in the regulation of cell energy metabolism, was recently reported by us a core regulator on EMT process in the context of kidney fibrosis. It arose the speculation that FOXK1 participates in reshaping the metabolic landscape of TECs along with kidney fibrosis progression. In this study, an expression pattern of fibrosis associated FOXK1 induction and upregulation in TECs was observed in fibrotic kidneys from either CKD patients or animal model. Meanwhile, pro-fibrotic stimulus triggered FOXK1 expression and nuclear translocation in cultured HK-2 cells. Genetic modification of FOXK1 expression in TECs in vivo or in vitro resulted in remarkable alteration of glycolytic metabolism and fibrotic effects. A set of glycolysis-related genes, including Ldha, were then identified as the direct targets of FOXK1 in the TECs by chromatin immunoprecipitation analysis. Mechanistically, Nuclear translocated FOXK1 bound to the target motif of the glycolysis-related genes to promote transcription through a mechanism of liquid-liquid phase separation. The core intrinsically disordered regions (IDRs) of FOXK1 responsible for phase separation formation were identified. We also found that RNA Pol II was incorporated into the condensates initiated by FOXK1 to spark the target gene transcription. Collectively, our findings revealed a novel role of FOXK1 in driving kidney fibrosis through bolstering glycolysis transition in tubular cells and shed light in exploring potential therapeutic target for renal fibrosis.
DOI: 10.17632/rwznmmbxzz.1
title: Guo et al. A modified laser ablation-isotope ratio mass spectrometry method for in situ analysis of sulfur isotope composition of sulfides

description: data from Guo et al. RCM 2024 entitled "A modified laser ablation-isotope ratio mass spectrometry method for in situ analysis of sulfur isotope composition of sulfides".
DOI: 10.17632/75h5d7mv4d.2
title: Visible Light-Responsive Antibacterial Packaging Films for Improving Food Quality and Safety

description: We developed a novel visible-light-responsive packaging film that can generate reactive oxygen species (ROS) that can inactivate bacteria. Our data shows that the material can inactive both gram-positive and gram-negative bacteria under various light intensities effectively, The quantification data also shows the sensitized TiO2 can generate ROS more effectively than the dye sensitizer and TiO2 alone.
DOI: 10.17632/bxyt9sc29n.1
title: Sun et al. 2024_Oxygen isotope anomalies (Δ17O) in nitrate formed during ultraviolet photochemical reaction in low-oxygen atmosphere an experimental study

description: data from Sun et al. 2024 submitted to GCA entitled "Oxygen isotope anomalies (Δ17O) in nitrate formed during ultraviolet photochemical reaction in low-oxygen atmosphere: an experimental study"
DOI: 10.17632/svr45t2xtj.1
title: Sedimentological and geochronological data for the fan deltaic Nemčiňany Formation, Upper Miocene, Danube Basin (Slovakia)

description: This dataset supports the stratigraphic, sedimentological and cosmogenic nuclide geochronological study of the sandy-gravelly deposits of fan deltaic origin, which were deposited during ca. 11.6-9.4 Ma in the eastern margin of the Danube Basin, which is the northernmost depocenter of the Pannonian Basin System (Central Europe). The study was focused on verification of the stratigraphic position of this formation, of the depositional processes and duration of the deposition. The dataset includes a detailed description of laboratory sample processing for the authigenic 10Be/9Be dating, which allows the reproducibility of the analyzes. Furthermore, the dataset contains a list of archival boreholes used for correlation in geological sections, including the information necessary to access the original manuscripts in a digital archive. The analyzed outcrops are characterized in this dataset by digital elevation model maps using Lidar data. A generalized log of facies distribution is provided for the Nemčiňany site, together with a sedimentological scheme and a photopanel showing sampling points for dating. The sedimentological and paleogeographic interpretations are included in the related paper Šujan et al. (2023) Geologica Carpathica, https://doi.org/10.31577/GeolCarp.2023.25
DOI: 10.17632/y684wpsz8s.1
title: Data for "Study on intrinsic point defects of MnCO3-doped ZnO ceramics based on first principles"

description: The dataset comprises the computed results of formation energy, ZnO lattice structure, energy band characteristics, and electron state density distribution. Zinc interstitials and oxygen vacancies are identified as the primary intrinsic point defects influencing the electrical properties of ZnO varistor ceramics. The data demonstrates that Mn2+ substitution doping can effectively modulate the occurrence of zinc interstitials and oxygen vacancies among intrinsic defects. These findings are consistent with experimental results and enhanced insights into material behavior that MnCO3-doped ZnO ceramics electrical properties is improved.
DOI: 10.17632/ndtxpb3vmg.1
title: Source code for smartphone-enabled digital CRISPR device

description: Source code for smartphone-enabled digital CRISPR device:
1. Source code of the smartphone app (developed by MIT App Inventor 2)
2. Source code of the TinyPICO ESP32 microcontroller (developed by Arduino IDE)
DOI: 10.17632/c36ywkzrm9.1
title: Improving the annotation process in computational pathology: from manual to semi-automatic approaches in digital nephropathology

description: The development of reliable artificial intelligence (AI) algorithms in pathology depends on solid ground truth provided by meticulous annotation of whole slide images (WSI), a time-consuming and operator-dependent process. A benchmark of the available annotation tools is performed to standardize and streamline this process.
DOI: 10.17632/9hywbzt8zd.1
title: Data for: Structural Dynamics, Phonon Spectra and Thermal Transport in the Silicon Clathrates

description: This repository provides additional data to accompany the paper:

"Structural Dynamics, Phonon Spectra and Thermal Transport in the Silicon Clathrates"

B. Wei, J. M. Flircroft and J. M. Skelton
Molecules 27 (19), 6431 (2022), DOI: 10.3390/molecules27196431

This article examines the structural dynamics, phonon spectra and thermal transport of bulk diamond Si and five Si clathrate framework structures. This repository makes available a full set of data from these calculations, including:

* Optimised structures;
* Phonon calculations;
* Simulated infrared (IR) and Raman spectra; and
* Thermal conductivity calculations performed within the single-mode relaxation-time approximation.

The repository also contains sample input files for the Vienna Ab initio Simulation Package (VASP) code.

For details of how this data was generated, users are referred to the published article and supporting information. Brief details of file formats and links to further documentation are given in the included README file.
DOI: 10.17632/cm5gty9x59.1
title: LDHU3_02.0130

description: Hypothetical protein - conserved; Leishmania donovani (HU3 strain)
DOI: 10.17632/4w3gb83rcr.3
title: Spatiotemporal evolution of aeolian sedimentary landscapes in the southern Tibetan Plateau during the late Quaternary

description: This dataset includes chronological data from 38 aeolian sections for probability density function analysis, geochemical data from 48 different loose sediments for fingerprinting analysis, map data depicting the distribution of aeolian sand and loess, and detrital zircon U-Pb ages of 2 fluval samples and 2 loess samples in the southern Tibetan Plateau.
DOI: 10.17632/svr45t2xtj.2
title: Sedimentological and geochronological data for the fan deltaic Nemčiňany Formation, Upper Miocene, Danube Basin (Slovakia)

description: This dataset supports the stratigraphic, sedimentological and cosmogenic nuclide geochronological study of the sandy-gravelly deposits of fan deltaic origin, which were deposited during ca. 11.6-9.4 Ma in the eastern margin of the Danube Basin, which is the northernmost depocenter of the Pannonian Basin System (Central Europe). The study was focused on verification of the stratigraphic position of this formation, of the depositional processes and duration of the deposition. The dataset includes a detailed description of laboratory sample processing for the authigenic 10Be/9Be dating, which allows the reproducibility of the analyzes. Furthermore, the dataset contains a list of archival boreholes used for correlation in geological sections, including the information necessary to access the original manuscripts in a digital archive. The analyzed outcrops are characterized in this dataset by digital elevation model maps using Lidar data. A generalized log of facies distribution is provided for the Nemčiňany site, together with a sedimentological scheme and a photopanel showing sampling points for dating. The sedimentological and paleogeographic interpretations are included in the related paper Šujan et al. (2023) Geologica Carpathica, https://doi.org/10.31577/GeolCarp.2023.25
DOI: 10.17632/2356m76ktj.1
title: Friction coefficient data of open-cell AlSi10Mg and AlSi10Mg-Al2O3 materials with different pore sizes by pin-on-disk test and machine learning prediction

description: The data folders and files are organized in the repository as follows:

Pin-on-disk_data folder contains three subfolders (Raw_files; Processed_files; COF_calculation).
The Raw_files subfolder contains 12 DWF files with the raw data for each specimen.
The Processed_files subfolder contains 12 XLSX files with the processed data for each specimen.
The COF_calculation subfolder contains eight XLSX files with the average COF and time data for each material, two PNG files with the plots of the average COF vs time for each material pair, and one python script for calculating and visualizing the average COF and time data.
Prediction folder contains three subfolders (Input_files; Output_data; Python_COF_prediction).
The Input_files subfolder contains four XLSX files with the input data for the python script to make the predictions of COF vs sliding time for each material.
The Output_data subfolder contains eight XLSX files with the actual and predicted values of COF for two different sets (test and validation) of each material, four TXT files with the performance metrics of the predicted COF for each material, and four PNG files with the plots of the actual vs predicted COF as a function of time for each material.
The Python_COF_prediction subfolder contains one python script for making and evaluating the predictions of COF vs sliding time using a XGBoost model.

The data were collected by performing dry wear tests at room temperature with linear velocity 0.5 m∙s−1, load 50 N and sliding time of 420 s. The labels of the specimen indicate the following:

• AC_3_2, AC_3_3, AC_3_4, are three datasets used for pin-on-disk tests conducted with open-cell AlSi10Mg-Al2O3 composite with pore size of 800 ÷ 1000 μm (AC);
• C_5_1, C_5_2, C_5_3, are three datasets used for pin-on-disk tests conducted with open-cell AlSi10Mg material with pore size of 800 ÷ 1000 μm (C);
• AE_3_2, AE _4_1, AE _6_6, are three datasets used for pin-on-disk tests conducted with open-cell AlSi10Mg- Al2O3 composite with pore size of 1000 ÷ 1200 μm (AE);
• E_3_1, E _6, E _6_3, are three datasets used for pin-on-disk tests conducted with open-cell AlSi10Mg material with pore size of 1000 ÷ 1200 μm (E).
DOI: 10.17632/w3943fx6c6.1
title: Data for: Methane concentration and bacterial communities’ dynamics during the anoxic desulfurization of landfill biogas under diverse nitrate sources and hydraulic residence times

description: This dataset supports the article "González-Cortés, J. J., Quijano, G., Ramírez, M., & Cantero, D. (2023). Methane concentration and bacterial communities’ dynamics during the anoxic desulfurization of landfill biogas under diverse nitrate sources and hydraulic residence times. Journal of Environmental Chemical Engineering, 11(2), 109285."
DOI: 10.17632/xn63xpnkbx.5
title: Characterisation data for sediments collected from Peel Place Quarry, Cumbria, UK – A Sellafield nuclear site analogue

description: The data contained in this repository describes biogeochemical and physicochemical characterisation data in samples collected from adjacent to the United Kingdom’s Sellafield Nuclear Site. It includes particle size distribution and textural classification, pH measurements, water and organic carbon content (loss on ignition), BET surface area, bioavailability of iron, cation exchange, permeability measurements, X-ray analysis for phase (X-ray diffraction, XRD) and element (X-ray fluorescence, XRF) identification, ion chromatography, thin sectioning and 16S Ribosomal (rRNA) gene analysis.
DOI: 10.17632/yyn3j5vg5d.1
title: Acoustic velocities natural aragonites

description: Acoustic velocity data of three natural aragonite samples measured by Brillouin spectroscopy at the Brillouin laboratory at GFZ, Potsdam. Sample Arag-T has 0.1mol% Sr, Arag-NT 0.3mol% Sr and Arag-S contains 1.5mol% Sr. This dataset is related to the manuscript 'Elasticity of natural aragonite samples by Brillouin spectroscopy' by Pennacchioni L., Speziale S., Winkler B.
DOI: 10.17632/gnmm8zcj25.1
title: High-dimensional profiling of pediatric immune responses to solid organ transplantation

description: CyTOF data from pediatric solid organ transplant recipients with either stable graft function or within 30 days of experiencing a rejection episode
DOI: 10.17632/hs7d7kpd3z.1
title: Crop and weed dataset

description: Weed and crop images from green house.
DOI: 10.17632/hs7d7kpd3z.2
title: A Novel Automated Cloud-Based Image Datasets for High Throughput Phenotyping in Weed Identification.

description: A greenhouse-based automatic data acquisition system generated a dataset encompassing six weed species and eight crop varieties. The dataset has been made publicly accessible to facilitate advancements in weed and crop detection research utilizing computer vision and AI techniques.
DOI: 10.17632/hs7d7kpd3z.3
title: A Novel Automated Cloud-Based Image Datasets for High Throughput Phenotyping in Weed Identification.

description: A greenhouse-based automatic data acquisition system generated a dataset encompassing six weed species and eight crop varieties. The dataset has been made publicly accessible to facilitate advancements in weed and crop detection research utilizing computer vision and AI techniques. 

If you want to used this data please cite our paper G C, S., Koparan, C., Upadhyay, A., Ahmed, M. R., Zhang, Y., Howatt, K., and Sun, X. (2024). A Novel Automated Cloud-Based Image Datasets for High Throughput Phenotyping in Weed Classification. Data in Brief .