cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4307883
title: The Buzsaki Lab Databank - Public electrophysiological datasets from awake animals

description: The Buzsaki Lab is proud to present a large selection of experimental data available for public access: https://buzsakilab.com/wp/database/. We publicly share more than a thousand sessions (about 40TB of raw and spike- and LFP-processed data) via our public data repository. The datasets are from freely moving rodents and include sleep-task-sleep sessions (3 to 24 hrs continuous recording sessions) in various brain structures, including metadata. We are happy to assist you in using the data. Our goal is that by sharing these data, other users can provide new insights, extend, contradict, or clarify our conclusions. The databank contains electrophysiological recordings performed in freely moving rats and mice collected by investigators in the Buzsaki Lab over several years (a subset from head-fixed mice). Sessions have been collected with extracellular electrodes using high-channel-count silicon probes, with spike sorted single units, and intracellular and juxtacellular combined with extracellular electrodes. Several sessions include physiologically and optogenetically identified units. The sessions have been collected from various brain region pairs: the hippocampus, thalamus, amygdala, post-subiculum, septal region, and the entorhinal cortex, and various neocortical regions. In most behavioral tasks, the animals performed spatial behaviors (linear mazes and open fields), preceded and followed by long sleep sessions. Brain state classification is provided. <strong>Getting started</strong> The top menu “Databank” serves as a navigational menu to the databank. The metadata describing the experiments is stored in a relational database which means that there are many entry points for exploring the data. The databank is organized by projects, animal subjects, and sessions. <strong>Accessing and downloading the datasets</strong> We share the data through two services: our public Globus.org endpoint and our webshare: buzsakilab.nyumc.org. A subset of the datasets is also available at CRCNS.org. If you have an interest in a dataset that is not listed or is lacking information, please contact us. We pledge to make our data available immediately after publication. <strong>Support</strong> For support, please use our Buzsaki Databank google group. If you have an interest in a dataset that is not listed or is lacking information, please send us a request. Feel free to contact us, if you need more details on a given dataset or if a dataset is missing.
DOI: 10.5281/zenodo.7838397
title: Rat gadoxetate MRI signal dataset for the IMI-WP2-TRISTAN Reproducibility study

description: Dataset to accompany the manuscript "Assessment of hepatic transporter function in rats using dynamic gadoxetate-enhanced MRI: A reproducibility study" by Ebony R. Gunwhy, Catherine D. G. Hines, Claudia Green, Iina Laitinen, Sirisha Tadimalla, Paul D. Hockings, Gunnar Schütz, J. Gerry Kenna, Steven Sourbron, and John C. Waterton  (referred to as the 'Reproducibility' study).

data.zip

After extracting the contents within the data.zip folder, the MRI signal data acquired in this study are provided in csv format and can be found inside the data/Reproducibility/01_signals subfolder. Each csv file contains the liver and spleen region of interest (ROI) time curve data for a single rat from a specific substudy and day, after administration of the test compound of interest.

The corresponding filename for each file is formatted as a string containing study descriptors (metadata) separated by underscores, i.e., filename = substudy_compound_site_RatNumber_dayNumber_dataType, e.g., 1_Rifampicin_D_Rat5_2_Signals.

results.zip

The results and figures relating to this manuscript were created using the outputs contained in results/Reproducibility/2023-04-17.

01_model_ouputs contains all outputs generated as a result of the tracer kinetic model fitting. Within this, plotted signal time curves for each acquistion per rat may be found in figures/per_rat, while average deltaR1 curves per substudy may be found in figures/per_substudy. All estimated parameter variables from the fitting are stored in all_parameters.csv. The folder relaxation_rates_and_signals contains the fitted MRI signal data in a similar format to the original csv data in data/01_signals. Additional columns have been included showing the MRI signals converted to R1. fit_errors.txt contains an ID list for any computational fitting errors found during quality control of the tracer kinetic modelling.

02_analyses contains results of the statistical analysis performed on the tracer kinetic modelling output. These are summarised in tabular csv format within the repeatability/ and reproducibility/ folders, while graphical distributions are provided within the figures/ folder. Summary results for benchmark values and from the mixed ANOVA are also provided in benchmarks.csv and mixed_anova.csv, respectively. Please see the manuscript for further details on these results.
DOI: 10.5281/zenodo.7931444
title: CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning

description: CREMP: A resource generated for the rapid development and evaluation of machine learning models for macrocyclic peptides. CREMP contains 36,198 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this dataset contains nearly 31.3 million unique macrocycle geometries, each annotated with energies derived from semi-empirical tight-binding DFT calculations. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics.

We provide the data in two available formats, either as Python pickle files, which provide quick read access with RDKit version 2022.09.5 or later, and as text-based SDF files with associated metadata in JSON format. Each file is named based on its amino acid sequence, with residues separated by periods, using standard one-letter codes with lowercase letters representing D-amino acids and "Me" prefixes representing N-methylated amino acids. The sequences are in no particular order, e.g., "C.R.E.M.P" and "R.E.M.P.C" correspond to the same peptide macrocycle. The filename extensions are ".pickle", ".sdf", and ".json".

Each file in the “pickle” folder contains a Python dictionary with amino acid sequence, SMILES, CREST metadata, and a single RDKit molecule object containing all conformers. All files in the folder were compressed into a single “pickle.tar.gz” archive. In the “sdf_and_json” folder, each individual SDF file contains all conformers, each associated with its own JSON file that contains CREST metadata. Similarly, all are compressed into another single archive, “sdf_and_json.tar.bz2”. A single summary CSV file is also provided containing ”sequence”, “smiles”, “num_monomers”, “num_atoms”, “num_heavy_atoms”, along with the CREST metadata “totalconfs”, “uniqueconfs”, “lowestenergy”, “poplowestpct”, “temperature”, “ensembleenergy”, “ensembleentropy”, and “ensemblefreeenergy”. The number of unique conformers with different 3D structures is given by “uniqueconfs”, while “totalconfs” includes the number of rotamers in addition.

The unzipped sizes of the archives are approximately 32 GB for "pickle.tar.gz" and 210 GB for "sdf_and_json.tar.bz2". If you encounter errors when trying to load the pickle files, please make sure your RDKit version is at least 2022.09.5. If that doesn't work, try other Python versions.
description: This version fixes the corrupted pickle.tar.gz file.
DOI: 10.5281/zenodo.8013531
title: SMILE GaN microLED Comsol simulation models

description: Comsol models with results and Matlab postprocessing scripts for ray tracing simulation of GaN-based micro-LED arrays. These models have been developed in H2020 Project SMILE, grant no. 952135. The zip archive contains the following files: <strong>refined_model_phi.mph</strong>: parameterized micro-LED array model, including results, without micro-lenses, with or without sapphire substrate <strong>in_GaN_ulenses.mph</strong>: parameterized micro-LED array model, including results, with GaN micro-lenses, using a single dipole emitter <strong>in_GaN_ulenses_more_sources.mph</strong>: parameterized micro-LED array model, including results, with GaN micro-lenses, using an array of dipole emitters <strong>postprocessing/angular_dist</strong> (directory): Matlab script to obtain angular distribution of far field <strong>postprocessing/gaussian_fit</strong> (directory): Matlab script to create a gaussian fit of the spatial intensity distribution at the substrate/air interface
DOI: 10.5281/zenodo.801828
title: Rdp Taxonomic Training Data Formatted For Dada2 (Rdp Trainset 16/Release 11.5)

description: These DADA2-formatted training fasta files were derived from the Ribosomal Database Project's Training Set 16 and the 11.5 release of the RDP database.

These fastas were generated by the following commands (using the dada2 R package version 1.5.1):


path &lt;- "~/Desktop/RDP/RDPClassifier_16S_trainsetNo16_rawtrainingdata"<br>
dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset16_022016.fa"), file.path(path, "trainset16_db_taxid.txt"), "~/tax/rdp_train_set_16.fa.gz")

dada2:::makeSpeciesFasta_RDP("~/Desktop/RDP/current_Bacteria_unaligned.fa", "~/tax/rdp_species_assignment_16.fa.gz")
DOI: 10.5281/zenodo.8126445
title: Milan 1958-1962: Music Topography of a City (main dataset)

description: This data set contains information about 8288 music performances held in Milan from 1958 to 1962. It was collected from the "shows of the day" page on Italian newspapers <em>Il Giorno </em>and <em>Il Corriere della Sera. </em>Its collection, analysis and visualization is part of the PhD research project "Milan 1958-1962: Music Topography of a City". Project website
DOI: 10.5281/zenodo.8128162
title: Database of New Phase Change Materials

description: Database of structural and optical properties of Gallium sulfide (GaS), Antimony sulfide (Sb2S3), Gallium Selenide (GaSe), Selenium (Se), and Molybdenum oxide (MoOx) thin film phase change materials. Contains Raman spectra and room temperature optical constants from spectroscopic ellipsometry for amorphous and polycrystalline phases. Also includes temperature dependent optical constants measured in-situ during thermal annealing to induce crystallization. Thin films fabricated by chemical vapor deposition, exfoliation, and solution processing methods. Provided by the PHEMTRONICS project (Deliverable 2.7).
DOI: 10.5281/zenodo.8132166
title: Excel data for MTT assay by promega

description: This data represent the Excel data of cell line results by promega
DOI: 10.57758/3zd1-j310
title: Pekár published papers 2012-2015
DOI: 10.57758/gb07-ah82
title: Data from published papers of Pekar 2007-2011
DOI: 10.6084/m9.figshare.21746804
title: Spotsize vs the half receiving FOV.zip

description: This zip contains parameters of the beam spot size on the detector in the array varies with the half receiving FOV. <br> This data is associated with the figure 7 in our paper "Design of the Quadrangular prism Beam Splitting Receiving System in MEMS-Based Scanning Lidar".
DOI: 10.6084/m9.figshare.23576478
title: out-final

description: output file from newAD2 software
DOI: 10.6084/m9.figshare.24082116.v6
title: Shortest Routes from DA Centroids to 24-hr EDs (Shapefile)

description: This file provides a Shapefile that displays the routes identifed for the shortest distance between DA centroid and the closest 24-hr-emergency department.
DOI: 10.6084/m9.figshare.24893019
title: Supplementary Material for: MASLD and MetALD increase the risk of developing hepatocellular carcinoma and incident or decompensated cirrhosis: a Korean nationwide study

description: Introduction: This study aimed to investigate the liver-related outcomes of newly suggested metabolic dysfunction-associated steatotic liver disease (MASLD) and MASLD with increased alcohol intake (MetALD), as well as alcohol-associated liver disease (ALD).
Methods: From a National Health Insurance Service Health Screening Cohort, we included 369,094 participants who underwent health check-ups between 2009 and 2010 in South Korea. SLD was defined as a fatty liver index ≥60. The risk of primary liver cancer (PLCa), hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), incident cirrhosis, and decompensated cirrhosis was compared with no steatotic liver disease (SLD). The subdistribution hazard ratio (SHR) was calculated using the Fine–Gray model regarding competing risks.
Results: A total of 3,232 participants (0.9%) developed PLCa during the median follow-up of 3,227,176 person-years: 0.5% with no SLD, 1.1% with MASLD, 1.3% with MetALD, and 1.9% with ALD. Competing risk analysis revealed that compared with no SLD, MASLD (SHR, 1.65; 95% CI, 1.44−1.88), MetALD (SHR, 1.87; 95% CI, 1.52−2.29), and ALD (SHR, 1.86; 95% CI, 1.39−2.49) were associated with an increased risk of PLCa. MASLD (SHR, 1.96; 95% CI, 1.67−2.31), MetALD (SHR, 2.23; 95% CI, 1.75−2.84), and ALD (SHR, 2.34; 95% CI, 1.67−3.29) were associated with a higher risk of HCC. No significant difference was observed in the risk of iCCA. The risk of incident cirrhosis and decompensated cirrhosis increased in the order of no SLD, MASLD, MetALD, and ALD.
Conclusion: MASLD, MetALD, and ALD have an increased risk of PLCa, HCC, incident cirrhosis, and decompensated cirrhosis but not iCCA. These findings may serve as a robust ground for the prognostic value of the newly suggested MASLD and MetALD.
DOI: 10.6084/m9.figshare.24894405
title: AOSLO images across devices and modalities

description: The masked dataset used in "Quantifying Image Quality for AOSLO Images"; image status (e.g. device, modality, or pathology) is provided in an excel file in the same folder.
DOI: 10.6084/m9.figshare.25100018
title: data records

description: Data records for the Nacob project
DOI: 10.6084/m9.figshare.25138136
title: Supplementary Material for: A Case of Lateral Meningocele Syndrome without Lateral Meningoceles

description: Introduction: Lateral meningocele syndrome (LMS), also known as Lehman syndrome, is caused by pathogenic variants in exon 33 of NOTCH3. Variants in this final exon of NOTCH3 interrupt the regulatory PEST domain, leading to enhanced NOTCH3 signaling due to prolonged cellular half-life. Individuals with LMS are expected to have multiple lateral meningoceles, developmental delay, neonatal hypotonia, dysmorphic facial features, and feeding difficulties.

Case Presentation: We report an 8-year-old male with a history of autism, feeding difficulties, developmental delay, severe intellectual disability, and self-injurious behavior. Genetic testing revealed a NOTCH3 c.6663C&gt;G (p.Y2221*) pathogenic variant in exon 33, consistent with a diagnosis of LMS. A follow up spine MRI showed a ventral sacral extradural arachnoid cyst but no lateral meningoceles. This individual’s most recent exam noted multiple dysmorphic features including prominent metopic ridging, broad forehead, down-slanting palpebral fissures, high arched palate, long narrow philtrum, mild pectus excavatum, and wide-based gait.

Discussion/Conclusion: This individual shares the dysmorphic facial features, ongoing G-tube dependence, failure to thrive, and developmental delay seen in other individuals with LMS. His lack of lateral meningoceles expands the phenotype for this condition, as all previously reported individuals with molecularly confirmed LMS had multiple lateral meningoceles before age 8 years with an average age of identification at 4 years.
DOI: 10.6084/m9.figshare.25480477
title: Supplementary Material for: A bioinformatically initiated approach to evaluate GATA1 regulatory regions in samples with weak D, Del or D– phenotypes despite normal RHD exons

description: Introduction: With over 360 blood group antigens recognized, there are antigens, such as RhD, which demonstrate a quantitative reduction in antigen expression due to nucleotide variants in the non-coding region of the gene that result in aberrant splicing or a regulatory mechanism. 
This study aimed to evaluate bioinformatically predicted GATA1-binding regulatory motifs in the RHD gene for samples presenting with weak RhD antigen expression but showing normal RHD exons. 
Methods: Publicly available open chromatin region data were overlayed with GATA1 motif candidates in RHD. Genomic DNA from weak D, Del or D– samples with normal RHD exons (n=13) was used to confirm RHD zygosity by quantitative PCR. Then, RHD promoter, intron 1 and intron 2 regions were amplified for Sanger sequencing to detect potential disruptions in the GATA1 motif candidates. Electrophoretic mobility shift assay (EMSA) was performed to assess GATA1-binding. Luciferase assays were used to assess transcriptional activity. 
Results: Bioinformatic analysis identified five of six GATA1 motif candidates in the promoter, intron 1 and intron 2 for investigation in the samples. Luciferase assays showed an enhancement in transcription for GATA1 motifs in intron 1 and for intron 2 only when the R2 haplotype variant (rs675072G&gt;A) was present. GATA1 motifs were intact in 12 of 13 samples. For one sample with a Del phenotype, a novel RHD c.1–110A&gt;C variant disrupted the GATA1 motif in the promoter which was supported by a lack of a GATA1 supershift in the EMSA and 73% transcriptional activity in the luciferase assay. Two samples were D+/D– chimeras. 
Conclusion: The bioinformatic predictions enabled the identification of a novel DEL allele, RHD c.1–110A&gt;C, which disrupted the GATA1 motif in the proximal promoter. Although the majority of the samples investigated here remain unexplained, we provide GATA1 targets which may benefit future RHD regulatory investigations.
DOI: 10.6084/m9.figshare.26139349
title: Dispersion Data.xlsx

description: Dispersion Data generated using FEM method
DOI: 10.13026/c2294b
title: MIMIC-III Waveform Database Matched Subset

description: The MIMIC-III Waveform Database Matched Subset contains 22,317 waveform
records, and 22,247 numerics records, for 10,282 distinct ICU patients. These
recordings typically include digitized signals such as ECG, ABP, respiration,
and PPG, as well as periodic measurements such as heart rate, oxygen
saturation, and systolic, mean, and diastolic blood pressure.

This database is a subset of the [MIMIC-III Waveform
Database](/content/mimic3wdb/), representing those records for which the
patient has been identified, and their corresponding clinical records are
available in the [MIMIC-III Clinical Database](/content/mimiciii/).

  *[ICU]: Intensive care unit
  *[ECG]: Electrocardiogram
  *[ABP]: Arterial blood pressure
  *[PPG]: Photoplethysmogram
DOI: 10.15156/bio/sh0957490.10fu
title: SH0957490.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.1594/pangaea.804589
title: Spectral reflectance library of selected biotic and abiotic coral reef features in Heron Reef

description: Underwater spectral reflectance was measured for selected biotic and abiotic coral reef features of Heron Reef from June 25-30, 2006. Spectral reflectance's of 105 different benthic types were obtained in-situ. An Ocean Optics USB2000 spectrometer was deployed in an custom made underwater housing with a 0.5 m fiber-optic probe mounted next to an artificial light source. Spectral readings were collected with the probe(bear fibre) about 5 cm from the target to ensure that the target would fill the field of view of the fiber optic (FOV diameter ~4.4 cm), as well as to reduce the attenuating effect of the intermediate water (Roelfsema et al., 2006). Spectral readings included for one target included: 1 reading of the covered spectral fibre to correct for instrument noise, 1 reading of spectralon panel mounted on divers wrist to measure incident ambient light, and 8 readings of the target. Spectral reflectance was calculated for each target by first subtracting the instrument noise reading from each other reading. The corrected target readings were then divided by the corrected spectralon reading resulting in spectral reflectance of each target reading. An average target spectral reflectance was calculated by averaging the eight individual spectral reflectance's of the target. If an individual target spectral reflectance was visual considered an outlier, it was not included in the average spectral reflectance calculation. See Roelfsema at al. (2006) for additional info on the methodology of underwater spectra collection.
description: The original file version in excel format is linked at "Other version:"Higher resolution photos of selected coral reef target features taken from Heron Reef from June 25-30, 2006 are provided in a pdf-file linked at "Further details:"The data publication workflow is documented in http://issues.pangaea.de/browse/PDI-3643.
DOI: 10.1594/pangaea.915747
title: Top of Atmosphere, Hyperspectral Synthetic Dataset for PACE (Phytoplankton, Aerosol, and ocean Ecosystem) Ocean Color Algorithm Development

description: This synthetic dataset was created to provide a measurement error-free hyperspectral (350-800 nm, 5 nm resolution) dataset as part of research performed by the first NASA PACE (Plankton, Aerosols, Cloud, and Ocean Ecosystem) Science Team (NNH13ZDA001N-PACEST). A synthetic dataset of sea surface and top of atmosphere (TOA) radiances were constructed by a Coupled Ocean Atmosphere Radiative Transfer (COART) model (Du and Lee, 2014) based on the SBDART (Santa Barbara DISORT Atmospheric Radiative Transfer) code (Ricchiazzi et al. 1998), with ocean contribution simulated by Hydrolight (Mobley, 2008). Water-leaving radiance (Lw) was forward modelled with Hydrolight with a solar zenith angle of 30°, cloudless sky, a sea surface state corresponding to a wind speed of 5 m/s, and realistic concentrations of optically active water constituents. The Hydrolight component of the model was constrained using inherent optical properties (IOPs) whose dynamic ranges and spectral qualities were based on real, in situ data acquired from the NASA SeaBASS dataset (https://seabass.gsfc.nasa.gov/) and that represent realistic in situ conditions. Certain characteristics of the IOPs were semi-randomly modelled based on principles outlined in IOCCG Report No.5 (2006) and summarised in the accompanying pdf document provided along with this dataset. Atmospheric conditions were simulated by coupling the water-leaving radiances to an atmosphere with and without absorbing gases, and with an aerosol optical depth (AOD) that varied between 0.1-0.8.
DOI: 10.22002/7aer7-qhf77
title: FPM-INR: Fourier ptychographic microscopy image stack reconstruction using implicit neural representations

description: Preprocessed and raw data for "FPM-INR: Fourier ptychographic microscopy image stack reconstruction using implicit neural representations"