cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21227/0xtb-fn23
title: Thaat and Raga Forest (TRF) Dataset

description: The "Thaat and Raga Forest (TRF) Dataset" represents a significant advancement in computational musicology, focusing specifically on Indian Classical Music (ICM). While Western music has seen substantial attention in this field, ICM remains relatively underexplored. This manuscript presents the utilization of Deep Learning models to analyze ICM, with a primary focus on identifying Thaats and Ragas within musical compositions. Thaats and Ragas identification holds pivotal importance for various applications, including sentiment-based recommendation systems and music categorization.The dataset comprises recordings from renowned musicians encompassing diverse musical forms such as solos, performances, choruses, instrumentals, and movie songs, available in both mp3 and wav formats. Organized meticulously, the dataset is categorized into ten primary Thaats, each containing a diverse array of Ragas. This comprehensive collection offers a valuable resource for researchers and practitioners alike, facilitating in-depth exploration and analysis of Indian Classical Music through computational means.
DOI: 10.5281/zenodo.10850398
title: Processed datasets used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics"

description: These are the processed anndata objects used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics".

These datasets are stored as .h5ad files and are intended to be used with the Scanpy package in Python. They contain all relevant cell type annotation, unnormalized and transformed gene expression counts, as well as the inferred intercellular fow networks inferred by FlowSig.
DOI: 10.5281/zenodo.10850397
title: Processed datasets used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics"

description: These are the processed anndata objects used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics".

These datasets are stored as .h5ad files and are intended to be used with the Scanpy package in Python. They contain all relevant cell type annotation, unnormalized and transformed gene expression counts, as well as the inferred intercellular fow networks inferred by FlowSig.
DOI: 10.5281/zenodo.10850471
title: Quark and Gluon Nsubs

description: A dataset consisting of 45 N-subjettiness observables for 100k quark and gluon jets generated with Pythia 8.230. Following 1704.08249, the observables are in the following order:

$$\{\tau_1^{(\beta=0.5)},\tau_1^{(\beta=1.0)},\tau_1^{(\beta=2.0)},\tau_2^{(\beta=0.5)},\tau_2^{(\beta=1.0)},\tau_2^{(\beta=2.0)},\ldots,\tau_{15}^{(\beta=0.5)},\tau_{15}^{(\beta=1.0)},\tau_{15}^{(\beta=2.0)}\}.$$

 

The dataset contains two members: 'X' which is a numpy array of the nsubs that has shape (100000,45) and 'y' which is a numpy array of quark/gluon labels (quark=1 and gluon=0).
DOI: 10.5281/zenodo.10850472
title: Quark and Gluon Nsubs

description: A dataset consisting of 45 N-subjettiness observables for 100k quark and gluon jets generated with Pythia 8.230. Following 1704.08249, the observables are in the following order:

$$\{\tau_1^{(\beta=0.5)},\tau_1^{(\beta=1.0)},\tau_1^{(\beta=2.0)},\tau_2^{(\beta=0.5)},\tau_2^{(\beta=1.0)},\tau_2^{(\beta=2.0)},\ldots,\tau_{15}^{(\beta=0.5)},\tau_{15}^{(\beta=1.0)},\tau_{15}^{(\beta=2.0)}\}.$$

 

The dataset contains two members: 'X' which is a numpy array of the nsubs that has shape (100000,45) and 'y' which is a numpy array of quark/gluon labels (quark=1 and gluon=0).
DOI: 10.5281/zenodo.10850331
title: Data from: Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of cyp27c1 expression

description: Code and Data associated with "Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of cyp27c1 expression"

Abstract

The wide-ranging photic conditions found across aquatic habitats may act as selective pressures potentially driving rapid evolution and diversity in the visual system of teleost fishes. Fine-tuning of visual sensitivities in many fish species relies on regulating the two components of visual pigments, the opsin protein and the chromophore. Many studies have focused on opsin gene expression or opsin sequence divergence in fishes inhabiting contrasting habitats. However, variation in chromophore usage across photic habitats has received less attention. Species from the Nicaraguan Midas cichlid complex, Amphilophus cf citrinellus [Günther 1864], have independently colonized seven isolated crater lakes of varying photic conditions resulting in repeated examples of small adaptive radiations. Here, we investigate variation in cyp27c1, the main enzyme involved in chromophore exchange, in response to photic environments in the wild, we measure its genetic component using laboratory-reared fish and test the effect of different rearing light conditions on cyp27c1 expression. We found that photic environments significantly predict variation in cyp27c1 expression in wild populations and that this variation seems to be genetically assimilated in two populations. We found that light-induced cyp27c1 expression is variable across populations (i.e., genotype-by-environment interactions) and correlated with local photic conditions thus highlighting cyp27c1 as a key factor of visual ecology in cichlid fishes.

Keywords: cyp27c1 gene expression, sensory ecology, visual plasticity, Neotropical cichlids
DOI: 10.5281/zenodo.10850332
title: Data from: Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of cyp27c1 expression

description: Code and Data associated with "Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of cyp27c1 expression"

Abstract

The wide-ranging photic conditions found across aquatic habitats may act as selective pressures potentially driving rapid evolution and diversity in the visual system of teleost fishes. Fine-tuning of visual sensitivities in many fish species relies on regulating the two components of visual pigments, the opsin protein and the chromophore. Many studies have focused on opsin gene expression or opsin sequence divergence in fishes inhabiting contrasting habitats. However, variation in chromophore usage across photic habitats has received less attention. Species from the Nicaraguan Midas cichlid complex, Amphilophus cf citrinellus [Günther 1864], have independently colonized seven isolated crater lakes of varying photic conditions resulting in repeated examples of small adaptive radiations. Here, we investigate variation in cyp27c1, the main enzyme involved in chromophore exchange, in response to photic environments in the wild, we measure its genetic component using laboratory-reared fish and test the effect of different rearing light conditions on cyp27c1 expression. We found that photic environments significantly predict variation in cyp27c1 expression in wild populations and that this variation seems to be genetically assimilated in two populations. We found that light-induced cyp27c1 expression is variable across populations (i.e., genotype-by-environment interactions) and correlated with local photic conditions thus highlighting cyp27c1 as a key factor of visual ecology in cichlid fishes.

Keywords: cyp27c1 gene expression, sensory ecology, visual plasticity, Neotropical cichlids
DOI: 10.6084/m9.figshare.25456678
title: Monitoring the Establishment of Small Hive Beetle on Oahu Hawaii (20-3-24).pdf

description: Raw data of initial infestation of small hive beetle (Aethina tumida) to an apiary on Oahu, Hawaii. Data was used for publication submitted to the Journal of Applied Entomology.
DOI: 10.5281/zenodo.10791353
title: Figure 1: autophagy flux in RUBCN KOs [FINAL]
DOI: 10.5281/zenodo.10791354
title: Figure 1: autophagy flux in RUBCN KOs [FINAL]
DOI: 10.5281/zenodo.10732696
title: Polarisation camera dSTORM datasets of actin in fixed HeLa cells labeled with phalloidin-Alexa Fluor 647

description: Polarisation camera dSTORM dataset of the actin of fixed HeLa cells labeled with phalloidin-Alexa Fluor 647.

Image acquisition was performed as follows:

Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 638 nm laser at quasi-TIRF, with a measured power density at the image plane of 3.51 kW/cm^2. A multiband dichroic (Di03-R405/488/561/635-t1, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass filter (BLP01-635R, Semrock) before detection. An exposure time of 30 ms was used.

Samples were prepared as follows:

Cell culture: HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C + 5 % CO_2. Cells were periodically tested for mycoplasma contamination and passaged 3 times per week. Cells were plated at low density on high-precision glass coverslips (MatTek, P35G-0.170-14-C) 1 day prior to fixation for dSTORM experiments.

Labeling: Cells were simultaneously fixed and permeabilized in cytoskeleton buffer (CBS, 10 mM MES, 138 mM KCl, 3 mM MgCl_2, 2 mM EGTA, 4.5 % sucrose w/v, pH 7.4), + 4 % paraformaldehyde (PFA) and 0.2 % Triton for 6 minutes at 37 °C, and further fixed in CBS + 4 % PFA for 14 minutes at 37 °C. Post-fixation, cells were washed x3 in PBST (PBS supplemented with 0.1 % Tween) and permeabilized a second time in PBS + 0.5 % Triton for 5 minutes at room temperature. The samples were then washed 3 times in PBST and blocked for 30 minutes in 5 % BSA. Cells were washed x3 in PBST and then incubated with Alexa Fluor™ 647 Phalloidin (A22287, Invitrogen, 1:50 in PBS) for 1 h in the dark, followed by x2 washes in PBS. Prior to dSTORM imaging, PBS was replaced with dSTORM imaging buffer (base buffer consisting of 0.56 M glucose, 50 mM Tris (pH 8.5), and 10 mM NaCl supplemented with 5 U/mL pyranose oxidase (Sigma, P4234), 10 mM cysteamine (Sigma, 30070), 40 µg/mL catalase (Sigma, C100) and 2 mM cyclooctatetraene (Sigma, 138924).
DOI: 10.5281/zenodo.10607237
title: Images of mouse VTA and SNc sections labeled for neurotransmitter phenotype markers via RNAscope

description: 48 coronal sections from 3 male and 3 female C57Bl/6J mice were labeled for mRNAs encoding the canonical vesicular transporters for dopamine (VMAT2), GABA (VGAT), and glutamate (VGLUT2). These sections were then imaged via confocal microscopy and saved as CZI files, editable with Zeiss Zen software. These image files include 'event marker' graphics, indicating where neurons positive for one or more of the above transporters are. 

The protocols used for sample preparation, labeling, imaging, and counting are linked in the Related Works section. 

Cell count data are organized by subregion (SUBREGION counts for R.csv), anterior-posterior (e.g. VGATVTA.csv), or anterior-posterior and medial-lateral distribution (e.g. 'snc triple.csv' or 'snc vmat2 AP and ML.csv').

The R code provided uses these csv files to visualize expression patterns across VTA and SNc. 
description: Count graphics are named according to transporter(s) (e.g. "vmat2" or "vmat2 and vgat"). Note that these are not markings of cell types, rather just transporter expression. For example, neurons labeled "vmat2" belong to all cell types with VMAT2: vmat2 only, vmat2 + vgat only, vmat2 + vglut2 only, and triple. 

Sometimes multiple count graphics for a single transporter show up (e.g. "vmat2 part2" or "vmat2 addition". The additional graphics are for neurons that were missed in the initial count due to accidental exiting of the Count tool.

Sometimes an extra event counter was created or placed in the wrong location. In these cases the graphic will have a note saying how many miscounts there are (e.g. "VMAT2 -1" for one miscount). There will be a correction graphic (a black rectangle) after covering the miscount (e.g. "VMAT2 correction").

T1: VMAT2T2: VGATT3: VGLUT2T4: DAPI

Animals alpha, epsilon, and mu are male; beta, sigma, and delta are female. All were 8-9 weeks old at time of sacrifice.

Fiber regions:ml: medial lemiscusfr: fasciculus retroflexusmt: medial terminal nucleus of the accessory optic tractpm: principal mammilary tract vtgx: ventral tegmental decussation

Cellular regions:CLi: Caudal linear nucleus DR: Dorsal rapheIF: Interfascicular nucleus IPN: Interpeduncular nucleusPBP: Parabrachial pigmented nucleus PIF: Parainterfascicular nucleusPN: Paranigral nucleus RLi: Rostral linear nucleusRN: red nucleus SNCD: SNc, dorsalSNCL: SNc, lateral SNCM: SNc, medialSNCV: SNc, ventral VTAR: VTA, rostral
DOI: 10.5281/zenodo.10607238
title: Images of mouse VTA and SNc sections labeled for neurotransmitter phenotype markers via RNAscope

description: 48 coronal sections from 3 male and 3 female C57Bl/6J mice were labeled for mRNAs encoding the canonical vesicular transporters for dopamine (VMAT2), GABA (VGAT), and glutamate (VGLUT2). These sections were then imaged via confocal microscopy and saved as CZI files, editable with Zeiss Zen software. These image files include 'event marker' graphics, indicating where neurons positive for one or more of the above transporters are. 

The protocols used for sample preparation, labeling, imaging, and counting are linked in the Related Works section. 

Cell count data are organized by subregion (SUBREGION counts for R.csv), anterior-posterior (e.g. VGATVTA.csv), or anterior-posterior and medial-lateral distribution (e.g. 'snc triple.csv' or 'snc vmat2 AP and ML.csv').

The R code provided uses these csv files to visualize expression patterns across VTA and SNc. 
description: Count graphics are named according to transporter(s) (e.g. "vmat2" or "vmat2 and vgat"). Note that these are not markings of cell types, rather just transporter expression. For example, neurons labeled "vmat2" belong to all cell types with VMAT2: vmat2 only, vmat2 + vgat only, vmat2 + vglut2 only, and triple. 

Sometimes multiple count graphics for a single transporter show up (e.g. "vmat2 part2" or "vmat2 addition". The additional graphics are for neurons that were missed in the initial count due to accidental exiting of the Count tool.

Sometimes an extra event counter was created or placed in the wrong location. In these cases the graphic will have a note saying how many miscounts there are (e.g. "VMAT2 -1" for one miscount). There will be a correction graphic (a black rectangle) after covering the miscount (e.g. "VMAT2 correction").

T1: VMAT2T2: VGATT3: VGLUT2T4: DAPI

Animals alpha, epsilon, and mu are male; beta, sigma, and delta are female. All were 8-9 weeks old at time of sacrifice.

Fiber regions:ml: medial lemiscusfr: fasciculus retroflexusmt: medial terminal nucleus of the accessory optic tractpm: principal mammilary tract vtgx: ventral tegmental decussation

Cellular regions:CLi: Caudal linear nucleus DR: Dorsal rapheIF: Interfascicular nucleus IPN: Interpeduncular nucleusPBP: Parabrachial pigmented nucleus PIF: Parainterfascicular nucleusPN: Paranigral nucleus RLi: Rostral linear nucleusRN: red nucleus SNCD: SNc, dorsalSNCL: SNc, lateral SNCM: SNc, medialSNCV: SNc, ventral VTAR: VTA, rostral
DOI: 10.5281/zenodo.10470794
title: Polarisation camera TAB-PAINT dataset of alpha-synuclein fibrils using Nile red

description: Alpha-synuclein fibrils were deposited on PLL-coated and argon plasma-cleaned coverslides. A low concentration of Nile Red (~1 nM) was added for PAINT imaging, and fluorescent beads for post-acquisition drift correction.

The data was collected on a fluorescence microscope (Eclipse Ti-U, Nikon) with a polarisation camera (CS505MUP, Thorlabs). The molecules were excited with a 515 nm laser using epi-illumination with a measured power density at the sample plane of 6.08 kW/cm^2. An exposure time of 50 ms was used. The following filters were used: dichroic (Di03-R514-t1, Semrock) and emission filter (FF01-515/LP and FF01-650/200, Semrock). A 60x oil-immersion objective (Plan Apo, 60xA/1.40 Oil, DIC H, inf/0.17 WD 0.21, Nikon) was used for detection.
DOI: 10.5281/zenodo.10471495
title: Polarisation camera movies of T cells on a cover glass

description: The plasma membrane of live T cells (J8 LFA-1) was labelled using the Nile red-derivative NR4A, and 3D movies were recorded using a polarisation camera. Two unprocessed datasets are included here:



Tcell_NR4A_EPI_stack: A 3D stack of a single T cell, imaged with the excitation in EPI configuration.

Tcell_NR4A_HILO_stack_movie: A 3D movie of live T cells interacting with an OKT3 antibody-coated cover glass, imaged with the excitation in HILO configuration.


For each .tif file, the corresponding Micro-Manager metadata file is included.

Optical setup:

Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 515 nm laser, coupled into a square-core multi-mode fiber (M97L02, Thorlabs) with a custom vibration-motor-based mode scrambler. The measured power density at the image plane was on the order of 0.004 kW/cm^2. A dichroic (Di03-R514-t1, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass filter (FF01-515/LP, Semrock) and bandpass filter (FF01-650/200, Semrock) before detection.

Sample preparation:

J8 LFA-1 cells were incubated overnight (~18 h) in complete-RPMI (StableCell RPMI-1640 media (Sigma) supplemented with 10 % (v/v) fetal calf serum (FCS), 1 % (v/v) HEPES buffer, and 1 % (v/v) pen/strep antibiotics. 1 mL of cells were collected by centrifugation and resuspended in phenol-red free RPMI supplemented with 1 % HEPES.

Round coverslips were rinsed with IPA, MilliQ, dried, and Ar-plasma cleaned for 20 minutes. Grace Bio-Labs CultureWells were attached, and the slide was incubated with OKT3 antibody (provided by the Human Immunology Unit, WIMM, Oxford) for 30 minutes. The slide was washed 5 times with phenol-red free RPMI supplemented with 1 % HEPES and a final wash with phenol-red free RPMI supplemented with 1 % HEPES and 200 nM NR4A before imaging.
DOI: 10.5281/zenodo.10630751
title: Data for LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread

description: Data that was analyzed and used to create figures in the paper.
description: Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson’s disease (PD). These mutations elevate LRRK2 kinase activity, making LRRK2 kinase inhibitors an attractive therapeutic target. LRRK2 kinase activity has been consistently linked to specific cell signaling pathways, mostly related to organelle trafficking and homeostasis, but its relationship to PD pathogenesis has been more difficult to define. LRRK2-PD patients consistently present with loss of dopaminergic neurons in the substantia nigra but show variable development of Lewy body or tau tangle pathology. Animal models carrying LRRK2 mutations do not develop robust PD-related phenotypes spontaneously, hampering the assessment of LRRK2 inhibitors’ efficacy against disease processes. We hypothesized that mutations in LRRK2 may not be directly related to a single disease pathway, but instead may elevate susceptibility to multiple disease processes, depending on the disease trigger. To test this hypothesis, we have previously evaluated progression of α-synuclein and tau pathologies following injection of proteopathic seeds. We demonstrated that transgenic mice overexpressing mutant LRRK2 show alterations in the brain-wide progression of pathology, especially at older ages. Here, we assess tau pathology progression in relation to long-term LRRK2 kinase inhibition. Wildtype or LRRK2G2019S knock-in mice were injected with tau fibrils and treated with control diet or diet containing LRRK2 kinase inhibitor MLi-2 targeting the IC50 or IC90 of LRRK2 for 3 to 6 months. Mice were evaluated for tau pathology by brain-wide quantitative pathology in 665 brain regions and subsequent linear diffusion modeling of progression. Consistent with our previous work, we found systemic alterations in the progression of tau pathology in LRRK2G2019S mice that were most pronounced at 6 months. Importantly, LRRK2 kinase inhibition reversed these effects in LRRK2G2019S mice, but had minimal effect in wildtype mice, suggesting that LRRK2 kinase inhibition is likely to reverse specific disease processes in G2019S mutation carriers, but additional work may be necessary to determine the potential effect in non-carriers. This work supports a protective role of LRRK2 kinase inhibition in G2019S carriers and provides a rational workflow for systematic evaluation of brain-wide phenotypes in therapeutic development.
DOI: 10.5281/zenodo.10630752
title: Data for LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread

description: Data that was analyzed and used to create figures in the paper.
description: Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson’s disease (PD). These mutations elevate LRRK2 kinase activity, making LRRK2 kinase inhibitors an attractive therapeutic target. LRRK2 kinase activity has been consistently linked to specific cell signaling pathways, mostly related to organelle trafficking and homeostasis, but its relationship to PD pathogenesis has been more difficult to define. LRRK2-PD patients consistently present with loss of dopaminergic neurons in the substantia nigra but show variable development of Lewy body or tau tangle pathology. Animal models carrying LRRK2 mutations do not develop robust PD-related phenotypes spontaneously, hampering the assessment of LRRK2 inhibitors’ efficacy against disease processes. We hypothesized that mutations in LRRK2 may not be directly related to a single disease pathway, but instead may elevate susceptibility to multiple disease processes, depending on the disease trigger. To test this hypothesis, we have previously evaluated progression of α-synuclein and tau pathologies following injection of proteopathic seeds. We demonstrated that transgenic mice overexpressing mutant LRRK2 show alterations in the brain-wide progression of pathology, especially at older ages. Here, we assess tau pathology progression in relation to long-term LRRK2 kinase inhibition. Wildtype or LRRK2G2019S knock-in mice were injected with tau fibrils and treated with control diet or diet containing LRRK2 kinase inhibitor MLi-2 targeting the IC50 or IC90 of LRRK2 for 3 to 6 months. Mice were evaluated for tau pathology by brain-wide quantitative pathology in 665 brain regions and subsequent linear diffusion modeling of progression. Consistent with our previous work, we found systemic alterations in the progression of tau pathology in LRRK2G2019S mice that were most pronounced at 6 months. Importantly, LRRK2 kinase inhibition reversed these effects in LRRK2G2019S mice, but had minimal effect in wildtype mice, suggesting that LRRK2 kinase inhibition is likely to reverse specific disease processes in G2019S mutation carriers, but additional work may be necessary to determine the potential effect in non-carriers. This work supports a protective role of LRRK2 kinase inhibition in G2019S carriers and provides a rational workflow for systematic evaluation of brain-wide phenotypes in therapeutic development.