Find research datasets worth reusing

Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (Mito channel)

This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondia over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only Mito channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.

Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (ER channel)

This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondria over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only ER channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.

Three-color whole cell LLSM imaging data of ER, H2B, and Lyso over 980 time points during mitosis (Lyso channel)

This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Lysosomes over 980 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Lamp1-Halo during mitosis (only Lyso channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.

Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (H2B channel)

This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondia over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only H2B channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.

openother-openMay 2022View details →

InSecTT BLE Channel Sniff Dataset

This dataset provides Bluetooth Low Energy (BLE) measurements for a single BLE channel, observed with a Software Defined Radio (SDR) in close proximity to several BLE devices. Since BLE uses channel hopping, not every message is detected if only a single channel is observed. In general, we do not know the access address, the connection interval, or the hopping pattern of the connections [1]. This measurement set provides the raw bitstream of the received BLE messages, as well as the already extracted measurements of the BLE connections including the header and measured timestamp. For each measurement set, we provide metadata with information about the BLE devices that are part of the setup. In BLE there are currently two different channel hop algorithms used [1]. The first one is the Channel Selection Algorithm 1 (CSA1), which was released with the first BLE specification, and the second is the Channel Selection Algorithm 2 (CSA2) which was implemented with the BLE version 5.0. This dataset provides measurements with BLE devices using both algorithms. The intention of this dataset, is to show that even though channel hopping is used, it is possible to reconstruct certain communication parameters and predict future channel access of the BLE connections by only passively listening to the channel. This dataset is a work from <a href="https://silicon-austria-labs.com/">Silicon Austria Labs GmbH</a> (SAL) and the <a href="https://www.jku.at/en/institute-for-communications-engineering-and-rf-systems/">Institute for Communications Engineering and RF-Systems</a> (NTHFS) of the Johannes Kepler University (JKU) in Linz for the <a href="https://www.insectt.eu/">InSecTT project</a>.

opencc-by-4.0Dec 2021View details →

Text-fig. 4. a: Conglomeratic to massive sandstone facies 1, facies A are composed of Andesit (AF), Clay (CF) and Sandstone (SF) fragments lain on medium-sandstone. b: Conglomeratic to massive sandstone facies, outcropping of massive sandstone facies comprises of fine to medium grain size of grey to yellowish sandstone. c: Heterolithic sandstone-mudstone facies, intercalation of fine sand with silt and shale as type form of heterolithic sandstone mudstone as indicated by a high sand/shale ratio. d: Example outcrops of heterolithic sandstone-mudstone 2 indicated by low sand/shale ratio. e: Heterolithic fine sand and mudstone and mudstone facies, intercalation of thin sandstone and shale. f: Representative of slump deposits outcrops belong to conglomeratic to massive sandstone facies, which is indicated by the intercalation of sandstone and shale and some disturbed beds or layers as seen in slump deposits. The facies type is normally deposited within the basin floor, channel margin or as a product of the overbank deposits. In this figure the slump deposit is shown as internal bedding, some occurred on the bedding-plane. Trend slope measurement of the fold-axis revealed values N 135°E and N 108°E. in Lithofacies And Ichnofacies Of Turbidite Deposits, West Java, Indonesia

Text-fig. 4. a: Conglomeratic to massive sandstone facies 1, facies A are composed of Andesit (AF), Clay (CF) and Sandstone (SF) fragments lain on medium-sandstone. b: Conglomeratic to massive sandstone facies, outcropping of massive sandstone facies comprises of fine to medium grain size of grey to yellowish sandstone. c: Heterolithic sandstone-mudstone facies, intercalation of fine sand with silt and shale as type form of heterolithic sandstone mudstone as indicated by a high sand/shale ratio. d: Example outcrops of heterolithic sandstone-mudstone 2 indicated by low sand/shale ratio. e: Heterolithic fine sand and mudstone and mudstone facies, intercalation of thin sandstone and shale. f: Representative of slump deposits outcrops belong to conglomeratic to massive sandstone facies, which is indicated by the intercalation of sandstone and shale and some disturbed beds or layers as seen in slump deposits. The facies type is normally deposited within the basin floor, channel margin or as a product of the overbank deposits. In this figure the slump deposit is shown as internal bedding, some occurred on the bedding-plane. Trend slope measurement of the fold-axis revealed values N 135°E and N 108°E.

openodc-byMay 2019View details →

Youtube cookery channels viewers comments in Hinglish

The data was collected from the famous cookery Youtube channels in India. The major focus was to collect the viewers' comments in Hinglish languages. The datasets are taken from top 2 Indian cooking channel named Nisha Madhulika channel and Kabita’s  Kitchen channel. Both the datasets comments are divided into seven categories:- Label 1- Gratitude Label 2- About the recipe Label 3- About the video Label 4- Praising Label 5- Hybrid Label 6- Undefined Label 7- Suggestions and queries All the labelling has been done manually.   Nisha Madhulika dataset: Dataset characteristics: Multivariate Number of instances: 4900 Area: Cooking Attribute characteristics: Real Number of attributes: 3 Date donated: March, 2019 Associate tasks: Classification Missing values: Null   Kabita Kitchen dataset: Dataset characteristics: Multivariate Number of instances: 4900 Area: Cooking Attribute characteristics: Real Number of attributes: 3 Date donated: March, 2019 Associate tasks: Classification Missing values: Null   There are two separate datasets file of each channel named as preprocessing and main file . The files with preprocessing names are generated after doing the preprocessing and exploratory data analysis on both the datasets. This file includes: <ul> <li> Id</li> <li>Comment text</li> <li>Labels</li> </ul> <ul> <li>Count of stop-words</li> <li>Uppercase words</li> <li>Hashtags</li> <li>Word count</li> <li>Char count</li> <li>Average words</li> <li>Numeric</li> </ul>   The main file includes: <ul> <li>Id</li> <li>comment text</li> <li>Labels</li> </ul> Please cite the paper https://www.mdpi.com/2504-2289/3/3/37   MDPI and ACS Style Kaur, G.; Kaushik, A.; Sharma, S. Cooking Is Creating Emotion: A Study on Hinglish Sentiments of Youtube Cookery Channels Using Semi-Supervised Approach. Big Data Cogn. Comput. 2019, 3, 37.

opencc-by-4.0Dec 2020View details →

Рис. 2. А – Тусингайское водохранилиЩе; В – оросительный канал Дустлик у г. Гулистан. Фото Н. РуЗикуловой, 2020 г. Fig. 2. A – Tusingay water reservoir; B – irrigation channel Dustlik near the Gulistan Town. Photo by N. Ruzikulova, 2020. in Patterns of ecology and life cycles of aquatic molluscs from Central Asia

Рис. 2. А – Тусингайское водохранилиЩе; В – оросительный канал Дустлик у г. Гулистан. Фото Н. РуЗикуловой, 2020 г. Fig. 2. A – Tusingay water reservoir; B – irrigation channel Dustlik near the Gulistan Town. Photo by N. Ruzikulova, 2020.

opencc-by-4.0Jan 2022View details →

РИС. 8. Примеры проблем с иЗображением при работе на СЭМ. А, В. Засветка раЗличных частей раковин глохидиев (А. Anodonta anatina (=Colletopterum), оЗ. Красное, ХакасиЯ. В. Inversiunio reinianus, оЗ. Бива, о-в Хонсю, ЯпониЯ). C. РаЗнаЯ скорость сканированиЯ (слева – очень быстраЯ, справа – медленнаЯ) наружной поверхности глохидиЯ (Anodonta cygnea, р. Ялма, МосковскаЯ обл.). D. Артефакты в виде гориЗонтальных полос вследствие накоплениЯ отрицательного ЗарЯда при недостаточном напылении внутренней поверхности глохидиЯ (Nodularia douglasiae, ПетровскаЯ протока, бассейн р. Амур, Хабаровский кр.). МасШтаб 50 мкм (А, В), 2 мкм (С), 5 мкм (D). Микроскопы Zeiss EVO 40 (А, С, D), Zeiss MERLIN (В), напыление углеродом (А, С), хромом (В, D). FIG. 8. Illustration of different problems with SEM images. A, B. Overall illumination of some glochidia shells parts (A. Anodonta anatina (= Colletopterum), Krasnoe Lake, Khakassia. B. Inversiunio reinianus, Biwa Lake, Honshu Island, Japan). C. Different scanning speed (faster on the left and slower on the right) of the exterior glochidia valve (Anodonta cygnea, Yalma River, Moscow Oblast). D. Artifacts as horizontal stripes because of additional accumulation of a negative charge due to insufficient coating of the interior glochidia valve (Nodularia douglasiae, Petrovskaya channel, Amur River basin, Khabarovsk Krai). Scale bars 50 μm (A, B), 2 μm (C), 5 μm (D). Zeiss EVO 40 (A, C, D) and Zeiss MERLIN (B) microscopes, sputter coating with carbon (A, C) and chromium (B, D). in Методика подготовки раковин глохидиев (Bivalvia, Unionidae) длЯ работы на сканируюЩем Электронном микроскопе

РИС. 8. Примеры проблем с иЗображением при работе на СЭМ. А, В. Засветка раЗличных частей раковин глохидиев (А. Anodonta anatina (=Colletopterum), оЗ. Красное, ХакасиЯ. В. Inversiunio reinianus, оЗ. Бива, о-в Хонсю, ЯпониЯ). C. РаЗнаЯ скорость сканированиЯ (слева – очень быстраЯ, справа – медленнаЯ) наружной поверхности глохидиЯ (Anodonta cygnea, р. Ялма, МосковскаЯ обл.). D. Артефакты в виде гориЗонтальных полос вследствие накоплениЯ отрицательного ЗарЯда при недостаточном напылении внутренней поверхности глохидиЯ (Nodularia douglasiae, ПетровскаЯ протока, бассейн р. Амур, Хабаровский кр.). МасШтаб 50 мкм (А, В), 2 мкм (С), 5 мкм (D). Микроскопы Zeiss EVO 40 (А, С, D), Zeiss MERLIN (В), напыление углеродом (А, С), хромом (В, D). FIG. 8. Illustration of different problems with SEM images. A, B. Overall illumination of some glochidia shells parts (A. Anodonta anatina (= Colletopterum), Krasnoe Lake, Khakassia. B. Inversiunio reinianus, Biwa Lake, Honshu Island, Japan). C. Different scanning speed (faster on the left and slower on the right) of the exterior glochidia valve (Anodonta cygnea, Yalma River, Moscow Oblast). D. Artifacts as horizontal stripes because of additional accumulation of a negative charge due to insufficient coating of the interior glochidia valve (Nodularia douglasiae, Petrovskaya channel, Amur River basin, Khabarovsk Krai). Scale bars 50 μm (A, B), 2 μm (C), 5 μm (D). Zeiss EVO 40 (A, C, D) and Zeiss MERLIN (B) microscopes, sputter coating with carbon (A, C) and chromium (B, D).

dryad40/100

Data from: Interactions of wood accumulations, channel dynamics, and geomorphic heterogeneity within a river corridor

Natural rivers are inherently dynamic. Spatial and temporal variations in water, sediment, and wood fluxes both cause and respond to an increase in geomorphic heterogeneity within the river corridor. We analyze 16 two-kilometer river corridor segments of the Swan River in Montana, USA to examine relationships between wood accumulations (wood accumulation distribution density, count, and persistence), channel dynamism (total sinuosity and average channel migration), and geomorphic heterogeneity (density, aggregation, interspersion, and evenness of patches in the river corridor). We hypothesize that i) more dynamic river segments correlate with a greater presence, persistence, and distribution of wood accumulations; ii) years with higher peak discharge correspond with greater channel dynamism and wood accumulations; and iii) all river corridor variables analyzed play a role in explaining river corridor spatial heterogeneity. Our results suggest that decadal-scale channel dynamism, as reflected in total sinuosity, corresponds to greater numbers of wood accumulations per surface area and greater persistence of these wood accumulations through time. Second, higher peak discharges correspond to greater values of wood distribution density, but not to greater channel dynamism. Third, persistent values of geomorphic heterogeneity, as reflected in the heterogeneity metrics of aggregation, interspersion, patch density, and evenness, are explained by potential predictor variables analyzed here. Our results reflect the complex interactions of water, sediment, and large wood in river corridors; the difficulties of interpreting causal relationships among these variables through time; and the importance of spatial and temporal analyses of past and present river processes to understand future river conditions

opencc-zeroMay 2024View details →

opencc-by-4.0Apr 2024View details →

Data for "Numerical simulation study of the evolution of lightning channel decay and reactivation processes" by Zheng et al.

All data of the manuscript "Numerical simulation study of the evolution of lightning channel decay and reactivation processes" submitted to Journal of Geophysical Research: Atmospheres. The data supports the manuscript entitled "Numerical simulation study of the evolution of lightning channel decay and reactivation processes”. Microsoft Notepad can open the *.txt files and the *.DAT files, they contain the channel information of two intracloud flashes (IC1 and IC2) and the channel elctrical parameters at different channel segments.  The data can be used freely for scientific purposes with the appropriate citation.

opencc-by-4.0May 2024View details →

Manual quantification of peroxisome counts in yeast from 2-channel fluorescence Z-stacks

This dataset contains fluorescence microscopy imaging data from various strains of Saccharomyces cerevisiae. The images were used to test software called perox-per-cell, which automatically quantifies peroxisome features in yeast cells based on microscopy data. There are 44 imaging instances in the dataset, each consisting of two Z-stacks, one capturing signal from calcofluor white to identify cell boundaries (blue channel), and one capturing signal from GFP tagged with peroxisome targeting sequence 1 (PTS1) to locate peroxisomes (green channel). These raw microscopy imaging sets are provided as ZVI files in Zstacks.zip. We compared perox-per-cell's automatically-generated peroxisome counts to those derived manually by two individuals. For manual counting, images were deconvolved with theoretically generated point spread functions using Axiovision software V4.9.1 SP2 followed by the generation of maximum intensity Z-projections (MIP) of both blue and green channels. All the deconvolved MIP images from WT and mutant strains were blinded and labelled as ‘1-44’, and their grey levels were set to ‘best fit’ in the Axiovision software prior to providing them to two individuals who manually counted peroxisomes in cells using the ‘measure events’ tool in Axiovision. The maximum intensity projection images used for manual counting are provided as ZVI files in MaxIntensityProjections.zip. Each individual's manual counts are included in this dataset within the CSV file ManualPeroxisomeCounts.csv. Please note that cell IDs in this file are only indicative of the order in which each individual counted peroxisomes, they do not indicate a specific cell within an image. For example, "Cell5" in Image 3 that was processed by manual counter 1 may not be the same cell as "Cell5" in Image3 processed by manual counter 2. These two entries have the same cell ID only because for both manual counters, they were the 5th cell counted. For our software test, we used wild-type (WT) yeast strains as well as several mutant strains with known peroxisomal defects. The strains used for each image are indicated in the ImageAndStrainTable.csv file. Experimental details: Saccharomyces cerevisiae cells were grown in synthetic defined medium (SD: 6.7 g/L Yeast nitrogen base without amino acids + 0.79 g/L CSM) with 2% Dextrose in flask cultures shaken at 250 rpm at 30 °C until log phase after which they were pelleted and resuspended in 50 µg/ml calcofluor white stain (Sigma, Cat No. 18909) for 5-10 min followed by imaging at room temperature. 3D images consisting of 26 XY images with a Z-slice spacing of 0.204 µm (total Z-stack thickness 5.1 µm) were acquired at 100× magnification using a fluorescence microscope (Axioskop 2 MOT plus, Carl Zeiss, Inc.) equipped with a Plan Apochromat 100×/1.4 Oil DIC objective, an Axio Cam HRm camera and an HBO 100 Mercury lamp. Identical exposure times (50 ms) were used to acquire the green channel images whereas the exposure time for blue channel was adjusted for individual images based on the intensity of calcofluor staining.

opencc-by-4.0Dec 2023View details →

Fig. 1 in First report of kdr mutations in the voltage-gated sodium channel gene in the arbovirus vector, Aedes aegypti, from Nouakchott, Mauritania

Fig. 1 The combinations of kdr point mutations S989P, V1016G, and F1534C in adult female Aedes aegypti mosquitoes in Nouakchott, Mauritania

opencc-by-4.0Feb 2024View details →

Molecular Dynamics Simulations of Hydrophilic (QTY) Potassium Ion Channels in Water

You can find here the molecular dynamics (MD) trajectories of QTY proteins in water performed for the "Computational engineering of water-soluble potassium ion channels through QTY transformation" manuscript. Please cite our paper and the previous Zenodo dataset when referring to or using this data. If you have any questions, please contact me (Eva Smorodina) at ribes.ev@gmail.com. Thank you! Smorodina, E. (2024). Molecular Dynamics Simulations of Hydrophobic (cryo-EM and Native) and Hydrophilic (QTY) Potassium Ion Channels [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10592842

dryad40/100

Piezo1 ion channels are capable of conformational signaling

Piezo1 is a mechanically activated ion channel that senses forces with short latency and high sensitivity. Piezos undergo large conformational changes, induce far-reaching deformation onto the membrane, and modulate the function of two-pore potassium (K2P) channels. Taken together, this led us to hypothesize that Piezos may be able to signal their conformational state to other nearby proteins. Here, we use chemical control to acutely restrict Piezo1 conformational flexibility and show that Piezo1 conformational changes, but not ion permeation through it, are required for modulating the K2P channel TREK1. Super-resolution imaging and stochastic simulations further reveal that both channels do not co-localize, which implies that modulation is not mediated through direct binding interactions; however, at high Piezo1 densities, most TREK1 channels are within the predicted Piezo1 membrane footprint, suggesting the footprint may underlie conformational signaling. We speculate that physiological roles originally attributed to Piezo1 ionotropic function could, alternatively, involve conformational signaling.

opencc-zeroJun 2024View details →

Fig. 4 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 4 Phylogenetic trees based on cox1 mtDNA (left tree) and ITS rDNA (right tree) sequences using the ML method with 1000 bootstraps

Fig. 3 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 3 Excysted Cryptocotyle lingua metacercariae at different degrees of contraction a in whiting from the English Channel, b in cod from Danish waters

Fig. 2 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 2 Morphology of excysted Cryptocotyle lingua metacercariae (ventral view) from Gadus morhua and Merlangius merlangius. Abbreviations: bi.i, bifurcation of intestine; e, oesophagus; ex.c, excretory canal; ex.p, excretory pore; ic, intestinal caecum; pp, prepharynx; ph, pharynx; ov, ovary; os, oral sucker; s.r, seminal receptacle; t, testis; vg.c, ventrogenital complex; vi, vitellaria; ① distance from oral sucker to end of pharynx; ② distance from oral sucker to intestinal branches; ③ width 1; ④ width 2; ⑤ oral sucker diameter; ⑥ ventrogenital complex diameter; ⑦ total length

Fig. 1 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 1 Infected Atlantic cod (Gadus morhua) (a) and microscope observation of encysted metacercariae in caudal fin (b)