Find research datasets worth reusing

The HAInich: A multidisciplinary vision data-set for a better understanding of the forest ecosystem

We present a multidisciplinary forest ecosystem 3D perception dataset. The dataset was collected in the Hainich-Dün region in central Germany, which includes two dedicated areas, which are part of the Biodiversity Exploratories - a long term research platform for comparative and experimental biodiversity and ecosystem research. The dataset combines several disciplines, including computer science and robotics, biology, bio-geochemistry, and forestry science. We present results for common 3D perception tasks, including classification, depth estimation, localization, and path planning. We combine the full suite of modern perception sensors, including high-resolution fisheye cameras, 3D dense LiDAR, differential GPS, and an inertial measurement unit, with ecological metadata of the area, including stand age, diameter, exact 3D position, and species. The dataset consists of three hand held measurement series taken from sensors mounted on a UAV during each of three seasons: winter, spring, and early summer. This enables new research opportunities and paves the way for testing forest environment 3D perception tasks and mission set automation. We do not focus on even more accurate and better forest data collection, our focus is automated forest inventory for robots.

opencc-by-4.0Jan 2022View details →

Data set for the article 'Robust replication initiation from coupled homeostatic mechanisms'

This data set contains the data of the submitted article "Robust replication initiation from coupled homeostatic mechanisms". The data was generated using simulations in python that are linked below. Experiments indicate that E. coli controls replication initiation via titration and activation of the initiator protein DnaA. We study by mathematical modelling how these two mechanisms interact to generate robust replication-initiation cycles.

opencc-by-4.0Aug 2022View details →

Vesicular release probability sets the strength of individual Schaffer collateral synapses

This repository contains the data used to generate the figures of the manuscript entitled 'Vesicular release probability sets the strength of individual Schaffer collateral synapses' and all the data used for the quantal analysis.

Excitation energy transfer and vibronic coherence in intact phycobilisomes — multidimensional electronic spectroscopy data set and MATLAB and Julia analysis code

Data sets used in the article "Excitation energy transfer and vibronic coherence in intact phycobilisomes" by Sil et al. The phycobilisomes were isolated from the short-filament mutant (SF33) of Fremyella diplosiphon UTEX 481 (also known as Tolypothrix sp. PCC 7601). Multidimensional electronic spectroscopy was performed with 6.7 fs mid-visible pulses (520–700 nm) using a pump–probe optical configuration using adaptive pulse shaping techniques. In addition to the full set of two-dimensional spectra and analysis files generated using global and target modeling and analysis of coherences (3DES oscillation maps), we provide here a linear absorption spectrum with phycobiliprotein component analysis as well as a set of 2D excitation–emission fluorescence spectra of intact and broken phycobilisome preparations.  Sil, S.; Tilluck, R. W.; Mohan TM, N.; Leslie, C. H.; Rose, J. B.; Domínguez-Martín, M. A.; Lou, W.; Kerfeld, C. A.; Beck, W. F. Excitation energy transfer and vibronic coherence in intact phycobilisomes. Nat. Chem. (2022), DOI: 10.1038/s41557-022-01026-8. <a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41557-022-01026-8__;!!HXCxUKc!yaVwTZFk8T-j3ROhygpOGW5Xy_E2wQvf-QgNGr9FZZbp4oNpfp_ZmhkdWYLdg2mKSDP8yYrNAZs$">https://www.nature.com/articles/s41557-022-01026-8</a>

An SEM Approach to Validating the Psychological Model of Musical Groove (Data Set)

Data set for the study "An SEM Approach to Validating the Psychological Model of Musical Groove"

Multi-crystal cubic insulin example data set recorded on i24

Data collected as part of routine commissioning on Diamond Light Source beamline i24 15th August 2022 with samples prepared by Felicity Bertram at Diamond following standard techniques. Data are individually incomplete but combined make for a reasonably complete and reasonable data set.    Purpose of the data upload is to make data available for tutorials using the DIALS toolchain (see e.g. examples at https://github.com/graeme-winter/dials_tutorials) however data are available for all purposes without limitation.

NGS in the clinical microbiology settings

This dataset contains bam files from 16s rRNA targeted NGS sequencing from a variety of clinical specimens. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing.  NGS: We sequenced the amplified V1-2 or V4 regions of 16s rRNA gene with Ion S5™ System (Thermo Fisher Scientific).  Data were analyzed using the Ion Reporter bioinformatics Software pipeline (Thermo Fisher Scientific), using a threshold of 1000 mapped reads for designating significant pathogens. BAM files uploaded to the Ion Reporter were mapped to the Silva 138 SSU database.

IODAQ Exploration Data Set

This repository contains the data underlying the results concerning the exploration of reactions starting from iodine and water presented in Türtscher, P. L.; Reiher, M. 2022 arXiv:2209.04039 [physics.chem-ph].

Fotopersbureau De Boer Training Set on Scene Detection

This dataset was created as part of the projects HisVis and <a href="https://noord-hollandsarchief.nl/fotografischgeheugen">Fotografisch Geheugen</a> conducted by the Noord-Hollands Archief and University of Amsterdam in the Netherlands. These projects examined to what extent Computer Vision, and more specifically, scene detection could be applied to a collection of historical press photographs. A computer was trained to automatically recognize specific scenes on historical press photographs, like a ‘protest’, ‘marriage’, ‘shopping street’ or ‘baseball game’. The key aspect of scene recognition is to identify the place in which the objects seat. The specific aim of the enrichments provided by scene detection was to benefit users of the archive and cultural historians studying historical photographs. The training set contains historical press photographs of the collection of Fotopersbureau De Boer (1945-2005). This file includes the training data used for the training of a scene detection model as well as a model to detect whether a picture was taken indoors or outdoors. The model cards, data sheet, and label sheet include more information on the dataset. - examples.tar.gz contains example images for each label. The label sheet contains more information - indoor_out.tar.gz contains the training set for the indoor / outdoor model - scene_detection.tar.gz contains the training set for the scene detection model. - no_description_found.tar.gz contains images that were not linked to any class during annotation. - HisVis2-0.1.beta.tar.gz contains the source code for the software. It stems from this GitHub repo: https://github.com/melvinwevers/HisVis2 - models.tar.gz contains the trained models. These should be placed in the repo. The models are not included here because of their size.   More information on the data is available in the <a href="https://github.com/melvinwevers/HisVis2/blob/main/docs/data_sheet.md">data sheet</a>:

Data set - What Defines Quality of Life for Older Patients Diagnosed with Cancer? A Qualitative Study

Data set from- What Defines Quality of Life for Older Patients Diagnosed with Cancer? A Qualitative Study Abstract of the study: The treatment of cancer can have a significant impact on quality of life in older patients and this needs to be taken into account in decision making. However, quality of life can consist of many different components with varying importance between individuals. We set out to assess how older patients with cancer define quality of life and the components that are most significant to them. This was a single-centre, qualitative interview study. Patients aged 70 years or older with cancer were asked to answer open-ended questions: What makes life worthwhile? What does quality of life mean to you? What could affect your quality of life? Subsequently, they were asked to choose the five most important determinants of quality of life from a predefined list: cognition, contact with family or with community, independence, staying in your own home, helping others, having enough energy, emotional well-being, life satisfaction, religion and leisure activities. Afterwards, answers to the open-ended questions were independently categorized by two authors. The proportion of patients mentioning each category in the open-ended questions were compared to the predefined questions. Overall, 63 patients (median age 76 years) were included. When asked, “What makes life worthwhile?”, patients identified social functioning (86%) most frequently. Moreover, to define quality of life, patients most frequently mentioned categories in the domains of physical functioning (70%) and physical health (48%). Maintaining cognition was mentioned in 17% of the open-ended questions and it was the most commonly chosen option from the list of determinants (72% of respondents). In conclusion, physical functioning, social functioning, physical health and cognition are important components in quality of life. When discussing treatment options, the impact of treatment on these aspects should be taken into consideration. Reference of research paper: Seghers PAL, Kregting JA, van Huis-Tanja LH, Soubeyran P, O'Hanlon S, Rostoft S, Hamaker ME, Portielje JEA. What Defines Quality of Life for Older Patients Diagnosed with Cancer? A Qualitative Study. Cancers. 2022; 14(5):1123. https://doi.org/10.3390/cancers14051123 Content of the data set: The first Tab describes what questions were asked, the second tab shows all individual anonymised answers to the open questions, the fourth shows the definitions that were used to classify all answers. Q1-Q4 show how the answers were categorised.

Vamos: VNTR annotation using efficient motif sets, 64-haplotype motifs

This is the efficient motif set for 382,492 VNTR loci in 64 haplotype-resolved assemblies (10.1126/science.abf7117). The initial release is with compression parameter (delta) = 0.1

opencc-by-4.0Dec 2021View details →

Text-fig. 9. a: Arenicolites isp., BK 13, Layer No. 6; b–f: Bifungites isp., a set of specimens showing variability in chamber shape, b – field photograph, Layer No. 23, c – field photograph, Layer No. 23, d – field photograph, Layer No. 23, e – parallel-orientated specimens, field photograph, Layer No. 23, f – field photograph, Layer No. 23; g: Didymaulichnus isp., convex epirelief, field photograph, Layer No. 1. Scale bar = 1 cm. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic

Text-fig. 9. a: Arenicolites isp., BK 13, Layer No. 6; b–f: Bifungites isp., a set of specimens showing variability in chamber shape, b – field photograph, Layer No. 23, c – field photograph, Layer No. 23, d – field photograph, Layer No. 23, e – parallel-orientated specimens, field photograph, Layer No. 23, f – field photograph, Layer No. 23; g: Didymaulichnus isp., convex epirelief, field photograph, Layer No. 1. Scale bar = 1 cm.

opencc-by-4.0Dec 2021View details →

Text-fig. 9. Progyrolepis heyleri POPLIN, 1999. a: right dentalosplenial of adult specimen in lateral view, GMC 1, scale bar 5 mm; b: left dentalospelenial and suboperculum in medial view, GMC 1, scale bar 5 mm; c: set of bones of the right side of the cheek displaying maxilla, preoperculum, hyomandibula, left and right ceratohyal, epibranchial and neural spine from the axial skeleton, G 123, scale bar 5 mm; d: drawing of the right frontal in dorsal view, GMC 81, scale bar 5 mm; e: right operculum in lateral view, GMC 10, scale bar 5 mm. Abbreviations: Cbr – ceratobranchial, Cer – ceratohyal, Ds – dorsal spine, Hy – hyomandibula, Md – mandible, Mx – maxilla, Op – operculum, Pop – preoperculum. in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central

Text-fig. 9. Progyrolepis heyleri POPLIN, 1999. a: right dentalosplenial of adult specimen in lateral view, GMC 1, scale bar 5 mm; b: left dentalospelenial and suboperculum in medial view, GMC 1, scale bar 5 mm; c: set of bones of the right side of the cheek displaying maxilla, preoperculum, hyomandibula, left and right ceratohyal, epibranchial and neural spine from the axial skeleton, G 123, scale bar 5 mm; d: drawing of the right frontal in dorsal view, GMC 81, scale bar 5 mm; e: right operculum in lateral view, GMC 10, scale bar 5 mm. Abbreviations: Cbr – ceratobranchial, Cer – ceratohyal, Ds – dorsal spine, Hy – hyomandibula, Md – mandible, Mx – maxilla, Op – operculum, Pop – preoperculum.

data sets of "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland"

data sets from "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland" Monthly means ozone profiles data sets of MCH homogenized Dobson D051 and of Brewer B040 used in the article entitled: "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland" by Eliane Maillard Barras, Alexander Haefele, René Stübi, Achille Jouberton, Herbert Schill, Irina Petropavlovskikh, Koji Miyagawa, Martin Stanek, and Lucien Froidevaux. <a href="https://doi.org/10.5194/acp-2022-344">https://doi.org/10.5194/acp-2022-344</a>

opencc-zeroOct 2022View details →

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Evoking the N400 Event-Related Potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)

During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.

Data Used in [~Re] Setting Inventory Levels in a Bike Sharing Network

Data used to reproduce the publication "Setting an Inventory Levels in a Bike Sharing Network" by Datner et al. This data correspond to the scenarios generated from the parameters given by the authors.

Data set for "Cortical sensory processing across motivational states during goal-directed behavior"

Data set for: Matteucci G, Guyoton M, Mayrhofer JM, Auffret M, Foustoukos G, Petersen CCH, El-Boustani S, Cortical sensory processing across motivational states during goal-directed behavior (2022). Neuron https://doi.org/10.1016/j.neuron.2022.09.032 There are 2 files in this upload: 1. The file named "Matteucci2022.pdf" is the Open Access pdf file of the manuscript published in Neuron. 2. The file named "Matteucci_data_code.zip" (~26.5 GB) is a zipped version of a folder "Matteucci_data_code" (~33 GB), which contains the data analysed in the study along with Matlab code used to generate all main figures of the paper. The analysis code is in a subfolder named "code". This subfolder in turn has three subfolders "analysis_scripts", “analysis_functions” (containing the original code for intermediate data processing) and “paper_figures_scripts” (containing the code for generating each figure panel from pre-processed data). The main script “reproduce_figures.m” will call the subscripts contained in the  “paper_figures_scripts” folder to reproduce the plots contained in all main figures of the paper (and take care of adding the relevant code and data folders and subfolders to Matlab file path). The raw and pre-processed data analysed in the study can be found in the folder named "data". A “README.txt” file provides further details on the content of each subfolder.

Data set for the journal article: Tandem electrocatalytic CO2 reduction with Fe-porphyrins and Cu nanocubes enhances ethylene production

Copper-based tandem schemes have emerged as promising strategies to promote the formation of multi-carbon products of the electrocatalytic CO2 reduction reaction. In such approaches, the CO-generating component of the tandem catalyst increases the local concentration of CO and thereby enhances the intrinsic carbon-carbon (C-C) coupling on copper. However, the optimal characteristics of the CO-generating catalyst for maximizing eventual C2 production are currently unknown. In this work, we developed tunable tandem catalysts comprising iron porphyrin (Fe-Por), as the CO-generating component, and Cu nanocubes (Cucub) to understand how the turnover frequency for CO (TOFCO) of the molecular catalysts impacts C-C coupling on the Cu surface. First, we tuned the TOFCO of the Fe-Por by varying the number of orbitals involved in the π-system. Then, by coupling these molecular catalysts with the Cucub, we assessed the current densities and faradaic efficiencies, discovering that all of the designed Fe- Por boost ethylene production. The most efficient Cucub/Fe-Por tandem catalyst was the one including the Fe-Por with the highest TOFCO and exhibited a nearly 22-fold increase in the ethylene selectivity and 100 mV positive shift of the onset potential with respect to the pristine Cucub. These results reveal that coupling the TOFCO tunability of molecular catalysts along with copper nanocatalysts opens up new possibilities towards the development of Cu-based catalysts with enhanced selectivity for multi-carbon product generation at low overpotential.

opencc-zeroOct 2022View details →

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Social learning data in a foraging setting for Heliconius erato

Insects may acquire social information by active communication and through inadvertent social cues. In a foraging setting, the latter may indicate the presence and quality of resources. Although social learning in foraging contexts is prevalent in eusocial species, this behaviour has been hypothesised to also exist between conspecifics in non-social species with sophisticated behaviours, including Heliconius butterflies. Heliconius are the only butterfly genus with active pollen feeding, a dietary innovation associated with a specialised, spatially faithful foraging behaviour known as trap-lining. Long-standing hypotheses suggest that Heliconius may acquire trap-line information by following experienced individuals. Indeed, Heliconius often aggregate in social roosts, which could act as 'information centres', and present conspecific following behaviour, enhancing opportunities for social learning. Here, we provide a direct test of social learning ability in Heliconius using an associative learning task in which naïve individuals completed a colour preference test in the presence of demonstrators trained to feed randomly or with a strong colour preference. We found no evidence that Heliconius erato, which roost socially, used social information in this task. Combined with existing field studies our results add to data which contradict the hypothesised role of social learning in Heliconius foraging behaviour.

In-silico PCR results for PSSC primer sets exhibiting >50% amplification rate

using in-silico PCR, 2,161 genomes from the Pseudomonas syringae species complex were amplified using 16 established PCR primer sets, allowing one mismatch per primer. Each file here contains amplicons generated from a single primer set, with each amplicon sequence named with the GenBank accession number for the associated genome.