Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

Unearthed from old soils: New records of Antarctic tardigrades, nematodes, and rotifers in the Prince-Charles Mountains

Supplementary display items genarted by running the code associated with the pre-print "Unearthed from old soils: New records of Antarctic tardigrades, nematodes, and rotifers in the Prince-Charles Mountains". Sequence records will be availble via an online resource upon submission.

opencc-by-4.0Oct 2024View details →

Miocene construction of the High Andes recorded by exhumation of the Frontal Cordillera, La Ramada Massif of western Argentina (32°S) (Supporting Information)

Supporting datasets for Howlett et al., "Miocene construction of the High Andes recorded by exhumation of the Frontal Cordillera, La Ramada Massif of western Argentina (32°S)" in TECTONICS.

opencc-by-4.0Oct 2024View details →

Demonstration record for discoverable IPCC WGIII data

This is a record used to demonstrate the concept of discoverable data for IPCC AR7 WGIII.

opencc-zeroSep 2024View details →

River flow and catchment rainfall records for the River Garry at Invergarry (Inverness-shire), Scotland, 1913-1915

Daily mean flows for the River Garry at Invergarry (Inverness-shire), Gauge A1, spanning the period 1913-01-01 to 1915-12-31. Data collected by Capt. W. N. McClean via his organisation River Flow Records, assisted by local observers. We acknowledge the sponsorship of Scottish Hydro-Electric and the Scottish Environment Protection Agency in suporting the costs of creating digital time series. Subsequent to the colletion of these records, the River Garry was developed by the construction of dams and hydro power stations below Loch Quoich and Loch Garry. The Scottish Environment Protection Agency (SEPA) subsequently opened a river flow gauging station on the River Garry at Craigard in 1997, approximately 3 km upstream of McClean's gauge, operated until May 2011.

opencc-by-4.0Jul 2021View details →

Modelling of excitation propagation on computer models of insoles colonised by fungal mycelium. Videos and potential difference recordings.

We used an artistic image of the mycelium network projected onto a $364 \times 985$ nodes grid.  The original image $M=(m_{ij})_{1 \leq j \leq n_i, 1 \leq j \leq n_j}$, $m_{ij} \in \{ r_{ij}, g_{ij}, b_{ij} \}$, where $n_i=364$ and $n_j=985$, and $1 \leq r, g, b \leq 255$, was converted to a conductive matrix $C=(m_{ij})_{1 \leq i,j \leq n}$ derived from the image as follows: $m_{ij}=1$  if $r_{ij}>170$, $g_{ij}>170$ and $b_{ij}<200$; a dilution operation was applied to $C$.  FitzHugh-Nagumo (FHN) equations is a qualitative approximation of the Hodgkin-Huxley model of electrical activity of living cells: \begin{eqnarray} \frac{\partial v}{\partial t} & = & c_1 u (u-a) (1-u) - c_2 u v + I + D_u \nabla^2 \\ \frac{\partial v}{\partial t} & = & b (u - v), \end{eqnarray} where $u$ is a value of a trans-membrane potential, $v$ a variable accountable for a total slow ionic current, or a recovery variable responsible for a slow negative feedback, $I$ {is} a value of an external stimulation current. The current through intra-cellular spaces is approximated by $D_u \nabla^2$, where $D_u$ is a conductance. The term $D_u \nabla^2 u$ governs a passive spread of the current. The terms $c_2 u (u-a) (1-u)$ and $b (u - v)$ describe the ionic currents. The term $u (u-a) (1-u)$ has two stable fixed points $u=0$ and $u=1$ and one unstable point $u=a$, where $a$ is a threshold of an excitation. We integrated the system using the Euler method with the five-node Laplace operator, a time step $\Delta t=0.015$ and a grid point spacing $\Delta x = 2$, while other parameters were $D_u=1$, $a=0.13$, $b=0.013$, $c_1=0.26$. We controlled excitability of the medium by varying $c_2$ from 0.05 (fully excitable) to 0.015 (non excitable). Boundaries are considered to be impermeable: $\partial u/\partial \mathbf{n}=0$, where $\mathbf{n}$ is a vector normal to the boundary.  To record dynamics of excitation in the network, as if in laboratory experiments, we simulated electrodes by calculating a potential $p^t_x$ at an electrode location $x$ as $p_x = \sum_{y: |x-y|<2} (u_x - v_x)$. Configuration of electrodes $1, \cdots, 16$ is shown in Fig.~\ref{fig:mycelium}c.  Time-lapse snapshots provided in the paper were recorded at every 100\textsuperscript{th} time step, and we display sites with $u >0.04$; videos and figures were produced by saving a frame of the simulation every 100\textsuperscript{th} step of the numerical integration and assembling the saved frames into the video with a play rate of 30 fps.  Insole_01: Excitation started at electrode E2 Insole_10: Excitation started at electrode E1 Insole_11: Excitation started at electrodes E1 and E2

opencc-by-4.0Aug 2021View details →

Black Lives, British Justice: Black people in London Criminal Justice Records 1720-1841

This dataset brings together all 698 known references to ‘Black’ or possibly Black African heritage people or groups in records of London criminal justice (1720-1841). Each entry includes references to primary sources mentioning the person(s), including in the Old Bailey Proceedings, Ordinary’s Accounts, and Middlesex Criminal Registers. Individuals are trial witnesses, victims, defendants, and people mentioned in passing during testimony. For each entry, a confidence level is offered by the authors, as a person’s ethnicity cannot always be determined with certainty. Evidence for making that judgment is provided. This dataset is useful for anyone interested in Black history in Britain, Black people and justice, or Black London during the age of enslavement. Significant background material is available on the Old Bailey Online website, which provides additional context for these records. The authors also recommend the following works:     * Kathleen Chater. Untold Histories: Black People in England and Wales during the Period of the British Slave Trade, c. 1660-1807 (Manchester, 2011).     * Norma Myers, Reconstructing the Black Past (Frank Cass, 1996).     * Marika Sherwood. ‘Blacks in the Gordon Riots’, History Today, vol. 47 (1997), 24-28. Each record includes details on the name of the Black individual(s), as well as information on up to three sources in which he/she/they have been identified, and an indication by the authors on the likelihood the person is actually Black. Each entry has 17 columns of data, all of which are described in full in the ReadMe.txt file.

opencc-by-4.0Aug 2021View details →

Protein tagged from Covid-19 trial records in ClinicalTrials.gov

Top 200 proteins appeared in the Covid-19 trial records in https://clinicaltrials.gov/, grouped by CATH classification, with URL linking back to the trial record at https://clinicaltrials.gov/.

opencc-by-4.0Oct 2022View details →

Model Output and Figure Scripts for: "Uncertainty in reconstructing paleo-elevation of the Antarctic Ice Sheet from temperature-sensitive ice core records"

New climate model output and figure scripts for the paper "Uncertainty in reconstructing paleo-elevation of the Antarctic Ice Sheet from temperature-sensitive ice core records".

WoS and Scopus records for the bibliometric analysis in the output D2.2 Digital transformation of research and innovation roadmap of the reSEArch-EU project

These files represent the exported WoS and Scopus records, used in the output D2.2 Digital transformation of research and innovation roadmap  of the Horizont project reSEArch-EU, implemented by the SEA-EU university alliance.

Microearthquake sequence recorded close to the Montello thrust system (Southeastern Alps)

Seismic catalogues (QuakeML format) of a microearthquake sequence occurred on August 2021 in the Montello thrust area and recorded by the Collalto seismic network (<a href="https://doi.org/10.7914/SN/EV">10.7914/SN/EV</a>); the seismic catalogues are provided, separately, for different earthquake location codes (h71=Hypo71; hel=Hypoellipse; hypoDD=HypoDD; migraloc=Migraloc). DATA_tgz_SAC.tar contains earthquake waveforms (SAC format) with P and S arrival times used for the locations. Other details in Peruzza et al. (2022, doi: 10.3389/feart.2022.1044296).

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Health records

Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation.  ------------------------------------------------------------------------------------- This dataset contains GWAS summary statistics for infection, inflammation, and allergy related traits in 487,297 individuals

How to find data at the Danish National Archives [Webinar recording]

The Danish National Archives have launched Digidata (https://digidata.rigsarkivet.dk/) which makes it easier for researchers and students to find and gain access to our large collection of research data (approx. 3000 datasets, primarily from surveys) and administrative data (approx. 6000 datasets, e.g. registers such as the Conscription Register and the Taxpayer Register). In the webinar, the presenter showed show how you could use Digidata platform to search for a dataset. Note: Portal presented at the event is in the Danish language. The video is available on the <a href="https://www.youtube.com/watch?v=vsKaT3_TDSM">CESSDA Training YouTube channel.</a>

opencc-by-4.0May 2023View details →

New records of the Atlantic blue crab Callinectes sapidus Rathbun, 1896 in European waters

New records of the Atlantic blue crab Callinectes sapidus Rathbun, 1896 in European waters (between 2019 and 2022).

opencc-by-4.0Dec 2022View details →

OpenChart-SE: A corpus of artificial Swedish electronic health records for imagined emergency care patients written by physicians in a crowd-sourcing project

Electronic health records (EHRs) are a rich source of information for medical research and public health monitoring. Information systems based on EHR data could also assist in patient care and hospital management. However, much of the data in EHRs is in the form of unstructured text, which is difficult to process for analysis. Natural language processing (NLP), a form of artificial intelligence, has the potential to enable automatic extraction of information from EHRs and several NLP tools adapted to the style of clinical writing have been developed for English and other major languages. In contrast, the development of NLP tools for less widely spoken languages such as Swedish has lagged behind. A major bottleneck in the development of NLP tools is the restricted access to EHRs due to legitimate patient privacy concerns. To overcome this issue we have generated a citizen science platform for collecting artificial Swedish EHRs with the help of Swedish physicians and medical students. These artificial EHRs describe imagined but plausible emergency care patients in a style that closely resembles EHRs used in emergency departments in Sweden. In the pilot phase, we collected a first batch of 50 artificial EHRs, which has passed review by an experienced Swedish emergency care physician. We make this dataset publicly available as OpenChart-SE corpus (version 1) under an open-source license for the NLP research community. The project is now open for general participation and Swedish physicians and medical students are invited to submit EHRs on the project website (<a href="https://github.com/Aitslab/openchart-se">https://github.com/Aitslab/openchart-se</a>), where additional batches of quality-controlled EHRs will be released periodically.     Dataset content OpenChart-SE, version 1 corpus (txt files and and dataset.csv) The OpenChart-SE corpus, version 1, contains 50 artificial EHRs (note that the numbering starts with 5 as 1-4 were test cases that were not suitable for publication). The EHRs are available in two formats, structured as a .csv file and as separate textfiles for annotation. Note that flaws in the data were not cleaned up so that it simulates what could be encountered when working with data from different EHR systems. All charts have been checked for medical validity by a resident in Emergency Medicine at a Swedish hospital before publication.   Codebook.xlsx The codebook contain information about each variable used. It is in XLSForm-format, which can be re-used in several different applications for data collection.   suppl_data_1_openchart-se_form.pdf OpenChart-SE mock emergency care EHR form.   suppl_data_3_openchart-se_dataexploration.ipynb This jupyter notebook contains the code and results from the analysis of the OpenChart-SE corpus.   More details about the project and information on the upcoming preprint accompanying the dataset can be found on the project website (<a href="https://github.com/Aitslab/openchart-se">https://github.com/Aitslab/openchart-se</a>).

Aggregated number of officially recorded COVID-19 deaths in 2020 in Poland by county (powiat) with indication of sources

This is a complimentary dataset for the article "Deaths during the first year of the COVID‑19 pandemic: insights from regional patterns in Germany and Poland" by Myck, Oczkowska, Garten, Krol, Brandt in BMC Public Health (DOI: 10.1186/s12889-022-14909-9).

3DED/MicroED datasets of hemozoin recorded by a SINGLA detector

32 diffraction datasets were collected using a Thermo Scientific Glacios operated at 200 kV with a stage temperature of ~80 K. The gun lens was reduced to the minimum (8), and spot size (11) with a C2 aperture of 50 µm was used. The beam was brought to parallel corresponding to a beam diameter of approximately 1.7 µm. The diffraction images were recorded by a DECTRIS SINGLA detector in the h5 format. NeXus format header files were subsequently generated using Nexgen (https://github.com/dials/nexgen). The diffraction patterns were collected at a nominal camera length of 677 mm according to the microscope control software (estimated to be to 809 mm at the detector). The sample was rotated through 90° over 18s with the camera collecting data at 50 Hz, producing images representing 0.1°. Subsequently, the oscillation angle was refined to 0.11°. The dose rate under these conditions was 0.01 e- Å-2 s-1. A data processing script is provided to index, integrate and scale 64 lattices across the datasets using DIALS 3.13

A collection of fully-annotated soundscape recordings from the southern Sierra Nevada mountain range

This collection contains 100 soundscape recordings of 10 minutes duration, which have been annotated with 10,296 bounding box labels for 21 different bird species from the Western United States. The data were recorded in 2015 in the southern end of the Sierra Nevada mountain range in California, USA. This collection has been featured as test data in the 2020 BirdCLEF and Kaggle Birdcall Identification competition and can primarily be used for training and evaluation of machine learning algorithms. Data collection The recordings were made in Sequoia and Kings Canyon National Parks, two contiguous national parks in the southern Sierra Nevada mountain range in California, USA. The focus of the acoustic study was the high-elevation region of the Parks; specifically, the headwater lake basins above 3,000 km in elevation. The original intent of the study was to monitor seasonal activity of birds and bats at lakes containing trout and lakes without trout, because the cascading impacts of trout on the adjacent terrestrial zone remain poorly understood. Soundscapes were recorded for 24 h continuously at 10 lakes (5 fishless, 5 fish-containing) throughout Sequoia and Kings Canyon National Parks during June-September 2015. Song Meter SM2+ units (Wildlife Acoustics, USA) powered by custom-made solar panels were used to obviate the need to swap batteries, due to the recording locations being extremely difficult to access. Song Meters continuously recorded mono-channel, 16-bits uncompressed WAVE files at 48 kHz sampling rate. For this collection, recordings were resampled at 32 kHz and converted to FLAC. Sampling and annotation protocol A total of 100 10-minute segments of audio between July 9 and 12, 2015 from morning hours (06:10-09:10 PDT) from all 10 sites were selected at random. Annotators were asked to box every bird call they could recognize, ignoring those that are too faint or unidentifiable. Every sound that could not be confidently assigned an identity was reviewed with 1-2 other experts in bird identification. To minimize observer bias, all identifying information about the location, date and time of the recordings was hidden from the annotator. Raven Pro software was used to annotate the data. Provided labels contain full bird calls that are boxed in time and frequency. In this collection, we use eBird species codes as labels, following the 2021 eBird taxonomy (Clements list). Unidentifiable calls have been marked with “????” and were added as bounding box labels to the ground truth annotations. Parts of this dataset have previously been used in the 2020 BirdCLEF and Kaggle Birdcall Identification competition. Files in this collection Audio recordings can be accessed by downloading and extracting the “soundscape_data.zip” file. Soundscape recording filenames contain a sequential file ID, recording date and timestamp in PDT (UTC-7). As an example, the file “HSN_001_20150708_061805.flac” has sequential ID 001 and was recorded on July 8th 2015 at 06:18:05 PDT. Ground truth annotations are listed in “annotations.csv” where each line specifies the corresponding filename, start and end time in seconds, low and high frequency in Hertz and an eBird species code. These species codes can be assigned to scientific and common name of a species with the “species.csv” file. The approximate recording location with longitude and latitude can be found in the “recording_location.txt” file. Acknowledgements  Compiling this extensive dataset was a major undertaking, and we are very thankful to the domain experts who helped to collect and manually annotate the data for this collection (individual contributors in alphabetic order): Anna Calderón, Thomas Hahn, Ruoshi Huang, Angelly Tovar

Extreme precipitation records in Antarctica [Dataset]

This is the dataset associated to the research 'Extreme precipitation records in Antarctica' published in International Journal of Climatology. This repository contains: <ul> <li>Precipitation extremes for each model at every grid point for a duration of xxx days. Files named: <ul> <li>[model]_PCP_max_[xxx]d.csv <ul> <li>Dimensions for ERA5: [lons, lats]</li> <li>Dimensions for RACMO2: [grid_x, grid_y]</li> <li>Units: mm</li> </ul> </li> </ul> </li> <li>Dimensions to plot the precipitation extremes: lons (longitudes), lats (latitudes) and duration. Files named: <ul> <li>[model]_PCP_max_lats.csv <ul> <li>Dimensions for ERA5: [lats]</li> <li>Dimensions for RACMO2: [grid_x, grid_y]</li> <li>Units: degrees</li> </ul> </li> <li>[model]_PCP_max_lons.csv <ul> <li>Dimensions for ERA5: [lons]</li> <li>Dimensions for RACMO2: [grid_x, grid_y]</li> <li>Units: degrees</li> </ul> </li> <li>[model]_PCP_max_duration.csv <ul> <li>Dimensions: [time]</li> <li>Units: days</li> </ul> </li> </ul> </li> <li>World Precipitation Records from 1 day. File named: <ul> <li>Max_WR_from1day.csv (first row duration [days]; second row precipitation [mm])</li> </ul> </li> </ul>   How to cite If you use this dataset, please cite the accompanying paper as: González-Herrero, S.,Vasallo, F., Bech, J., Gorodetskaya, I., Elvira, B., & Justel, A. (2023). Extreme precipitation records in Antarctica.International Journal of Climatology, 43(7), 3125–3138. <a href="https://doi.org/10.1002/joc.8020">https://doi.org/10.1002/joc.8020</a>   Complementary code You can find the jupyter notebooks to complement the research in: <a href="https://github.com/sergigonzalezh/Extreme_PCP_Scaling_Antarctica">https://doi.org/10.1002/joc.8020</a>   Contact If you have any question, please contact with Sergi at <a href="mailto:sergi.gonzalez@slf.ch">sergi.gonzalez@slf.ch</a>

opencc-by-4.0Feb 2023View details →

Migration Data Inventory Records

This inventory includes metadata on various quantitative sources of information on migration that can be used for modelling purposes. Documentation: http://www.quantmig.eu/res/QuantMig_documentation_website.pdf Instructional video: https://www.youtube.com/watch?v=Lqm36f0lXho How to cite: Soto Nishimura A and Mooyaart J (2021) Migration Data Inventory Records: Data Inventory. Online resource, available at <a href="http://www.quantmig.eu/data_inventory/">http://www.quantmig.eu/data_inventory/.</a>