Find research datasets worth reusing

opencc-zeroSep 2020View details →

Data and code for: The evolution of siphonophore tentilla for specialized prey capture in the open ocean

Predator specialization has often been considered an evolutionary 'dead-end' due to the constraints associated with the evolution of morphological and functional optimizations throughout the organism. However, in some predators, these changes are localized in separate structures dedicated to prey capture. One of the most extreme cases of this modularity can be observed in siphonophores, a clade of pelagic colonial cnidarians that use tentilla (tentacle side branches armed with nematocysts) exclusively for prey capture. Here we study how siphonophore specialists and generalists evolve, and what morphological changes are associated with these transitions. To answer these questions, we: (1) measured 29 morphological characters of tentacles from 45 siphonophore species, (2) mapped these data to a phylogenetic tree, and (3) analyzed the evolutionary associations between morphological characters and prey type data from the literature. Instead of a dead-end, we found that siphonophore specialists can evolve into generalists, and that specialists on one prey type have directly evolved into specialists on other prey types. Our results show that siphonophore tentillum morphology has strong evolutionary associations with prey type, and suggest that shifts between prey types are linked to shifts in the morphology, mode of evolution, and genetic correlations of tentilla and their nematocysts. The evolutionary history of siphonophore specialization helps build a broader perspective on predatory niche diversification via morphological innovation and evolution. These findings contribute to understanding how specialization and morphological evolution have shaped present-day food webs.

Think Open Rovereto Workshop 2020 Registered participants from outside Italy

In this map there is shown the distribution of registered participants to the first edition of Think Open Rovereto Workshop (2020) coming from outside Italy.

opencc-zeroSep 2020View details →

Plant DNA metabarcoding records from three cores of lacustrine lakes along a open larch forest-forest tundra-tundra transect at the Omoloy region, north-eastern Siberia

Here, we provide the raw plant DNA metabarcoding data archived in three Siberian lake sediment cores spanning the mid-Holocene to the present (7.6-0 cal ka BP), from northern typical tundra to southern open larch forest in the Omoloy region. There are three cores: <ol> <li> 14-OM-20B, Lat. / °: 70.53, Lon. / °: 132.91, Ele. / m a.s.l.: 52, Modern vegetation: open larch forest, Lake area / km2: 0.26, Maximal depth / m: 3.4</li> <li> 14-OM-02B, Lat. / °: 70.72, Lon. / °: 132.67, Ele. / m a.s.l.: 58, Modern vegetation: forest tundra, Lake area / km2: 0.08, Maximal depth / m: 3.5</li> <li> 14-OM-12A, Lat. / °: 70.96, Lon. / °: 132.57, Ele. / m a.s.l.: 60, Modern vegetation: tundra, Lake area / km2: 0.09, Maximal depth / m: 4.5</li> </ol> Three lake sediment cores, 14OM12A (33 cm long), 14OM02B (49.5 cm long) and 14OM20B (86 cm long), were recovered from three sites using a UWITEC gravity corer (6 cm internal diameter) equipped with a hammer tool in July 2014. From the three cores, 16 bulk organic carbon samples were selected because of the lack of macrofossil remains and radiocarbon dated using accelerator mass spectrometry (AMS) at Poznań radiocarbon laboratory of Adam Mickiewicz University, Poland. In addition, 30 freeze-dried samples per core at 0.25 or 0.5 cm intervals between 0 and 15 cm were analysed for 210Pb/137Cs at the Liverpool University Environmental Radioactivity Laboratory. (The dating table has been submitted to PANGAEA) In this project, we analyse pollen (has been submitted to PANGAEA, doi: 10.1594/PANGAEA.922550) and sedaDNA from three lake sediment cores from the Omoloy region in north-eastern Siberia (northern Yakutia), which are currently surrounded by different vegetation types ranging from typical tundra to open larch forest. First, our aim is to compare sedaDNA with the pollen data to see whether both methods track the same pattern with respect to compositional changes and diversity changes across the northern Russian treeline zone or are complementary to each other. Second, we reconstruct the mid- to late-Holocene changes of vegetation composition along a north–south transect. Third, we use the sedaDNA data to reconstruct variations in species richness and relate this to vegetation and climate change.

Euro-Calliope model and results for "Open Source Energiewende" multi-model analysis

Contains the model version of Euro-Calliope applied in the multi-model analysis "Open Source Energiewende" and the aggregated results of six scenarios. See `./README.md` for more information.

The Evolving Nature of Developers' Contributions in Open Source Projects

Vídeo com a apresentação do artigo The Evolving Nature of Developers’ Contributions in Open Source Projects Autores: Talita Orfanó, Mariza Bigonha, Kecia Ferreira

opencc-by-4.0May 2020View details →

Integrating QSAR models predicting acute contact toxicity and mode of action profiling in honey bees (A. mellifera): Data curation using open source databases, performance testing and validation

This excel file (DOI: <a href="https://doi.org/10.5281/zenodo.3755675">https://doi.org/10.5281/zenodo.3755675</a>) provides the collection of raw data used for developing the first integrative Quantitative Structure-Activity Relationship (QSAR) model using EFSA's OpenFoodTox, US-EPA ECOTOX and Pesticide Properties DataBase i) to predict acute contact toxicity (LD50) and ii) to profile the Mode of Action (MoA) of pesticides active substances in honey bees (Apis mellifera). Chemical identifiers (e.g. SMILES, CAS n., InChI) and acute contact toxicity data (LD50) on honey bees were used to develop and validate i) a two-category QSAR model (toxic/non-toxic; n=411) (sensitivity =0.93), specificity =0.85), balanced accuracy =0.90), Matthews correlation coefficient MCC=0.78), and ii) a regression-based model (n=113) (R2=0.74; MAE=0.52). Similarly, current study proposes the first MoA profiling for 113 pesticides active substances and the first harmonised MoA classification scheme for acute contact toxicity in honey bees, including LD50s data points from three different databases such as EFSA's OpenFoodTox, US-EPA ECOTOX and Pesticide Properties DataBase. Such classification allows to further define MoAs and the target site of Plant Protection Products (PPPs) active substances, thus enabling regulators and scientists to refine chemical grouping and toxicity extrapolations for single chemicals and component-based mixture risk assessment of multiple chemicals. The full data collection and analysis of QSAR models, toxicity data (LD50) and Mode of Action (Moa) data are described in Carnesecchi et al., 2020 (DOI: doi.org/10.1016/j.scitotenv.2020.139243). This work was supported by the European Food Safety Authority (EFSA) [contract number: OC/EFSA/SCER/2018/01 and NP/EFSA/AFSCO/2016/02 (Edoardo Carnesecchi)].

Sample Dataset for the UN Open GIS Initiative - WG2 and WG3 QGIS 3.10-GeoAnalysis Practice

Sample Dataset for the UN Open GIS Initiative - WG2 and WG3 QGIS 3.10-GeoAnalysis Practice including 26 geoanalytic functions for PKO. vector: OpenStreetMap vector dataset (8 shapefiles) for the city of Seoul (version date 2018-07-22T20:00:02, CRS: WGS84) licensed under the Open Database 1.0 License. raster: (a)Landsat8 image (code: LC08_L1TP_115034_20180721_20180731_01_T1, CRS: WGS84/UTM zone 52N), 11 bands. (b) Aster Digital Elevation map (20 m, CRS: WGS84) for the city of Seoul See: <a href="https://qgis3-10-geoanalysis-un.readthedocs.io">UN Open GIS Initiative - WG2 and WG3 QGIS 3.10-GeoAnalysis Practice</a>

opencc-by-4.0Nov 2019View details →

OPEN-WINDOW: SOUND EVENT DATABASE FOR RESEARCH AND DEVELOPMENT

(1) Background: Situated in the domain of urban sound scene classification by humans and machines, the research in this project will be a first step towards mapping urban noise pollution experienced indoors and finding ways to reduce its negative impact in peoples' homes. The acoustic distinction between outdoor and indoor scenes is an active research field and can be automated with some success. A much subtler difference is the change in the indoor soundscape induced by an open window. Being able to determine this, however, would allow applications in warning systems and be a prerequisite for an app-based urban sound mapping project. Acoustic detection requires neither line of sight nor sensors at the window frame or knowledge of the number of windows or their size. The task, however, varies substantially in difficulty with the amount of sound inside and outside. From the point of machine classification, the lack of specificity is the most problematic aspect: Very few sounds if any can be assumed to originate exclusively from outside and be present at all times to aid automatic detection. The required generalisation ability, however, can be assumed for humans, who might also use very subtle cues in the change of reverberations.   (2) Dataset (a) Recording locations The recordings have been made at three different locations.  <ul> <li>Farm: A farm in Brook, Surrey, United Kingdom. The recordings were made in an open-plan studio flat area in the centre of the farm. The recordings in this location have the lowest levels of background noise, due mainly to a quiet environmental surrounding.</li> <li>Office 1: An office at the University of Surrey, Guildford, United Kingdom. The recordings were made in an open-plan office located on the first floor, at the Centre for Vision, Speech and Signal Processing (CVSSP). Since this office accommodates 16 researchers, recordings in this location have the highest level of background noise</li> <li>Office 2: An office at the University of Surrey, Guildford, United Kingdom. The recordings were made in a small size open-plan office at the CVSSP. This office accommodates 8 researchers and the recordings made in this office considered to have a medium level of background noise.</li> </ul> (b) Recording equipment The recordings made at the two offices and a studio flat in a farm used a dedicated laptop, Focusrite Clarett 4pre USB external sound card (44,100 Hz sample rate at 16 bits per sample) 1, and a Behringer ECM 8000 microphone. (c) Recording setup The Behringer ECM 8000 microphone is connected to the External Line Return (XLR) input of the Focusrite Clarett external sound card via an XLR cable. The external sound card is connected to the dedicated laptop and controlled using Ableton Live 10 software for setting configurations and exporting the recorded audio files. The microphone is located approximately 10 cm away from the window and fixed using a microphone holder. At each location 90 audio sessions are recorded; 60 one minute recordings for static state setup and 30 fifteen seconds recordings for transitional state setup. (d) File naming conventions The naming convention for audio recording is as follows: [Location] [State] [Time] [IDX] [State] will be one of the following: “O stands for open, C stands for Close, OC means a transition from Open to Close and CO stands for a transition from Close to Open.” [Time] stamp will be one of the following: “AM stands for morning between 9:00 to 12:00, N stands for noon which is between 13:00 to 15:00 and PM which stands for an afternoon which is between 17:00 to 20:00.” [IDX] is representing the file ID number. For example, “Farm C PM 01.wav”, means this file is recorded at the farm and in the afternoon when the window is closed and the file ID is 01. (e) Dataset acquisition: A recording kit consisting of a dedicated laptop and microphone will be given to volunteers. Custom-programmed software will remind the user to specify the window state (establishing the so-called ground truth). (f) Specifications   - Open-Window contains 270 audio recordings totalling 3.37 hours of audio.   - Each audio recording belongs to one of the four classes representing the window states; two stationary states (Open, Close) and two transitional states (Open-Close, Close-Open).   - The recordings were carried out in different locations and at different times of the day.       - Three locations: Office1, Office2, Farm       - Three periods of the day: Morning, Afternoon, Evening   - The recordings are split into six-folds.       - Fold 1 is the test set.       - Fold 2 is the validation set.       - Folds 3-6 comprise the training set.     Each fold is balanced in terms of the class and location distribution.   - The annotations/metadata can be found in annotations.csv.   - The recordings for the stationary states are approximately 60 seconds, while the recordings for the transitional states are approximate 15 seconds.   - The format of the recordings is 2-channel 16-bit PCM sampled at 44.1 kHz.

opencc-by-4.0Dec 2019View details →

Exploring the reach of open access content to non-academic audiences

Raw data from survey run on nature.com, springerlink and biomedcentral.com in association with VSNU. Relates to publication "Exploring the reach of open access content to non-academic audiences" <a href="https://www.doi.org/10.5281/zenodo.4143313">https://www.doi.org/10.5281/zenodo.4143313</a>

opencc-by-3.0Nov 2020View details →

A heterometallic [LnLn'Ln] lanthanide complex as a qubit with embedded quantum error correction. Open data set

Includes data relevant for publication with DOI <a href="https://doi.org/10.1021/acsnano.0c03167">10.1039/d0sc03107k</a> plus a table with information on how the data were obtained and processed.

opencc-zeroNov 2020View details →

Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein Tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights with potential therapeutic implications. Our findings demonstrate the power of iDAPT as a discovery platform for both the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

Student oriented subset of the Open University Learning Analytics dataset

The Open University (OU) dataset is an open database containing student demographic and click-stream interaction with the virtual learning platform. The available data are structured in different CSV files. You can find more information about the original dataset at the following link: <a href="https://analyse.kmi.open.ac.uk/open_dataset">https://analyse.kmi.open.ac.uk/open_dataset</a>. We extracted a subset of the original dataset that focuses on student information. 25,819 records were collected referring to a specific student, course and semester. Each record is described by the following 20 attributes:  code_module, code_presentation, gender, highest_education, imd_band, age_band, num_of_prev_attempts, studies_credits, disability, resource, homepage, forum, glossary, outcontent, subpage, url, outcollaborate, quiz, AvgScore, count. Two target classes were considered, namely Fail and Pass, combining the original four classes (Fail and Withdrawn and Pass and Distinction, respectively). The final_result attribute contains the target values. All features have been converted to numbers for automatic processing. Below is the mapping used to convert categorical values to numeric: <ul> <li>code_module: 'AAA'=0, 'BBB'=1, 'CCC'=2, 'DDD'=3, 'EEE'=4, 'FFF'=5, 'GGG'=6</li> <li>code_presentation: '2013B'=0, '2013J'=1, '2014B'=2, '2014J'=3</li> <li>gender: 'F'=0, 'M'=1</li> <li>highest_education: 'No_Formal_quals'=0, 'Post_Graduate_Qualification'=1, 'HE_Qualification'=2, 'Lower_Than_A_Level'=3, 'A_level_or_Equivalent'=4</li> <li>IMBD_band: 'unknown'=0, 'between_0_and_10_percent'=1, 'between_10_and_20_percent'=2, 'between_20_and_30_percent'=3, 'between_30_and_40_percent'=4, 'between_40_and_50_percent'=5, 'between_50_and_60_percent'=6, 'between_60_and_70_percent'=7, 'between_70_and_80_percent'=8, 'between_80_and_90_percent'=9, 'between_90_and_100_percent'=10</li> <li>age_band: 'between_0_and_35'=0, 'between_35_and_55'=1, 'higher_than_55'=2</li> <li>disability: 'N'=0, 'Y'=1</li> <li>student's outcome: 'Fail'=0, 'Pass'=1</li> </ul> For more detailed information, please refer to: Casalino G., Castellano G., Vessio G. (2021) Exploiting Time in Adaptive Learning from Educational Data. In: Agrati L.S. et al. (eds) Bridges and Mediation in Higher Distance Education. HELMeTO 2020. Communications in Computer and Information Science, vol 1344. Springer, Cham. <a href="https://www.google.com/url?q=https%3A%2F%2Fdoi.org%2F10.1007%2F978-3-030-67435-9_1&sa=D&sntz=1&usg=AFQjCNF7fUT9S4TcSpImSr4e_DjaLn3wtg">https://doi.org/10.1007/978-3-030-67435-9_1</a>

Making plasma science more open, collaborative, and reproducible

The reproducibility crisis of modern science is the inability of scientists to reproduce roughly half of the results published in scientific journals. This crisis has affected a broad range of fields, such as psychology, chemistry, and oncology. While physicists tend to have high confidence that physics research is reproducible, no comprehensive studies have been performed to support or refute this claim. Nevertheless, the scientific, cultural, and institutional practices that contribute to the reproducibility crisis in other fields are also present in plasma science. This tutorial will describe how to implement best practices for scientific reproducibility into plasma research. The talk will begin by outlining sources of irreproducibility, such as cognitive biases, improper use of statistics, publication bias, closed access policies for data and software, and the reward system for modern academia. The talk will then describe remedies for these problems such as open access data policies; open metadata standards; open source software; training on proper use of statistics; pre-registration of research methodologies; independent methodological and statistical support; and valuing the reproducibility of research in tenure, hiring, and funding decisions.

An open dataset of scholarly publications highlighted by journal editors

Abstract: We present a dataset of scholarly publications featured as outstanding by journal editors. This first version, which covers the last 10 years, includes papers referenced in (a) Breakthroughs of the year by Science Magazine (b) Les 10 découvertes de l'année by La Recherche Magazine (c) research highlights by Nature journal and (c) Editors' choice by Science magazine. The rationale and process of its creation are described in details in the  following pre-print: Mugabushaka, A.M. , Sadat, J and Dantas Faria, J.C. (2020). In Search of Outstanding Research Advances: prototyping the creation of an open dataset of "editorial highlights" .  <a href="https://arxiv.org/abs/2011.07910">Arxiv 2011.07910</a> Description of the dataset In this version, the datasets are released in 4 Microsoft Excel Files. 1. Science - Breakthroughs of the year 2. La Recherche - les dix découvertes de l'année 3. Nature Magazine - Research highlights 4. Science magazine - Editors' choices The entries for each year are recorded in a separate sheet. In each sheet, the highlighting article and its metadata are recorded as well as the referenced papers together with their identifiers (doi)

Process Not Product: How the Open Life Science Mentoring Program Creates Open Science Ambassadors

Episode Summary In this episode we talk to Yo Yehudi and Malvika Sharan, two of the co-founders and organisers of the Open Life Science training and mentoring program. We discuss why mentorship and community are so important in encouraging open science, what makes the program unique, and what the future for Open Life Science.  Episode Links <ul> <li><a href="https://openlifesci.org/">Open Life Science</a></li> <li><a href="https://about.me/malvikasharan">Malvika Sharan</a> <ul> <li><a href="https://twitter.com/MalvikaSharan">Twitter</a></li> </ul> </li> <li><a href="https://yo-yehudi.com/">Yo Yehudi</a> <ul> <li><a href="https://twitter.com/yoyehudi">Twitter</a></li> </ul> </li> </ul>

A Transformative Edge: How Transformative Learning Can Benefit Open Science

In this episode we talk to Ursel Biester and Marylin Mehlmann, two experts in adult education, about what Transformative Learning is and how it can be applied to creating meaningful change in the context of trainings, including those in the Open Science and RRI movement.  Episode Links <a href="http://www.hostingtransformation.eu/a-transformative-edge/">The Transformative Edge Book</a> <a href="http://www.hostingtransformation.eu/about/">Hosting Transformation Project</a>

Exploring the formation processes on open-air Palaeolithic sites: a late Middle Pleistocene Acheulean assemblage at Arbo site (Miño River basin, Spain)

Dataset (.shp file) of lithic industry and natural clasts  late Middle Pleistocene Acheulean assemblages at Arbo site.

opencc-by-sa-4.0Dec 2020View details →

Industrial Electronics 4.0: Is It Going to Be Free and Open?

The presentation addresses phenomena of free software and open hardware and it is based on twelve years of the author's experience in using free software, ten years of teaching a course that covers free software tools used in electrical engineering, about five years of experience with open hardware, and four years of teaching a reformed course in electrical measurements, which involves extensive use of free software. Teaching experiences are presented in the paper, plans for further improvements in existing courses, as well as some ideas about new courses that would cover free software and open hardware topics not covered already. Actual software tools are discussed. Also, the use of free software, open hardware, open data, and open culture in general, in research practice is presented, where open access articles and open public repositories are new means for disseminating scientific information supporting reproducibility and verifiability of the results, extending the information exchange beyond the paper form. In embedded systems, the method of building upon finds free software a useful tool, besides security and privacy advantages. Promising ongoing projects, like open instruction set architectures, are also discussed. In the time when Industry 4.0 and the fourth industrial revolution are discussed, it seems that open models of software, scientific, and intellectual production are unexpected winners, regardless indirect supporting business models. According to author's experience, free software is mature enough and offers numerous advantages to be a basic tool in education, and open culture practices require modification of curricula to address the situation already present.

opencc-zeroDec 2020View details →

Association of APOE gene polymorphisms with primary open angle glaucoma in Brazilian patients

Background: Primary open-angle glaucoma (POAG) is a multifactorial disease that affects 65.5 million people worldwide. In addition to the genetic variants already established as indicators of greater risk for POAG, the apolipoprotein (APOE) gene has been studied in some populations, with controversial results. The aim of this study is to investigate the frequency of the genetic variants of APOE in the Brazilian population, and to evaluate the association between these polymorphisms and the risk of POAG. Methods: APOE variants (rs429358; rs7412) were genotyped in 402 POAG patients and 401 controls. We evaluated the association between APOE genetic variants and the risk for POAG, as well as the correlation between the requirement of glaucoma surgery and the APOE polymorphisms. Results: Among the three APOE gene isoforms, we found a low frequency of APOE alleles ε2 (7.34%) and ε4 (11.76%), but a high frequency of ε3 (80.88%) in our population. When compared to ε3ε3 reference genotype, ε2 allele-carriers (OR=1.516; p-value=0.04) and ε2ε3 genotype (OR=1.655; p-value=0.02) were associated with a greater risk for POAG. An additive genetic model confirmed the influence of the ε2 allele in the risk of POAG in this sample of the Brazilian population (OR=1.502; p-value=0.04). There was no significant association between the analyzed genotypes and the requirement or number of glaucoma surgeries (p>0.05). Conclusion: Brazilian individuals carrying the APOEε2 allele may be at an increased risk for the development of POAG.