Find research datasets worth reusing

opencc-by-4.0Sep 2022View details →

Operator-Software Impact in Local Tie Networks: Case study at Geodetic Observatory Wettzell (Data set)

The operator-software impact describes the differences between results introduced by different operators using identical software packages but applying different analysis strategies to the same data. This contribution studies the operator-software impact in the framework of local tie determination, and compares two different analysis approaches. Both approaches are used in present local tie determinations and mainly differ in the consideration of the vertical deflection within the network adjustment. However, no comparison study has yet been made so far. Selecting a suitable analysis approach is interpreted as a model selection problem, which is addressed by information criteria within this investigation. A suitable model is indicated by a sufficient goodness of fit and an adequate number of model parameters. Moreover, the stiffness of the networks is evaluated by means of principle component analysis. Based on the date of a measurement campaign performed at the Geodetic Observatory Wettzell in 2021, the impact of the analysis approach on local ties is investigated. For that purpose, an innovated procedure is introduced to obtain reference points of space geodetic techniques defining the local ties. Within the procedure, the reference points are defined independently of the used reference frame, and are based on geometrical conditions. Thus, the results depend only on the estimates of the performed network adjustment and, hence, the applied network analysis approach. The comparison of the horizontal coordinates of the determined reference points shows a high agreement. The differences are less than 0.2 mm. However, the vertical components differ by more than 1 mm, and exceed the coverage of the estimated standard deviations. The main reasons for these large discrepancies are a network tilting and a network bending, which is confirmed by a residual analysis.

Replication Package: Model-Driven Engineering for the Interoperability of Simulation Modeling Languages: a Case Study in the Space Industry

Replication package "Architectural Support for Software Performance in Continuous Software Engineering: a Systematic Mapping Study".

Database on soil properties of the CS1 Study case

Soil properties dataset of the CS1 Study Case corresponding to the article "The combination of crop diversification and no tillage enhances key 1 soil quality parameters related to soil functioning without compromising crop yields in a low-input rainfed almond orchard under semiarid Mediterranean conditions" by Almagro et al.

opencc-by-4.0Nov 2022View details →

The linked data ecosystem for SSH and a case study from the cultural heritage domain

Semantic Web, an extension of the current web, focuses on the structure of data. The aim is to develop data structures that will be more effectively processable by computers, in contrast to the limited functionality of the contemporary scriptocentric web. Semantic Web, therefore, aims to transform the web into a global ‘database’ and lead the developments toward the Web of Data. The specifications developed or related to this aim, as well as the processes and rules for achieving it, are known as Linked Data, i.e. (inter)connected data from different sources. Linked Data creates a content-agnostic, as well as software-agnostic ecosystem, which can be used for encoding and publishing all types of information from various domains. The first presentation of this webinar introduces the basic concepts of Linked Data and shows that Linked Data are particularly suitable for Social Sciences and Humanities (SSH) since they do not emphasize metrics and quantifications but conceptualizations and reason. After presenting the paradigm shift introduced by linked data concerning the development of the web, a case study from the cultural heritage domain will be discussed. The second presentation showcases SearchCulture.gr, the Greek cross-domain Cultural Data Aggregator, as a state-of-the-art case, for the use of Linked data in the cultural domain. The National Documentation Centre of Greece (EKT) develops this service, which has collected a growing number of 800.000 digitized Cultural Heritage Objects (CHOs) from 73 cultural institutions. Moreover, it is the Accredited National Aggregator for Europeana having provided more than 580.000 CHOs so far. Addressing metadata heterogeneity has been a key target from the start. Controlled Linked Data vocabularies for item types, historical periods, subjects and persons have been developed over the course of the past years and are being used for the semantic enrichment of the CHOs’ metadata. This presentation addresses the challenges, methodology and tools used over the past 7 years for the process of enriching the aggregated CHOs’ metadata. This process classifies and disambiguates the aggregated data, provides multilinguality and adds significant browse and search functionalities to the portal and, therefore, opens new horizons for SSH research.

Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"

DATASETS Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber* * Correspondence: <a href="mailto:argruber@usp.br">argruber@usp.br</a> (AG); Tel. +55 11 3091 7274   Here we provide different data of Microviridae, Flavivirus and casposons used throughout the work: <ul> <li>Microviridae folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for Microviridae</li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for Microviridae</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the Microviridae family</li> <li>Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset</li> <li>Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 Alpavirinae sequences, 1,040 Gokushovirinae sequences and 295 Pichovirinae sequences</li> <li>Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein Microviridae dataset used in the experiment of Figure 4</li> </ul> </li> </ul> </li> <li>Flavivirus folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for Flavivirus</li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for Flavivirus <ul> <li>full-length – models constructed from full-length protein sequences</li> <li>short - models constructed from selected short alignment blocks of the protein sequences</li> </ul> </li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus Flavivirus</li> <li>Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset</li> <li>Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of Flavivirus, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses</li> <li>Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein Flavivirus dataset</li> </ul> </li> </ul> </li> <li>Casposons folder <ul> <li>casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.</li> <li>casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>casposons_crisprs.fasta – 106 Cas1 bona fide sequences derived from 52 CRISPRs and 54 casposons</li> <li>casposon_family_discrimination.aln - multiple sequence alignment of 52 bona fide CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.</li> <li>casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 bona fide CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons.</li> </ul> </li> </ul> </li> </ul>

Data set for publication Sikora P., Techman M., Federowicz K., El-Khayatt A.M., Saudi H.A., Abd Elrahman M., Hoffmann M., Stephan D., Chung S.-Y. Insight into the microstructural and durability characteristics of 3D printed concrete: Cast versus printed specimens. Case Studies in Construction Materials (2022), 17, e01320.

Open dataset for publication Sikora P., Techman M., Federowicz K., El-Khayatt A.M., Saudi H.A., Abd Elrahman M., Hoffmann M., Stephan D., Chung S.-Y. Insight into the microstructural and durability characteristics of 3D printed concrete: Cast versus printed specimens. Case Studies in Construction Materials (2022), 17, e01320. <a href="https://doi.org/10.1016/j.cscm.2022.e01320">https://doi.org/10.1016/j.cscm.2022.e01320</a> File 1 - Mechanical characteristics - *.opju (Origin) File 2 - Particle size distributions of used materials - *.opju (Origin) File 3 - Sorptivity measurement data - *.opju (Origin) File 4 - G-code for printing of 1 layered specimen - *txt File 5 - G-code for printing of 3 layered specimens - *txt

Benefits and limitations of environmental magnetism for completing citizen science on air quality: a case study in a street canyon.

Inside a street canyon in Montpellier (France) a total of 72 deposimeters were deployed in 29 households for a period of 3 months to measure local air quality. This street canyon was chosen because dwellers were already mobilized against the street traffic, and because they were in conflict on this issue with policy makers. The project aimed to include all the stakeholders through co-construction. The closure of the street during the metrological campaign and the absence of agreement curbed their involvement and motivation. However, the feedbacks from the citizen partners promote the fact that this study supported their claims and brought them a deeper understanding on the micro-scale air quality monitoring. Indeed, it is increasingly difficult for citizens, who seemed specifically interested in what is happening right outside their front door, to understand this measure with the emergence of ever more low-cost sensors. For that reason, we examined the citizen’s degree of confidence in magnetic monitoring of air quality and how can this technique be useful in their claims. The results show that magnetism can be a measurement technique favorable to citizen participation because it provides a large amount of data at the micro-scale of the street level, while the data from the certified associations for monitoring air quality requires a spatial interpolation to map variations on a neighborhood scale. In this study, we proposed a magnetic air quality index to standardize and democratize the magnetic monitoring of air quality to facilitate the dialogue with all stakeholders.

Supplementary Data and Code: Determinants of range sizes pinpoint vulnerability of groundwater species to climate change: a case study on subterranean amphipods from the Dinarides

Supplementary Data and R code for phylogenetic analyses for manuscript entitled Determinants of range sizes pinpoint vulnerability of groundwater species to climate change: a case study on subterranean amphipods from the Dinarides. The dataset contains beast.tree → data for import into R: maximum credibility phylogeny data_lambert.csv → data for import into R: data on habitat and distribution for 52 Niphargus species morpho.csv → data for import into R: morphometric data (body length) for 52 Niphargus species niphargus_ranges.Rmd → fully reproducible R markdown file niphargus_ranges.html → html output of Rmd file To be able to run the analysis put the data files into folder <data> and run the Rmd script.

opencc-zeroJan 2023View details →

Data for: Inadequate sampling of the soundscape leads to overoptimistic estimates of recogniser performance: A case study of two sympatric macaw species

Passive acoustic monitoring (PAM) offers the potential to dramatically increase the scale and robustness of species monitoring in rainforest ecosystems. PAM generates large volumes of data that require automated methods of target species detection. Species-specific recognisers, which often use supervised machine learning, can achieve this goal. However, they require a large training dataset of both target and non-target signals, which is time-consuming and challenging to create. Unfortunately, very little information about creating training datasets for supervised machine learning recognisers is available, especially for tropical ecosystems. Here we show an iterative approach to creating a training dataset that improved recogniser precision from 0.12 to 0.55. By sampling background noise using an initial small recogniser, we addressed one of the significant challenges of training dataset creation in acoustically diverse environments. Our work demonstrates that recognisers will likely fail in real-world settings unless the training dataset size is large enough and sufficiently representative of the ambient soundscape. We outline a simple workflow that can provide users with an accessible way to create a species-specific PAM recogniser that addresses these issues for tropical rainforest environments. Our work provides important lessons for PAM practitioners wanting to develop species-specific recognisers for acoustically diverse ecosystems.

Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study

Data and code for publication on Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study

Reproduction package for the paper "Prospects of Gravitational Wave Follow-up Through a Wide-field Ultra-violet Satellite: a Dorado Case Study"

This is a basic reproduction package for the paper "Prospects of Gravitational Wave Follow-up Through a Wide-field Ultra-violet Satellite: a Dorado Case Study" by [Dorsman et al. (2022)](https://doi.org/10.48550/arXiv.2206.09696). This package provides (1) data and software to reproduce the results from the Bayesian inference, (2) the pre-computed results from the Bayesian inference for the purpose of reproducing the plots, and (3) the plots.

opencc-by-4.0Apr 2022View details →

Case study of a rapid prototyping method for optimizing soft gripper structures with integrated piezoresistive sensors

Closed-loop control systems and monitoring the activities of soft robots in the natural environment require sensing elements in soft actuator modules. In this study, additive manufacturing is used for sensorized soft actuator modules to investigate the influence of the Shore hardness and design aspects of an open-source tendon-based gripper structure, in a time-efficient way. Additionally, the placement of the piezoresistive sensing element (tension or compression side on the bending soft gripper) was investigated. A user-friendly method, based on thermoplastic material extrusion, has been explored to improve the future design optimization in of active soft robotic structures successfully. A higher Shore hardness resulted in a higher total deflection and a higher force to bend the gripper structure. By increasing the geometrical stiffness of the gripper printed with low Shore hardness, the total deflection was increased, but the force needed to activate the movement was higher in comparison to high Shore hardness and low geometrical stiffness. Moreover, the sensing element on the substrate of higher Shore hardness, leads to low drift, monotonic response, with good sensitivity, independent of the sampling rate. The gripper of higher Shore hardness had a larger functional range, being capable of gripping small and larger objects.

opencc-zeroJan 2023View details →

Shifting environmental predictors of phenotypes under climate change: A case study of growth in high latitude seabirds

Climate change is altering species' traits across the globe. To predict future trait changes and understand the consequences of those changes, we need to know the environmental drivers of phenotypic change. In the present study, we use multi-decadal long datasets to determine periods of within-year environmental variation that predict growth of three seabird species. We evaluate whether these periods changed over time and use them to predict future growth under climate change. We find that predictions of trait change could be improved by considering that 1) the timing of environmental factors used to predict traits (predictive-environmental features) can change over time, and 2) the type of predictive-environmental features can change over time. We find evidence of changes in the timing of environmental predictors in all populations studied and evidence for a change in the type of predictor in the studied Arctic murre population. Environmental models of growth predict that warming conditions will decrease growth rates and bird body sizes in two species (black-legged kittiwakem Rissa tridactyla, and glaucous-winged gullm Larus glaucescens), but not the third (thick-billed murrem Uria lomvia). Consequently, climate change is likely to decrease fledging rates in the gulls and kittiwakes. Further, we find that ice-cover historically predicted murre chick growth well, but no longer does – instead air temperature is now a better predictor of murre growth. Our study highlights a need to investigate whether environmental determinants of trait variation commonly shift in a changing climate and whether such changes have implications for adaptation to novel environments.

Case Study Videos for DoppelTest

The video recording of 3 case studies discussed in the paper titled "Doppelganger Test Generation for Revealing Bugs in Autonomous Driving Software". These videos were recorded using <a href="https://doi.org/10.5281/zenodo.7622089">Apollo 7.0</a>

Case study for Sustainable agri-food supply chain planning through multi-objective optimisation

Case study used to solve the multi-objective model proposed in: Sustainable agri-food supply chain planning through multi-objective optimisation

Species distribution and abundance modelling with dynamicSDM: a case study analysis of the red-billed quelea (Quelea quelea).

GBIF_all_aves_2000_2020.csv A dataset containing e-Bird sampling events for all bird species across southern Africa between 2000-2020 (Fink et al., 2021, GBIF, 2021).  Fink, D., T. Auer, A. Johnston, M. Strimas-Mackey, O. Robinson, S. Ligocki, W. Hochachka, L. Jaromczyk, C. Wood, I. Davies, M. Iliff, L. Seitz. 2021. eBird Status and Trends, Data Version: 2020; Released: 2021. Cornell Lab of Ornithology, Ithaca, New York.  \doi{10.2173/ebirdst.2020} GBIF.org (12 July 2021) GBIF Occurrence Download \doi{10.15468/dl.ppcu6q} RBQ_full_analysis.R An R script for the generation of dynamic species distribution and abundance models for nomadic bird, the red-billed quelea (Quelea quelea) using dynamicSDM package functions.  Unfiltered_quelea_occurrence.csv A dataset containing species occurrence and abundance records for the bird species, the red-billed quelea (Quelea quelea) between 1976-2021 (GBIF 2021 & GBIF 2022 & sources listed in Table 1).  GBIF.org (12 July 2021) GBIF Occurrence Download \doi{10.15468/dl.ppcu6q} GBIF.org (25 July 2022) GBIF Occurrence Download \doi{10.15468/dl.k2kftv}   Table S1. Red-billed quelea (Quelea quelea) occurrence and abundance data sources. <table align="left"> <tbody> <tr> <td> Data type </td> <td> Sources </td> </tr> <tr> <td> Control operation </td> <td> <ul> <li>Information Core for Southern African Migrant Pests (ICOSAMP, 2001-2005).</li> <li>Centre for Overseas Pest Research (COPR), Natural History Museum, Tring.</li> <li>Botswana Ministries of Agriculture.</li> <li>Mozambique Ministry of Agriculture</li> </ul> </td> </tr> <tr> <td> Citizen science </td> <td> <ul> <li>Global Biodiversity Information Facility, including iNaturalist, eBird, South Africa Bird Atlas Project (SABAP) and South Africa Bird Ringing Unit (SAFRING) sources.</li> </ul> </td> </tr> <tr> <td> Independent research </td> <td> <ul> <li>EXCEL File "NfA-yearposRAC" (unpublished data set complied by R. A. Cheke, 2010).</li> </ul> </td> </tr> </tbody> </table>

Data for "Measuring Back: Bibliodiversity and the Journal Impact Factor brand. A Case study of IF-journals included in the 2021 Journal Citations Report."

This is the open data for the preprint "Measuring Back: Bibliodiversity and the Journal Impact Factor brand.  A Case study of IF-journals included in the 2021 Journal Citations Report."

Fig. 1 in Nest Entry Shape Change May Cause Nest Abandonment In Urban Cavity-Nesting Species: A Case Study Of The Tree Sparrow Passer Montanus

Fig. 1. Location of the study area (left) and examples of Tree Sparrow nests at the study sites (right). Site 1: Agricultural Practical Training Center, Chonnam National University,

opencc-zeroMar 2023View details →

Using geometric morphometrics to determine the 'fittest' floral shape: a case study in large-flowered buzz-pollinated Melastomataceae

PREMISE Floral shape, i.e. the relative arrangement and position of floral organs, is critical in mediating fit with pollinators and maximizing conspecific pollen transfer. This seems particularly true for functionally specialized systems. To date, however, few studies have attempted to quantify flowers as the inherently three-dimensional structures that they are, and determine the effect of intraspecific shape variation on pollen transfer. We here address this research gap using a functionally specialized system, buzz pollination, where bees extract pollen through vibrations, as a model. Our study species, Meriania hernandoi (Melastomataceae), undergoes a natural floral shape change from pseudo-campanulate corollas with more actinomorphically-arranged stamens (first day) to open corollas with more zygomorphic stamens (second day) over anthesis, providing a natural experiment to test how variation in floral shape affects male and female fitness. METHODS In one population of M. hernandoi, we bagged 51 pre-anthetic flowers and exposed half of them to bee pollinators when they were in either stage of their shape transition. We then collected flowers, obtained 3D flower models through X-ray Computed Tomography for 3D geometric morphometrics, and counted the amount of pollen grains remaining per stamen (male fitness) and stigmatic pollen loads (female fitness). KEY RESULTS We found significantly higher male fitness in open flowers with zygomorphic androecia than in pseudo-campanulate flowers. Female fitness did not differ among floral shapes. CONCLUSIONS These results suggest that there is an 'optimal' shape for male fitness, while the movement of bees around the flower when buzzing the spread-out stamens results in sufficient pollen deposition regardless of floral shape.