Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila

Data from sleep study of Drosophila Allnighter mutation. Relevant to Figure 7 of publication Shashank et al. Nature Communication (in press).  Ethoscopes were used for video tracking of Drosophila activity. Resulting activity records are contained in the current datasets.

opencc-by-4.0May 2023View details →

Twitter links to tweets from Flemish parties and chairmen in advance of the 2019 elections

This is a list of al tweets used in the Master's Thesis of Toon Tabruyn to obtain the degree of Master of Sociology.

opencc-by-4.0May 2023View details →

Code. Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology

The code used for the analyses for the paper entitled "Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology".

opencc-by-4.0Apr 2023View details →

Dataset for Requirements Classification in Traceability Link Recovery Datasets

The dataset contains a gold standard for classifying parts of requirements in five traceability link recovery benchmark datasets. Classification <ul> <li>For aspect classification: <ul> <li>functional aspects (F)</li> <li>quality aspects (Q)</li> </ul> </li> <li>For concerns in functional requirements (c.f. <a href="https://doi.org/10.1109/RE48521.2020.00028">NoRBERT publication</a>): <ul> <li>Function: A function that a system shall perform</li> <li>Behavior: Behavior, the system displays or reactions that are triggered by one or more stimuli</li> <li>Data: A data item or data structure that shall be part of a system's state</li> <li>UserRelated: Behavior of the user or functionality of the system attributable to the user</li> </ul> </li> </ul> Datasets The dataset comprises preprocessed requirements of the eTour, iTrust, SMOS, eAnci and LibEST datasets. As SMOS and eAnci's original requirements were written in Italian, the dataset comprises automatically translated versions of the requirements to English. The datasets were retrieved from the <a href="http://coest.org/">website</a> of the Center of Excellence for Software & Systems Traceability (CoEST). Attribution for the datasets: The original eTour dataset was provided for the TEFSE challenge at 6th International Workshop on Traceability in Emerging Forms of Software Engineering (TEFSE), 2011 and was retrieved from <a href="http://coest.org/">http://coest.org/</a> The iTrust dataset was retrieved from <a href="http://coest.org/">http://coest.org/</a> The original SMOS and eAnci datasets can be attributed to Gethers et al., On integrating orthogonal information retrieval methods to improve traceability recovery. In 2011 27th IEEE International Conference on Software Maintenance (ICSM), Sep. 2011 and were retrieved from <a href="http://coest.org/">http://coest.org/</a>  The LibEST dataset can be attributed to Moran et al., Improving the Effectiveness of Traceability Link Recovery using Hierarchical Bayesian Networks. In 2020 IEEE/ACM 42nd International Conference on Software Engineering (ICSE), May 2020 and was retrieved from <a href="https://gitlab.com/SEMERU-Code-Public/Data/icse20-comet-data-replication-package">https://gitlab.com/SEMERU-Code-Public/Data/icse20-comet-data-replication-package</a>

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity

We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH

We used Escherichia coli transformed with pJKR-H-tetR plasmids encoding an inducible GFP gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the GFP gene, used non-transformed E. coli as a negative control, and tested six different FISH protocols.

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping

We used rRNA FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of an active prophage with a sixth fluorophore.  We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump.

opencc-zeroJun 2023View details →

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

opencc-by-4.0Nov 2019View details →

Figure 3 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia

Figure 3. Periophthalmus variabilis, Sugihan estuary, southern Sumatra (© M. Iqbal).

The Moderating Effect of Employee Agility on the Link between Employee Vitality, Digital Literacy and Transformational Leadership with Job Performance: An Empirical Study of HR Practitioners in the Manufacturing Sector of Northern Malaysia.

This is a dataset for a study that examines the effects of employee vitality, digital literacy, and transformational leadership on job performance. Additionally, it investigates the moderating role of employee agility in these relationships. Data were collected from HR practitioners in manufacturing companies in the northern region of Malaysia for analysis. The results indicate that the job performance of HR practitioners is positively influenced by employee vitality, digital literacy and transformational leadership.

Comparison tables for evaluating FAIR Digital Object and Linked Data

RO-Crate and tables from the paper "Evaluating FAIR Digital Object and Linked Data as distributed object systems" <a href="https://doi.org/10.48550/arXiv.2306.07436">https://doi.org/10.48550/arXiv.2306.07436</a> We systematically evaluate FDO and its implementations as a global distributed object system, by using five different conceptual frameworks that cover interoperability, middleware, FAIR principles, EOSC requirements and FDO guidelines themself. <ul> <li>table1.html Considering FDO and Web according to the quality levels of the Interoperability Framework for Fast Data (Delgado 2016)</li> <li> table2.html Mapping the Metamodel concepts from the Interoperability Framework for Fast Data (Delgado 2016) to equivalent concepts for FDO and Web. </li> <li> table3.html Checking FDO guidelines (Bonino et al. 2019; Anders et al. 2023) against its current implementations as DOIP (DONA 2018) and Linked Data Platform (LDP) (Bonino da Silva Santos, Guizzardi, and Sales 2022), with suggestions for required additions </li> <li> table4.html Comparing FAIR Digital Object (with the DOIP 2.0 protocol (DONA 2018)) and Web technologies (using Linked Data) as middleware infrastructures (Zarras 2004) </li> <li> table5.html Assessing RDA’s FAIR Data Maturity Model (FAIR Data Maturity Model Working Group 2020; Bahim et al. 2020) (first 2 columns) against the FDO guidelines (Bonino et al. 2019), FDO implemented with the protocol DOIPv2 (DONA 2018), Linked Data Platform (LDP) (Bonino da Silva Santos, Guizzardi, and Sales 2022) and examples from Linked Data practices in general. (— indicates Unspecified, may be possible with additional conventions) </li> </ul> A web rendering of this RO-Crate is available at <a href="https://w3id.org/ro/doi/10.5281/zenodo.8075229">https://w3id.org/ro/doi/10.5281/zenodo.8075229</a>

opencc-zeroJun 2023View details →

The weaken-fill-repair model for cell budding: Linking cell wall biosynthesis with mechanics

The interplay between cellular mechanics and other biochemical processes leading to the cell cycle is poorly understood. Here, we propose a quantitative model of the mechanism of cell budding, particularly for Saccharomyces cerevisiae, as a ''weaken-fill-repair'' process. This model links Newtonian mechanics over the cell wall with biochemical processes that change the mechanical properties of the wall. Our model shows that: (1) The oscillatory behavior in the size of the mother compartment during cell division, as observed experimentally, is an inevitable consequence of the budding mechanism; (2) The asymmetry of cell division is necessary for the daughter cell to maintain mechanical stiffness; (3) Although different aspects of a cell are strictly constrained and intricately interconnected, the budding process is governed by a single reduced parameter that, when at an appropriate value, can automatically achieve homeostasis. Our quantitative model of the evolution of cell walls and their impact on cell division could provide valuable insights into cell morphology from a system perspective. This knowledge could be instrumental in developing effective antimicrobial treatments against microorganisms with cell walls and even in building synthetic cells.

opencc-zeroJul 2023View details →

Reproductive phenology is a repeatable, heritable trait linked to the timing of other life history events in a migratory marine predator

Population-level shifts in reproductive phenology in response to environmental change are common, but whether individual-level responses are modified by demographic and genetic factors remains less well understood. We used mixed models to quantify how reproductive timing varied across 1,755 female southern elephant seals (Mirounga leonina) breeding at Marion Island in the Southern Ocean (1989–2019) and to identify the factors that correlate with phenological shifts within- and between individuals. We found strong support for covariation in the timing of breeding arrival dates and the timing of the preceding moult. Breeding arrival dates were more repeatable at the individual-level, as compared to the population-level, even after accounting for individual traits (wean date as a pup, age and breeding experience) associated with phenological variability. Mother-daughter similarities in breeding phenology were also evident, indicating that additive genetic effects may contribute to between-individual variation in breeding phenology. Over 30 years, elephant seal phenology did not change towards earlier or later dates, and we found no correlation between annual fluctuations in phenology and indices of environmental variation. Our results show how maternal genetic (or non-genetic) effects, individual traits and linkages between cyclical life-history events can drive within- and between-individual variation in reproductive phenology.

opencc-by-4.0Jul 2023View details →

Effect of burosumab on muscle function and strength, and rates of ATP synthesis in skeletal muscle in adults with X-linked Hypophosphatemia

Abstract Context: Burosumab, a neutralizing antibody to FGF23, is approved for the treatment of X-linked hypophosphatemia. In clinical trials burosumab improves symptoms of pain, fatigue and stiffness and improves performance on certain muscle function studies. Objective: Determine if burosumab would increase ATP synthesis in skeletal muscle of treatment-naïve adults with XLH and if so whether that correlated with improved muscle function. Methods: Ten symptomatic adults, who had not received any treatment for XLH for years, had ATP synthesis rates assessed in the soleus/gastrocnemius muscle complex of the right calf using the 31P magnetic resonance spectroscopy saturation transfer technique. Baseline muscle function tests and symptoms of pain, fatigue, stiffness and lower extremity joint pain were quantified. All participants were treated with burosumab, 1 mg/kg every four weeks for 12 weeks. ATP synthesis rates and muscle function tests were repeated 2-weeks (“peak”) and 4-weeks (“trough”) after the third dose of burosumab. Results: Pain, fatigue, stiffness and lower extremity joint pain all improved with treatment. Performance on the 6-Minute Walk and Sit to Stand tests also improved significantly. Performance on the Timed Up and Go test did not significantly improve (p = 0.057). Muscle strength, measured by dynamometry, did not change significantly in either the upper or lower extremities during the study. ATP synthesis rates did not change over the three months of study in the group as whole. In a sub-analysis comparing individuals whose performances on the 6-Minute Walk Test and Sit to Stand tests were at or better than the mean outcome for those tests, to those whose outcomes were below the mean, no difference was observed in the rate of change in ATP synthesis rates. Despite profound and prolonged hypophosphatemia at baseline, intracellular muscle concentrations of phosphorus were normal. Conclusion: The improvement in the 6-Minute Walk Test and Sit to Stand tests without any observed change in either upper or lower extremity muscle strength or ATP synthesis rates, suggests that improvement in pain, fatigue and stiffness may explain, at least in part, the improved performance on these two tests. The preserved intracellular phosphate levels suggests that adaptive mechanisms are present in skeletal muscle that insulate intracellular phosphorus from life-long FGF23-mediaed hypophosphatemia.

opencc-zeroJul 2023View details →

Data from: Identifying links between the biodiversity impacts and monetary costs of alien birds

This dataset accompanies a published paper (Evans et al. 2023) which aims to identify links between the biodiversity impacts and monetary costs of alien bird species. In this paper we used mixed-effects models to test: (1) whether alien bird species with severe biodiversity impacts also had high monetary costs; (2) whether specific types of biodiversity impacts were associated with high monetary costs; and (3) whether certain factors caused alien bird species to have both severe biodiversity impacts and high monetary costs. This dataset includes all data used for the analysis, including biodiversity impact scores and monetary costs for each alien bird species, and the variables tested for their influence on these biodiversity impacts and costs. Please refer to Evans et al. (2023) for details on the methods used. The abstract to the published paper follows. <ol> <li>Alien species can be damaging to native biodiversity, human well-being and the economy. Identifying the complete range of impacts they cause, and the ways that these impacts are connected, may inform the prioritisation of management actions to mitigate impacts.</li> <li>Using datasets on the biodiversity impacts and monetary costs (damage and management costs) of alien birds, we aimed to establish whether species with the most severe biodiversity impacts also had the highest costs; whether types of biodiversity impact were associated with high costs; and whether specific factors associated with alien species are linked to both damaging biodiversity impacts and high costs.</li> <li>We identified a positive relationship between a specific type of biodiversity impact (predation) and costs, possibly because predation by alien birds can be severely damaging to native species and therefore attracts management actions. However, predation impacts are likely to occur more frequently and to be easier to identify than some other impact mechanisms such as hybridisation and transmission of diseases, and they are therefore likely to be more frequently managed, and hence to have costs.</li> <li>We identified a specific species characteristic (generalism) to be associated with severe biodiversity impacts and high costs, probably because generalist species have greater opportunity to cause impacts, whether they be on biodiversity or the economy, or both. We also found widely distributed alien birds to be associated with high costs, probably also because these species have greater opportunity to cause impacts.</li> <li>Management interventions that prevent the introduction of both predatory and generalist alien bird species, or that reduce their geographic distribution at early stages of invasions, may have significant biodiversity and economic benefits.</li> </ol>

opencc-zeroJul 2023View details →

Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds

Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.

opencc-zeroAug 2023View details →

Biological links between personality and plasticity: testing some alternative hypotheses

When organisms respond behaviorally to a stimulus, they exhibit plasticity, but some individuals respond to the same stimulus consistently differently than others, thereby also exhibiting personality differences. Parent house sparrows express individual differences in how often they feed offspring and how that feeding rate changes with nestling age. Mean feeding rate and its slope with respect to nestling age were positively correlated at median nestling ages but not at hatching, indicating that individuality is primarily in plasticity. Individual differences could arise due to 1) interactions between environmental variables, 2) differences in underlying state or 'quality', or 3) differences in the ability to update cues of changing nestling demand. Individual slopes were modestly repeatable across breeding attempts, hinting at the likely action of additional environmental variables, but only brood size was important. I also found few correlates suggesting quality differences. I used short-term brood size manipulations at two nestling ages to test divergent predictions between the three hypotheses. The pattern of correlations between response to the manipulation and individual slope did not fit any single hypothesis. Patterns of sparrow parental care reveal that personality and plasticity are not cleanly separable, and their biology is likely intertwined. New thinking may be needed about the factors parents use in decisions about care and the relevant fitness consequences.

opencc-by-4.0Aug 2023View details →

Datasets for Out-of-KB Mention Discovery with Entity Linking

The repository contains datasets for out-of-KB mention discovery from texts, documented in the work, Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking, on arXiv: <a href="https://arxiv.org/abs/2302.07189">https://arxiv.org/abs/2302.07189</a> (CIKM 2023). Each data setting (as a sub-folder) contains train, valid, and test files and also 100 random sample files for each data split for debugging. Data folder names with “syn_full” at the end are synonym augmented data (each synonym as an entity) for the setting. Ontology .jsonl files have two versions for each, "syn_attr" setting treats synonyms are attributes, "syn_full" setting treats synonyms as entities.   Data scripts are available at <a href="https://github.com/KRR-Oxford/BLINKout#data-scripts">https://github.com/KRR-Oxford/BLINKout#data-scripts</a>   Acknowledgement of the data sources below: ShARe/CLEF 2013 dataset is from <a href="https://physionet.org/content/shareclefehealth2013/1.0/">https://physionet.org/content/shareclefehealth2013/1.0/</a> MedMention dataset is from <a href="https://github.com/chanzuckerberg/MedMentions">https://github.com/chanzuckerberg/MedMentions</a> UMLS (versions 2012AB, 2014AB, 2017AA) is from <a href="https://www.nlm.nih.gov/research/umls/index.html">https://www.nlm.nih.gov/research/umls/index.html</a> SNOMED CT (corresponding versions) is from <a href="https://www.nlm.nih.gov/healthit/snomedct/index.html">https://www.nlm.nih.gov/healthit/snomedct/index.html</a> NILK dataset is from <a href="https://zenodo.org/record/6607514">https://zenodo.org/record/6607514</a> WikiData 2017 dump is from <a href="https://archive.org/download/enwiki-20170220/enwiki-20170220-pages-articles.xml.bz2">https://archive.org/download/enwiki-20170220/enwiki-20170220-pages-articles.xml.bz2</a>

opencc-by-4.0Aug 2023View details →

Links Between Optical and X-ray Light in Scorpius X-1

Optical data taken from the Argos photometer in 2006.