Find research datasets worth reusing

opencc-by-4.0May 2022View details →

Weighted Link Schedules in 100-node Fixed Topology Wireless Networks

This is a data repo for the data samples used for learning the link scheduling in a fixed-topology placed networks. This data set contains samples for 100-node networks, and the scheduling decisions are made from delayed column generation (DCG) algorithm.

opencc-by-4.0Feb 2023View details →

A microwave link simulation dataset for rainfall observation applications

A microwave link simulation dataset is developed for theoretical research of rainfall observation applications. The dataset is built based on electromagnetic propagation theory attenuation effects with measured raindrop size distribution data from a PARSIVEL disdrometer and air temperature, air pressure and humidity data from nearby weather stations. Frequencies from 6 to 180 GHz, horizontal or vertical polarization, link lengths from 0.1 km to 20 km, and quantization resolutions from 0 to 1 dB are all fully considered for various existing and future complications. The dataset can be utilised to validate the performance of the microwave link-based rainfall inversion process algorithm in various equipment configurations and to assess the potential of microwave link-based rainfall monitoring technology in future high-frequency communication infrastructure conditions on a theoretical level with a very low cost.

opencc-by-4.0Mar 2023View details →

Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study.

Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study. Angewandte Chemie, 2023

The origin of blinking in both mudskippers and tetrapods is linked to life on land

Blinking, the transient occlusion of the eye by one or more membranes, serves several functions including wetting, protecting, and cleaning the eye. This behavior is seen in nearly all living tetrapods and absent in other extant sarcopterygian lineages, suggesting that it might have arisen during the water-to-land transition. Unfortunately, our understanding of the origin of blinking has been limited by a lack of known anatomical correlates of the behavior in the fossil record and a paucity of comparative functional studies. To understand how and why blinking originates, we leverage mudskippers (Oxudercinae), a clade of amphibious fishes that have convergently evolved blinking. Using micro-computed tomography and histology, we analyzed two mudskipper species, Periophthalmus barbarus and Periophthalmodon septemradiatus, and compared them to the fully aquatic round goby, Neogobius melanostomus. Study of gross anatomy and epithelial microstructure shows that mudskippers have not evolved novel musculature or glands to blink. Behavioral analyses show the blinks of mudskippers are functionally convergent with those of tetrapods: P. barbarus blinks more often under high evaporation conditions to wet the eye, a blink reflex protects the eye from physical insult, and a single blink can fully clean the cornea of particulates. Thus, eye retraction in concert with a passive occlusal membrane can achieve functions associated with life on land. Osteological correlates of eye retraction are present in the earliest limbed vertebrates, suggesting blinking capability. In both mudskippers and tetrapods, therefore, the origin of this multifunctional innovation is likely explained by selection for increasingly terrestrial lifestyles.

opencc-by-4.0Mar 2023View details →

Data for "Structure and drivers of social networks and their links with health in older adults"

Data, supplementary material and scripts for the paper "Structure and drivers of social networks and their links with health in older adults" Social network is an important factor in promoting healthy aging. However, the mechanisms linking social capital to health are complex. Moreover, most of the social network analysis studies on older adults consider only participants’ relationships and not how these relationships are themselves connected. In this study, we went further than current ego-centered network studies by determining global social network metrics and the structure of relationships among older adult participants of the RECORD Cohort using the Veritas-Social questionnaire. The aim of this study is to identify key dimensions of social networks of older adults, and to evaluate how these dimensions relate to depressive symptoms, life satisfaction, and well-being. Using Principal Component Analyses (PCA), we identified four social network dimensions with psychological meanings. Dimension 1 (homophily) was positively linked with perceived accessibility to services in one’s residential neighborhood but negatively linked with the level of study. Dimension 2 (social integration) as Dimension 3 (social support) was only linked to the number of people living with ego. Dimension 4 was linked with perceived accessibility to local services. Finally, and rather surprisingly, we found that none of the four network dimensions, even the degree, was linked to the three health status metrics.

Linking trait network parameters with plant growth across light gradients and seasons

1. Reduced light availability induced by eutrophication has dramatically affected the growth of submerged macrophytes and caused their rapid decline globally in lakes. Functional traits have usually been used to predict ecological processes and explain plant adaptation. Trait networks, which are constructed from a series of nodes (traits) and edges (trait-trait correlations), can reveal complex relationships among traits. Plant traits belonging to different organs are considered relevant for overall plant performance. Therefore, variation in trait network topology at the whole-plant level can better reflect plant adaptation and response to environments than traditional methods, but the mechanisms underlying the decline of plants from a trait network perspective are not well understood. 2. In this study, based on a one-year manipulation experiment for Potamogeton maackianus cultured with four levels of light intensity, we constructed trait networks from 20 traits belonging to different organs. 3. Our results showed that trait network connectivity decreases in harsh environments, probably due to increased trait modules responding independently to stress. Network connectivity was positively related to the plant relative growth rate (RGR), as high trait connectivity and coordination should be beneficial for plants to acquire and transport resources efficiently across the whole plant. Additionally, we found that specific stem length, leaf:root mass ratios, and leaf total nonstructural carbohydrates were hub traits with high connectivity. These hub traits expressed high phenotypic plasticity, had close links with plant growth, and consistently held their higher importance within the network across light gradients or seasons. 4. We found that low phenotypic integration in stressful environments may constrain plant growth, which can provide important implications for understanding plant adaptation strategies to low-light stress and even predicting community dynamics in the context of global environmental change.

opencc-by-4.0Mar 2023View details →

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub2) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

Data from: Mitochondrial function declines with age within individuals but is not linked to the pattern of growth or mortality risk in zebra finch

Mitochondrial dysfunction is considered a highly conserved hallmark of ageing. However, most studies in both model and non-model organisms are cross-sectional in design; therefore, little is known, at the individual level, on how mitochondrial function changes with age, its link to early developmental conditions or its relationship with survival. Here we manipulated the postnatal growth in zebra finches (Taeniopygia guttata) via dietary modification that induced accelerated growth without changing adult body size. In the same individuals, we examined blood cells mitochondrial functioning (mainly erythrocytes) when they were young (ca 36 weeks) and again in mid-aged (ca 91 weeks) adulthood. Mitochondrial function was strongly influenced by age but not by postnatal growth conditions. Across all groups, within individual ROUTINE respiration, OXPHOS and OXPHOS coupling efficiency significantly declined with age, while LEAK respiration increased. However, we found no link between mitochondrial function and the probability of survival into relatively old age (ca 4 years). Our results suggests that the association between accelerated growth and reduced longevity, evident in this as in other species, is not attributable to age-related changes in any of the measured mitochondrial function traits.

opencc-by-4.0May 2022View details →

Weighted Link Schedules in sub-100 node Random Topology Wireless Networks

This is a data repo for the data samples used for learning the link scheduling in a randomly placed networks. This data set contains samples for sub 100-node networks, and the scheduling decisions are made from delayed column generation (DCG) algorithm.

opencc-by-4.0May 2022View details →

Weighted Link Schedules in sub-100 node Fixed Topology Wireless Networks

This data repo contains the link schedules in a multi-hop wireless networks that aims to maximize the weighted throughput. Each instance is represented by a numpy data file that contains the necessary data fields to reconstruct the original problem instance.   Note: 100_7_new.tar.xz should be in the repo https://zenodo.org/deposit/7671940.

Dissimilarity of turbulent transport of momentum and heat under unstable conditions linked to convective circulations

The dissimilarity between the turbulent transport of momentum and heat under unstable conditions and its physical mechanisms are investigated in this study, based on the multiple-level turbulence observation from Tianjin's 255-m meteorological tower. The transport dissimilarity is observed from the surface layer to the lower part of the mixed layer as atmospheric instability increases. Although the transport dissimilarity is accompanied by the development of plumes and thermals under unstable conditions, plumes and thermals can produce intense transport of momentum and heat simultaneously. It is convective circulations related to vigorous thermals that cause transport dissimilarity. The horizontal divergence induced by convective circulations imposes a dominant large-scale reduction in the along-wind velocity component near the surface, while the temporal variations in temperature mainly reflect the role of plumes and thermals. This difference in respective physical processes subsequently leads to dissimilar transport between momentum and heat under unstable conditions. Therefore, the influence of convective circulations on the momentum-flux estimation should be considered in atmospheric numerical models, particularly for the simulation and prediction of severe convective weather.

opencc-by-4.0Jan 2023View details →

Data for 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'

Underlying data for publication 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'.

opencc-zeroApr 2023View details →

Effects of long-term mowing on leaf- and root-associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe

<ol> <li>Long-term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing-induced plant trait plasticity affect plant microbiomes in natural grasslands. </li> <li>Here we examined the responses of leaf-/root-associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (6 replicates per species) to a 17-year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits and analyzed the relationships among mowing practice, bacterial community structures, and leaf/root trait parameters. </li> <li>We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment-induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. </li> <li> The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter-/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing-induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and aboveground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil-derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing. </li> <li>Our results demonstrate that the magnitude of plant-associated microbial community response to long-term mowing is plant compartment- and trait-variation-dependent, and advance our understanding of the leaf/root microbiome-trait relationships in complex plant communities.</li> </ol>

opencc-zeroDec 2022View details →

When death comes: Linking predator-prey activity patterns to timing of mortality to understand predation risk

The assumption that activity and foraging are risky for prey underlies many predator-prey theories and has led to the use of predator-prey activity overlap as a proxy of predation risk. However, the simultaneous measures of prey and predator activity along with timing of predation required to test this assumption have not been available. Here, we used accelerometry data on snowshoe hares (Lepus americanus) and Canada lynx (Lynx canadensis) to determine activity patterns of prey and predators and match these to precise timing of predation. Surprisingly, we found that lynx kills of hares were as likely to occur during the day when hares were inactive as at night when hares were active. We also found that activity rates of hares were not related to the chance of predation at daily and weekly scales, whereas lynx activity rates positively affected the diel pattern of lynx predation on hares and their weekly kill rates of hares. Our findings suggest that predator-prey diel activity overlap may not always be a good proxy of predation risk, and highlight a need for examining the link between predation and spatiotemporal behavior of predator and prey to improve our understanding of how predator-prey behavioral interactions drive predation risk.

opencc-by-4.0Apr 2023View details →

Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial & nuclear biology

This online depository corresponds to manuscript : Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial & nuclear biology. Authors: Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau, Claudia Manzoni Whilst the majority (~90-95%) of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. However, in the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring an increased risk of developing PD across the population.  A recently developed mitophagy screening assay of GWAS candidates, has functionally implicated the non-specific lethal (NSL) complex, a chromatin remodeler, in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. A multi-layered approach has been taken to; i) build the ‘mitochondrial’ NSL interactome, applying PD gene-set enrichment analysis to explore the relevance of the NSL mitochondrial interactome to PD and, ii) build the PD-oriented NSL interactome, using functional enrichment, to uncover biological pathways underpinning the NSL /PD association.

opencc-by-4.0Apr 2023View details →

Integrated multi-omics analysis of early lung adenocarcinoma links tumor biological features with predicted indolence or aggressiveness

This is a collection of datasets presented in the manuscript "Multi-omics data analysis identifies correlations between tumor biology features and predicted behaviors in early lung adenocarcinoma". This study provides a comprehensive profiling of LUAD indolence and aggressiveness at the biological bulk and single cell levels, as well as at the clinical and radiomics levels. This hypothesis generating study uncovers several potential future research avenues. It also highlights the importance and power of data integration to improve our systemic understanding of LUAD and to help reduce the gap between basic science research and clinical practice.

opencc-zeroApr 2023View details →

Linking critical thermal maximum to mortality from thermal stress in a cold-water frog

Estimates of organismal thermal tolerance are frequently used to assess physiological risk from warming, yet the assumption that these estimates are predictive of mortality has been called into question. We tested this assumption in the cold water-specialist frog, Ascaphus montanus. For seven populations, we used dynamic experimental assays to measure tadpole critical thermal maximum (CTmax) and measured mortality from chronic thermal stress for three days at different temperatures. We tested the relationship between previously–estimated population CTmax and observed mortality, as well as the strength of CTmax as a predictor of mortality compared to local stream temperatures capturing varying timescales. Populations with higher CTmax experienced significantly less mortality in the warmest temperature treatment (25℃). We also found that population CTmax outperformed stream temperature metrics as the top predictor of observed mortality. These results demonstrate a clear link between CTmax and mortality from thermal stress, contributing evidence that CTmax is a relevant metric for physiological vulnerability assessments.

opencc-by-4.0May 2023View details →

Freebase Datasets for Robust Evaluation of Knowledge Graph Link Prediction Models

Freebase is amongst the largest public cross-domain knowledge graphs. It possesses three main data modeling idiosyncrasies. It has a strong type system; its properties are purposefully represented in reverse pairs; and it uses mediator objects to represent multiary relationships. These design choices are important in modeling the real-world. But they also pose nontrivial challenges in research of embedding models for knowledge graph completion, especially when models are developed and evaluated agnostically of these idiosyncrasies. We make available several variants of the Freebase dataset by inclusion and exclusion of these data modeling idiosyncrasies. This is the first-ever publicly available full-scale Freebase dataset that has gone through proper preparation.  Dataset DetailsThe dataset consists of the four variants of Freebase dataset as well as related mapping/support files. For each variant, we made three kinds of files available:<ul><li>Subject matter triples file<ul><li>fb+/-CVT+/-REV One folder for each variant. In each folder there are 5 files: train.txt, valid.txt, test.txt, entity2id.txt, relation2id.txt Subject matter triples are the triples belong to subject matters domains—domains describing real-world facts.<ul><li>Example of a row in train.txt, valid.txt, and test.txt: <ul><li>2, 192, 0</li></ul></li><li>Example of a row in entity2id.txt:<ul><li>/g/112yfy2xr, 2</li></ul></li><li>Example of a row in relation2id.txt:<ul><li>/music/album/release_type, 192</li></ul></li><li>Explaination<ul><li>"/g/112yfy2xr" and "/m/02lx2r" are the MID of the subject entity and object entity, respectively. "/music/album/release_type" is the realtionship between the two entities. 2, 192, and 0 are the IDs assigned by the authors to the objects.</li></ul></li></ul></li></ul></li><li>Type system file<ul><li>freebase_endtypes: Each row maps an edge type to its required subject type and object type.<ul><li>Example<ul><li>92, 47178872, 90</li></ul></li><li>Explanation<ul><li>"92" and "90" are the type id of the subject and object which has the relationship id "47178872".</li></ul></li></ul></li></ul></li><li>Metadata files<ul><li>object_types: Each row maps the MID of a Freebase object to a type it belongs to.<ul><li>Example<ul><li>/g/11b41c22g, /type/object/type, /people/person</li></ul></li><li>Explanation<ul><li>The entity with MID "/g/11b41c22g" has a type "/people/person"</li></ul></li></ul></li><li>object_names: Each row maps the MID of a Freebase object to its textual label.<ul><li>Example<ul><li>/g/11b78qtr5m, /type/object/name, "Viroliano Tries Jazz"@en</li></ul></li><li>Explanation<ul><li>The entity with MID "/g/11b78qtr5m" has name "Viroliano Tries Jazz" in English.</li></ul></li></ul></li><li>object_ids: Each row maps the MID of a Freebase object to its user-friendly identifier.<ul><li>Example<ul><li>/m/05v3y9r, /type/object/id, "/music/live_album/concert"</li></ul></li><li>Explanation<ul><li>The entity with MID "/m/05v3y9r" can be interpreted by human as a music concert live album.</li></ul></li></ul></li><li>domains_id_label: Each row maps the MID of a Freebase domain to its label.<ul><li>Example<ul><li>/m/05v4pmy, geology, 77</li></ul></li><li>Explanation<ul><li>The object with MID "/m/05v4pmy" in Freebase is the domain "geology", and has id "77" in our dataset.</li></ul></li></ul></li><li>types_id_label: Each row maps the MID of a Freebase type to its label.<ul><li>Example<ul><li>/m/01xljxh, /government/political_party, 147</li></ul></li><li>Explanation<ul><li>The object with MID "/m/01xljxh" in Freebase is the type "/government/political_party", and has id "147" in our dataset.</li></ul></li></ul></li><li>entities_id_label: Each row maps the MID of a Freebase entity to its label.<ul><li>Example<ul><li>/g/11b78qtr5m, Viroliano Tries Jazz, 2234</li></ul></li><li>Explanation<ul><li>The entity with MID "/g/11b78qtr5m" in Freebase is "Viroliano Tries Jazz", and has id "2234" in our dataset.</li></ul></li><li>properties_id_label: Each row maps the MID of a Freebase property to its label.<ul><li>Example<ul><li>/m/010h8tp2, /comedy/comedy_group/members, 47178867</li></ul></li><li>Explanation<ul><li>The object with MID "/m/010h8tp2" in Freebase is a property(relation/edge), it has label "/comedy/comedy_group/members" and has id "47178867" in our dataset.</li></ul></li></ul></li><li>uri_original2simplified and uri_simplified2original: The mapping between original URI and simplified URI and the mapping between simplified URI and original URI repectively.<ul><li>Example<ul><li>uri_original2simplified<ul><li>"<a href="http://rdf.freebase.com/ns/type.property.unique">http://rdf.freebase.com/ns/type.property.unique</a>": "/type/property/unique"</li></ul></li><li>uri_simplified2original<ul><li>"/type/property/unique": "<a href="http://rdf.freebase.com/ns/type.property.unique">http://rdf.freebase.com/ns/type.property.unique</a>"</li></ul></li></ul></li><li>Explanation<ul><li>The URI "<a href="http://rdf.freebase.com/ns/type.property.unique">http://rdf.freebase.com/ns/type.property.unique</a>" in the original Freebase RDF dataset is simplified into "/type/property/unique" in our dataset.</li><li>The identifier "/type/property/unique" in our dataset has URI <a href="http://rdf.freebase.com/ns/type.property.unique">http://rdf.freebase.com/ns/type.property.unique</a> in the original Freebase RDF dataset.</li></ul></li></ul></li></ul></li></ul></li></ul>

opencc-by-4.0May 2023View details →

[DATA LINK] Clearing the way to the external world: do ants make optimal decisions when removing obstacles from their subterranean galleries?

Data repository of the submitted paper: “Clearing the way to the external world: do ants make optimal decisions when removing obstacles from their subterranean galleries?” Authors : Louis Devers (0009-0001-3726-1891), Clémentine Cléradin, Zoé Bescond-Michel, Gérard Latil and Vincent Fourcassié (0000-0002-3605-6351). Contains : <ul> <li>Extraction.csv  [database] : the observed orientations of the obstacle extraction</li> <li>Traction.csv [database] : censing the orientation of mandibular grasps and effective pulls observed</li> <li>Model_traction.csv [database] : censing the orientation of virtual pulls</li> <li>Model_extraction.csv [database] : censing the orientation of virtual extraction, resulting from sequential tractions presented in model_traction.csv</li> <li>TreatmentAndGraphs [R script] : script including statistical analysis, and survival analysis graphs</li> </ul>