Find research datasets worth reusing

opencc-zeroMay 2022View details →

Data from: Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH4) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH4 oxidation. CH4 oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH4 oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH4 uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH4 uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal Ralstonia pickettii associates with CH4 uptake across soils along with pertinent CH4 and inorganic N metabolism associated genes. This study highlights the critical relationship between CH4 and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.

opencc-by-4.0Aug 2021View details →

Linked Data Conversion using Microservices

Conference talk at the LINCS 2021 conference describing the motivations, design, and development process behind the creation of the NSSI (NERVE Secure Scalable Infrastructure) data conversion platform.

opencc-by-4.0Apr 2022View details →

Travel Time Statistics for Links with Locks from L&D 16 to L&D 20

This is an Excel spreadsheet that contains multiple travel time performance statistics for the Upper Mississippi River from L&D 16 to L&D 20.  It includes a map depicting the links in the table.

opencc-by-4.0Apr 2022View details →

Travel Time and Speed Statistics for Links Containing Locks 16 through 20

This is an Excel spreadsheet that records the travel times/speeds of each trip through a lock in the range of Lock & Dam 16 through Lock & Dam 20 in the Upper Mississippi River.  Each lock is part of a three sublink set: a sublink upriver from the lock, the lock itself, and a sublink downriver .  A table of links used by the study, a link map, and heat maps are also included.

opencc-by-4.0May 2022View details →

FI_WD20K & SI_WD20K: Datasets For Hyper-Relational Inductive Link Prediction

The datasets correspond to the work presented in <a href="https://arxiv.org/abs/2107.04894">"Improving Inductive Link Prediction Using Hyper-Relational Facts"</a>.

opencc-zeroMay 2022View details →

Higher intelligence is genetically linked with longevity

Epidemiological studies in different populations, in different countries, and in different epochs consistently showed that high intelligence is positively correlated with longevity. Despite the definitive association, the reason of the linkage between higher intelligence and longevity has remained unknown. Here, we show by using Drosophila melanogaster that both higher intelligence and longevity are genetically linked. The high intelligent D. melanogaster (INT) lived longer than non-intelligent flies (NINT), 26.40% and 21.35% in male and female, respectively. The bidirectional selective breeding based on intelligence extended lifespans gradually generation by generation in INT breeding and reverse in NINT breeding. The INT of F12 generation lived longer than NINT of F12 generation, 63.91% for male and 67.88% for female, as a result from slower aging. Whole-genome analysis showed that the genetic linkage of higher intelligence with longevity was determined by the genes of the pathways of ribosome, autophagy, and genome stability.

Community science reveals links between migration arrival timing advance, migration distance, and wing shape

Substantial global data show that many taxa are shifting their phenologies in response to climate change. For birds, migration arrival dates in breeding regions have been shifting earlier, and there is evidence that both evolutionary adaptation and behavioural flexibility influence these shifts. As more efficient flyers may be able to demonstrate more flexibility to respond to changing conditions during migratory flight, we hypothesize that differences among passerine species in flight efficiency, as reflected by morphology, may be associated with the magnitude of shifts in arrival date in response to climate warming. We applied a logistic model to eighteen years of eBird data to estimate mean arrival date for 44 common passerines migrating to northeast North America. We then used linear mixed-effects models to estimate changes in mean arrival date and compared these changes to morphological proxies for flight efficiency and migratory distance using phylogenetic generalized least squares models. On average, passerine species shifted their arrival dates 0.120 days earlier each year, with 27 of the 44 species shifting to significantly earlier arrival times, and two shifting to significantly later ones. Of the 15 species with non-significant shifts, 13 trended toward earlier arrivals. Longer migration distances and higher wing aspect ratios were associated with greater shifts towards earlier arrivals. Migration distance and aspect ratio were also significantly correlated to each other. This suggests that changes in arrival date are affected by factors pertaining to migratory flight over long distances namely, flight efficiency and migration distance. These traits may be able predict the magnitude of arrival date shift, and by extension identify species that are most at risk to climate change due to inflexible arrival timing.

Data and code from: Mixed infection, risk projection and misdirection: Interactions among pathogens alter links between host resources and disease

A growing body of literature links resources of hosts to their risk of infectious disease. Yet most hosts encounter multiple pathogens, and projections of disease risk based on resource availability could be fundamentally wrong if they do not account for interactions among pathogens within hosts. Here, we measured infection risk of grass hosts (Avena sativa) exposed to three naturally-co-occurring viruses either singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]: CYDV-RPV, BYDV-PAV, and BYDV-SGV) along experimental gradients of nitrogen and phosphorus supply. We asked whether disease risk (i.e., infection prevalence) differed in single versus co-inoculations, and whether these differences varied with rates and ratios of nitrogen and phosphorus supply. In single inoculations, the viruses did not respond strongly to nitrogen or phosphorus. However, in co-inoculations, we detected illustrative cases of 1) resource-dependent antagonism (RPV with increasing N; possibly due to competition), 2) resource-dependent facilitation (SGV with decreasing N:P; possibly due to immunosuppression), and 3) weak or no interactions within hosts (for PAV). Together, these within-host interactions created emergent patterns for co-inoculated hosts, with both infection prevalence and viral richness increasing with the combination of low nitrogen and high phosphorus supply. We demonstrate that knowledge of multiple pathogens is essential for predicting disease risk from host resources, and that projections of risk that fail to acknowledge resource-dependent interactions within hosts could be qualitatively wrong. Expansions of theory from community ecology theory may help anticipate such relationships linking host resources to diverse pathogen communities.

Following Darwin's footsteps: Evaluating the impact of an activity designed for elementary school students to link historically important evolution key concepts on their understanding of natural selection

While several researchers have suggested that evolution should be explored from the initial years of schooling, little information is available on effective resources to enhance elementary school students' level of understanding of evolution by natural selection (LUENS). For the present study, we designed, implemented and evaluated an educational activity planned for fourth graders to explore concepts and conceptual fields that were historically important for the discovery of natural selection. Observation field notes and students' productions were used to analyse how the students explored the proposed activity. Additionally, an evaluation framework consisting of a test, the evaluation criteria and the scoring process was applied in two fourth-grade classes to estimate elementary school students' LUENS before and after engaging in the activity. Our results suggest that our activity allowed students to effectively link all of the key concepts in the classroom and produced a significant increase in their LUENS. These results indicate that our activity had a positive impact on students' understanding of natural selection. They also reveal that additional activities and minor fine-tuning of the present activity are required to further support students' learning about the concept of differential reproduction. We also observed a low level of teleological predictions for both pre- and post-tests. --

The emblematic South African therocephalian Euchambersia in China: a new link in the dispersal of late Permian vertebrates across Pangea

Therapsids were widely distributed in Pangea in the late Permian. South Africa in Gondwana, and Russia in Laurasia are the principal areas recording tetrapods (including therapsids) of this age. More recent field explorations have increased the importance of Chinese late Permian fossil assemblages. This is clearly reflected in the discovery of several new therocephalians from the Naobaogou Formation in Nei Mongol. Here we report a therocephalian from that unit identified as a new species of the emblematic South African taxon Euchambersia. The new species, E. liuyudongi, is represented by a well-preserved skull and mandible showing a well-developed maxillary fossa and absence of postcanine teeth. This is the third akidnognathid recovered from the Naobaougou Formation, but oddly, the two basal Chinese akidnognathids previously known were recovered from a younger unit of the formation than the derived E. liuyudongi. This is the first time that the same therocephalian genus is recorded in northern and southern continents, making the record of the Naobaougou Formation key to understanding the evolution of late Permian continental faunas in general, and of akidnognathid therocephalians in particular.

opencc-zeroJul 2022View details →

The knock-down of the chloroquine resistance transporter PfCRT is linked to oligopeptide handling in Plasmodium falciparum

The chloroquine resistance transporter, PfCRT, is an essential factor during intraerythrocytic development of the human malaria parasite Plasmodium falciparum. PfCRT resides at the digestive vacuole of the parasite, where hemoglobin taken up by the parasite from its host cell is degraded. PfCRT can acquire several mutations that render PfCRT a drug transporting system expelling compounds targeting hemoglobin degradation from the digestive vacuole. The non-drug related function of PfCRT is less clear, although a recent study has suggested a role in oligopeptide transport based on studies conducted in a heterologous expression system. The uncertainty about the natural function of PfCRT is partly due to a lack of a null mutant and a dearth of functional assays in the parasite. Here, we report on the generation of a conditional PfCRT knock-down mutant in P. falciparum. The mutant accumulated oligopeptides 2 to at least 8 residues in length under knock-down conditions, as shown by comparative global metabolomics. The accumulated oligopeptides were structurally diverse, had an isoelectric point between 4.0 and 5.4 and were electrically neutral or carried a single charge at the digestive vacuolar pH of 5.2. Fluorescently-labeled dipeptides and live cell imaging identified the digestive vacuole as the compartment where oligopeptides accumulated. Our findings suggest a function of PfCRT in oligopeptide transport across the digestive vacuolar membrane in P. falciparum and associated with it a role in nutrient acquisition and the maintenance of the colloid osmotic balance.

opencc-by-4.0Jul 2022View details →

Brain-Derived Neurotrophic Factor and extracellular vesicle-derived miRNAs in an Italian cohort of individuals with obesity: a key to explain the link between depression and atherothrombosis.

This record contains raw data related to the article “Brain-Derived Neurotrophic Factor and Extracellular Vesicle-Derived miRNAs in an Italian Cohort of Individuals With Obesity: A Key to Explain the Link Between Depression and Atherothrombosis”  Abstract:  Background: Obesity and depression are intertwined diseases often associated with an increased risk of cardiovascular (CV) complications. Brain-Derived Neurotrophic Factor (BDNF), altered in the brain both of subjects with depression and obesity, provides a potential link between depression and thrombosis. Since the relationship among peripheral BDNF, depression and obesity is not well-defined, the aim of the present report has been to address this issue taking advantage of the contribution played by extracellular vesicle (EV)-derived miRNAs. Research Process: Associations among circulating BDNF, depression and EVderived miRNAs related to atherothrombosis have been evaluated in a large Italian cohort of obese individuals (n = 743), characterized by the Beck Depression Inventory (BDI-II) score. Results: BDI-II was negatively associated with BDNF levels without a significant impact of the rs6265 BDNF polymorphism; this association was modified by raised levels of IFN-g. BDNF levels were linked to an increase of 80 EV-derived miRNAs and a decrease of 59 miRNAs related to atherosclerosis and thrombosis. Network analysis identified at least 18 genes targeted by these miRNAs, 7 of which involved in depression and CV risk. The observation of a possible link among BDNF, depression, and miRNAs related to atherothrombosis and depression in obesity is novel and may lead to a wider use of BDNF as a CV risk biomarker in this specific subject group.

opencc-zeroJul 2022View details →

Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli

Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in E. coli. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.

opencc-zeroJul 2022View details →

Disentangling the interrelated abiotic and biotic pathways linking landscape composition and crop production

Landscape composition and its related functional agrobiodiversity (FAB) was severely simplified during the last decades. As landscape composition is expected to influence the interrelated microclimate and arthropod community at different scales, this simplification might have led to a decline in multiple agro-ecosystem services, with potential impacts for the growth of crops with different demands from the environment. To study landscape-scale effects on multi-crop yield and herbivory in combination with its potential drivers, including functional arthropod community and microclimate, we used standardised 1 m² mini-gardens planted with ten different vegetable crops as phytometers. The gardens were installed at locations varying in surrounding landscape composition and the vegetables were selected to have contrasting requirements in terms of growing conditions, pollination services, and susceptibility to pests. Monitoring of the mini-gardens was performed in 2018 and 2019 in Flanders (Belgium). We found no relationship between landscape composition in a 500 meter radius and crop yield. Considering possible mechanisms, we found that an increasing share of woody vegetation (> 3 m high) in the surrounding landscape is important to buffer the temperature and soil moisture variation in the mini-gardens. The share of agricultural land use and urban green (< 3 m high) is, respectively, positively and negatively related with the activity-density of natural enemies and pollinators. The growth of different crops responded differently to higher temperature ranges and we found no relation between natural enemies and herbivory. In conclusion, these abiotic and biotic pathways did not cause an overall relationship between landscape composition and yield.

Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data

guided walkthrough of poster at <a href="https://doi.org/10.5281/zenodo.6821815">https://doi.org/10.5281/zenodo.6821815</a> which provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata and the techniques for structuring this data as Linked Data. You can also watch the video in the browser on the <a href="https://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/">I3D:bio website</a>.

Experimental data linked to publication "Process optimization and study of the co-sintering behaviour of Cu-Ni multi-material 3D structures fabricated by spark plasma sintering (SPS)"

Those are all the experimental data used to produce the plots in the article

Target-focused library design by pocket-applied computer vision and fragment deep generative linking

Data inputs and outputs used in <pre>Target-focused library design by pocket-applied computer vision and fragment deep generative linking</pre> Code: https://github.com/kimeguida/POEM

opencc-by-4.0Mar 2022View details →

Dataset- Barking up the right tree: Using tree bark to track airborne particles in school environment and link science to society

Experimental data regarding magnetic properties measured in bio-sensors and air filters. Bio-sensors include tree bark samples, either collected in situ (courtyard tree bark) and exposed indoors-outdoors (bio-sensors) in the schools. Bio-sensors had their magnetic properties measured.  PM1, EC and OC concentrations and SIRM measured on air filters.

Supporting data for 'A shuttling-based two-qubit logic gate for linking distant silicon quantum processors'

Data supporting for paper 'A shuttling-based two-qubit logic gate for linking distant silicon quantum processors'. All the data are stored in the HDF5 format that can be conveniently loaded by the xarray Python package.