Find research datasets worth reusing

Extra-pair paternity enhances the reproductive fitness of urban Chinese blackbird

Urbanization is a human-induced process of rapid habitat change that can affect the reproductive success of animals. The occurrence of extra-partial paternity (EPP) may be sensitive to changes in urban ecological conditions. In this study, the Chinese blackbird (Turdus mandarinus), a common breeding bird in southern Chinese cities, was selected as the focus species to explore the EPP patterns of monogamous birds in developing cities and their relationship. Over four breeding seasons, 316 Chinese blackbird nestlings and 20 adults in both urban and rural areas were monitored and genotyped for 11 microsatellite loci to determine progeny affinity. We confirmed that both the brood size and hatching rate of EPP nests were significantly larger than those of within-pair paternity (WPP) nests. The body mass, beak length, head length, and body length of 12-day age extra-pair offspring (EPO) were significantly greater than those of within-pair offspring (WPO) suggesting important benefits of EPP. However, according to the analyses of nest ecological variables, we concluded that EPP occurs most often in areas with low urbanization levels indicating some constraints for this reproductive strategy in cities. Our findings provide interesting new insights into how this growing human-induced landscape change affects mating behavior in birds, an important aspect of avian ecology and evolution.

Data for: What you have, not who you know: food-enhanced social capital and changes in social behavioural relationships in a non-human primate

Social network position in non-human primates has far-reaching fitness consequences. Critically, social networks are both heterogenous and dynamic, meaning an individual's current network position is likely to change due to both intrinsic and extrinsic factors. However, our understanding of the drivers of changes in social network position is largely confined to opportunistic studies. Experimental research on the consequences of in situ, controlled network perturbations is limited. Here we conducted a food-based experiment in rhesus macaques to assess whether allowing an individual the ability to provide high-quality food to her group changed her social behavioural relationships. We considered both her social network position across five behavioural networks, as well as her dominance and kin interactions. We found that gaining control over a preferential food resource had far-reaching social consequences. There was an increase in both submission and aggression centrality and changes in the socio-demographic characteristics of her agonistic interaction partners. Further, we found that her grooming balance shifted in her favour as she received more grooming than she gave. Together, these results provide a novel, preliminary insight into how in situ, experimental manipulations can modify social network position and point to broader network-level shifts in both social capital and social power.

Magnetic field enhancements in the interplanetary solar wind: Diverse processes manifesting a uniform observation type?

Interlaced magnetic flux ropes are a subject of investigation in various space environments, including the solar corona, interplanetary solar wind, and magnetosheath. In this study, we utilize a Hall Magnetohydrodynamics (MHD) model to replicate these interactions within selected regions. By employing plasma flow to propel two flux ropes of various parameters towards each other, we examine the effect of their relative helicity on the ensuing process. Our simulations, coupled with vector analysis, found the existence of flux ropes with opposing helicity along their axes (counter-helical) in some of the resultant interactions. These findings underscore the need to identify and study counter-helical flux ropes in space. The study presented here contributes new comprehension of space plasma dynamics and new insights into the solar wind in control of space weather.

Community science enhances modelled bee distributions in a tropical Asian city

Bees and the ecosystem services they provide are vital to urban ecosystems, but little is understood about their distributions, particularly in the Asian tropics. This is largely due to taxonomic impediments and limited inventorying, monitoring, and digitization of occurrence records. While expert collections (EC) are demonstrably insufficient by themselves as a data source to model and understand bee distributions, the boom of community science (CS) in urban areas provides an untapped opportunity to learn about bee distributions within our cities. We used CS observations in combination with EC observations to model the distribution of bees in Singapore, a small tropical city-state in Southeast Asia. To address the restricted spatial context, we performed multiple bias corrections and show that species distribution models performed well when estimating the distribution of habitat specialists with distinct range limits detectable within Singapore. We successfully modelled 37 bee species, where model statistics improved for 23 species upon the incorporation of CS observations. Nine species had insufficient EC observations to obtain acceptable models, but could be modelled with the incorporation of CS observations. This is the first study to combine both EC and CS observations to map and model the occurrences of tropical Asian bee species for a highly urbanised region at such fine resolution. Our results suggest that urban landscapes with impervious surfaces and higher temperatures are less suitable for bee species, and such findings can be used to advise the management of urban landscapes to optimise the diversity of bee pollinators and other organisms.

opencc-by-4.0Mar 2024View details →

Enhancing comparative T-cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice

All data files used to generate the figures in the paper are shared in this project. Scripts are available on <a href="https://github.com/i3-unit/CRM_24" target="_blank" rel="noopener">GitHub</a>.

opencc-zeroMar 2024View details →

Incorporating generalist seagrasses enhances habitat restoration in a changing environment

Coastal habitat-forming species provide protection and essential habitat for fisheries but their ability to maintain these services are under threat from novel stressors including rising temperatures. Coastal habitat restoration is a powerful tool to help mitigate the loss of habitat-forming species, however, many efforts focus on reintroducing a single, imperiled species instead of incorporating alternatives that are more conducive to current and future conditions. Seagrass restoration has seen mixed success in halting local meadow declines but could begin to specifically utilize generalist seagrasses with climate change-tolerant and opportunistic life history traits including high reproduction rates and rapid growth. Here, we built on decades of successful eelgrass (Zostera marina) restoration in the Chesapeake Bay by experimentally testing seed-based restoration potential of widgeongrass (Ruppia maritima) – a globally distributed seagrass that can withstand wide ranges of salinities and temperatures. Using field experiments, we evaluated which seeding methods yielded highest widgeongrass survival and growth, tested if seeding widgeongrass adjacent to eelgrass can increase restoration success, and quantified how either seagrass species changes restored bed structure, invertebrate communities, and nitrogen cycling. We found widgeongrass can be restored via direct seeding in the fall, and that seeding both species maximized total viable restored area. Our pilot restoration area increased by 98% because we seeded widgeongrass in shallow, high temperature waters that are currently unsuitable for eelgrass survival and thus, would remain unseeded via only eelgrass restoration efforts. Restored widgeongrass had higher faunal diversity and double animal abundance per plant biomass than restored eelgrass, whereas restored eelgrass produced three times greater plant biomass per unit area and higher nitrogen recycling in the sediment. Synthesis and applications: Overall, we provide evidence that supplementing opportunistic, generalist species into habitat restoration is a proactive approach to combat climate change impacts. Specifically, these species can increase trait diversity which, for our study, increased total habitat area restored - a key factor to promote seagrass beds' facilitation cascades, stability, and grass persistence through changing environments. Now, we call for tests to determine if the benefits of restoration with generalist species alone or in conjunction with historically dominant taxa are broadly transferrable to restoration in other marine and terrestrial habitats.

opencc-zeroMar 2024View details →

Rapid responses of bees and butterflies but not birds to targeted urban road verge habitat enhancements

Cities provide opportunities for biodiversity conservation through the design of urban greenspaces as wildlife habitat. A significant proportion of urban public land is narrow linear road verges, though their small size and harsh environmental conditions (e.g. high soil temperatures) may limit their ability to support plants and animals. We worked with a municipal government in a highly urbanised area to test whether conversion of standard road verges (e.g. lawn) to predominantly native understorey plants (forbs, grasses, and shrubs) selected for their abilities to tolerate harsh growing conditions and provide habitat increased the abundance and richness of bees, butterflies, and birds. We used a before-after-control-impact experiment and characterised temporal dynamics of biodiversity responses one year prior to planting and four years post planting. We also tested whether traits known to influence species responses to urbanisation (body size and feeding specialisation) mediated responses to road verge plantings. Bee species richness and abundance increased at experimental plantings in the first post-planting year and remained stable thereafter despite fluctuations at control sites. Butterfly abundance but not richness increased, and there was no evidence of bird responses to plantings. Larger bee species, which are known to be most negatively impacted by urbanisation, benefited more from the road verge plantings, while there was no effect of feeding specialisation. Bird and butterfly traits did not mediate responses to plantings. Synthesis and applications: Road verges comprise a significant proportion of urban green spaces, and our results suggest that despite their small sizes and harsh environmental conditions they can provide habitat for bees and to a lesser extent butterflies. We demonstrated that habitat value can be rapidly enhanced by converting standard road verges to native understorey plants, and that these benefits may be greatest for the bee species most negatively impacted by urbanisation. Modifications such as additional plant species or wider verges may be required for urban road verges to provide habitat for a greater range of taxa including birds and butterflies.

opencc-zeroMar 2024View details →

Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics

Deforestation, exploitation, and other drivers of biodiversity loss in Madagascar leave its highly endangered and predominantly endemic wildlife at risk of extinction. Decreasing biodiversity threatens to compromise ecosystem functions and vital services provided to people. New, economical, and diverse methods of biodiversity monitoring can help to establish reliable baseline and long-term records of species richness. Metabarcoding with invertebrate-derived DNA (iDNA) has emerged as a promising new biosurveillance tool. An unexpected wet forest fragment tucked in the dry cliffs of Madagascar's southcentral plateau, the Ivohibory Protected Area (IPA), hosts a unique mosaic of species diversity, featuring both dry and wet forest species. Recently elevated to protected status, the IPA has been surveyed for flora and fauna with a range of inventory methods over three years and six expeditions (2016, 2017, & 2019). We collected 1,451 leeches over 12 days from the IPA to supplement known species richness and to compare results against current records. With iDNA, we pooled tissues, and isolated, and amplified bloodmeal DNA with five sets of primers. We detected 20 species of which four are species of frogs previously undetected and three of which are previously unknown to exist in this region. iDNA surveys can provide complementary data to traditional surveying methods like camera traps, line transects, and bioacoustic methods.

opencc-by-4.0Nov 2023View details →

Enhancing MnBi2Te4 stability by doping

Content of the files:   Python notebooks for analysis: mn_bi_hull_fig3.ipynb mn_bi_formation_fig2.ipynb   Data files: Kagome ordered neutral antisite structures: neutral-antisite-structures-kagome.hdf5   Structures with dopants, no antisites: defect-structures-kagome.hdf5   Structures with dopants, no antisites:All the structures used in the phase diagram determination all_phases.hdf5

Human seminal extracellular vesicles enhance endometrial receptivity through leukemia inhibitory factor

Seminal extracellular vesicles (EVs) contain different subgroups that have diverse effects on sperm function. However, the effect of seminal EVs—especially its subgroups, on the endometrial receptivity was largely unknown. Here, we found that the seminal EVs could be divided into high-density EV (EV-H), medium density EV (EV-M), and low-density EV (EV-L), after purification using iodixanol. Then we demonstrated that EV-H could promote the expression and secretion of leukemia inhibitor factor (LIF) in human endometrial cells. In EV-H-treated endometrial cells, we identified 1274 differentially expressed genes (DEGs). DEGs were enriched in cell adhesion and AKT, STAT3 pathways. Therefore, we illustrated that EV-H enhanced the adhesion of human choriocarcinoma JAr cell spheroids to endometrial cells through the LIF-STAT3 pathway. Collectively, our findings indicated that seminal EV-H could regulate endometrial receptivity through the LIF pathway, which would provide novel insights into male fertility.

opencc-by-4.0Apr 2024View details →

A Post-Synthetic Modification Strategy for Enhancing Pt adsorption Efficiency in MOF/Polymer Composites

Growing polymers inside porous metal-organic frameworks (MOFs) can allow incoming guests to access the backbone of otherwise non-porous polymers, boosting the number and/or strength of available adsorption sites inside the porous support. In the present work, we have devised a novel post-synthetic modification (PSM) strategy that allows one to graft metal-chelating functionality onto a polymer backbone while inside MOF pores, enhancing the material’s ability to recover Pt(IV) from complex liquids. For this, polydopamine (PDA) was first grown inside of a MOF, known as Fe-BTC (or MIL-100 Fe). Next, a small thiol-containing molecule, 2,3-dimercapto-1-propanol (DIP), was grafted to the PDA via a Michael addition. After the modification of the PDA, the Pt adsorption capacity and selectivity were greatly enhanced, particularly in the low concentration regime, due to the high affinity of the thiols towards Pt. Moroever, the modified composite was found to be highly selective for precious metals (Pt, Pd, and Au) over common base metals found in electronic waste (i.e., Pb, Cu, Ni, and Zn). X-ray photoelectron spectroscopy (XPS) and in situ X-ray absorption spectroscopy (XAS) provided insight into the Pt adsorption/reduction process. Last, the PSM was extended to various thiols to demonstrate the versatility of the chemistry. It is hoped that this work will open pathways for the future design of novel adsorbents that are fine-tuned for the rapid, selective retrieval of high-value and/or critical metals from complex liquids.

opencc-by-4.0May 2024View details →

An Exploratory Evaluation of Continuous Feedback to Enhance Machine Learning Code Smell Detection

Context: Code smells are symptoms of bad design choices implemented on the source code. To manage and enhance software quality, it is important to be aware of code smells and refactor them whenever possible. As a result, several code smell detection tools and techniques have been proposed over the years. These tools and techniques present different strategies to detect code smells. More recently, machine learning algorithms have also been proposed to support code smell detection. However, we lack empirical evidence on how expert feedback could improve detection of these machine learning based techniques. Objective: This paper aims to propose and evaluate a machine-learning based strategy to improve detection of code smells by means of continuous feedback provided by the system expert. Method: To evaluate the strategy, we follow an experimental design to compare results of the detection before and after the feedback, both when feedback is provided at once and continuously. We focus on four code smells - God Class, Long Method, Feature Envy, and Refused Bequest - detected in twenty Java systems by using five code smell detection tools. We also extracted class- and method-level metrics from the systems for training the machine learning algorithms. Results: We observed that continuous feedback improves the performance of code smell detection. For the detection of God Class, a code smell with a detection performance initially good, we achieved an average improvement of 0.13 in terms of F1. For Refused Bequest, another class-level code smell, we achieved an average improvement of 0.58 in terms of F1 after all interactions of the strategy. For the method-level code smells, Long Method and Feature Envy, we achieved an average improvement of 0.66 and 0.72 in terms of F1, respectively. Conclusions: Our promising results are a stepping stone towards the development of tools relying on continuous feedback for machine learning detection of code smells.

Data from: Tree diversity enhances predation by birds but not by arthropods across climate gradients

Tree diversity can promote both predator abundance and diversity. However, whether this translates into increased predation and top-down control of herbivores across predator taxonomic groups and contrasting environmental conditions remains unresolved. We used a global network of tree diversity experiments (<a href="https://www.treedivnet.ugent.be">www.treedivnet.ugent.be</a>; TreeDivNet) spread across three continents and three biomes to test the effects of tree species richness on predation across varying climatic conditions of temperature and precipitation. We recorded bird and arthropod predation attempts on plasticine caterpillars in monocultures and tree species mixtures. Both tree species richness and temperature increased predation by birds, but not by arthropods. Furthermore, the effects of tree species richness on predation were consistent across the studied climatic gradient. Our findings provide evidence that tree diversity strengthens top-down control of insect herbivores by birds, underscoring the need of implementing conservation strategies that safeguard tree diversity to sustain ecosystem services provided by natural enemies in forests.

opencc-by-4.0Jan 2023View details →

FIGURE 1 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)

FIGURE 1 (Continued)

opencc-by-4.0Mar 2024View details →

Exploring Beneficial Properties of Haskap Berry Leaf Compounds for Gut Health Enhancement

Data and the publication to which they are related

opencc-by-4.0Apr 2024View details →

Data sets to the paper "Weakening surface hydrogen to enhance permeation in hydrogen selective membranes", E. Billeter and A. Borgschulte, Appl. Surf. Sci. (2024)

Datasets to empirical data displayed in Figs. 1(c), 2(b), 3(a), 4(b), 4(c)

Monosaccharide transporter OsMST6 is activated by transcription factor OsERF120 to enhance chilling tolerance in rice seedlings

Chilling stress caused by extreme weather is threatening global rice (Oryza sativa L.) production. Identifying components of the signal transduction pathways underlying chilling tolerance in rice would advance molecular breeding. Here, we report that OsMST6, which encodes a monosaccharide transporter, positively regulates the chilling tolerance of rice seedlings. The mst6 mutants showed hypersensitivity to chilling, while the OsMST6 overexpression lines were tolerant. During chilling stress, OsMST6 transported more glucose into cells to modulate sugar and ABA signal pathways. We showed that the transcription factor OsERF120 could bind to the DRE/CRT element of the OsMST6 promoter and activate the expression of OsMST6 to positively regulate chilling tolerance. Genetically, OsERF120 was functionally dependent on OsMST6 when promoting chilling tolerance. In summary, OsERF120 and OsMST6 form a new downstream chilling regulatory pathway in rice in response to chilling stress, providing valuable findings for molecular breeding aimed at achieving global food security. The stored data is the analysis results of transcriptome data from ZH11 and mst6-1 after 0 hours and 4 hours of chilling treatment. These data form the basis for the transcriptome data visualization in the article.

Data from: Enhanced woody biomass production in a mature temperate forest under elevated CO2

This data set reports tree growth and net primary productivity in response to experimentally elevated atmospheric CO2 concentration in the free-air CO2 enrichment (FACE) of the Birmingham Institute of Forest Research (BIFoR FACE). Data ae reported for a pre-treatment period (2010-2016) and from the onset of CO2 treatment (2017-2023). The BIFoR FACE experiment is located in central England (52.801°N, 2.301°W, 107 m above sea level) within a deciduous forest dominated by 180-year old Quercus robur L. trees, which represent 92% of the forest's basal area. There are six experimental arrays of approximately 30 m diameter. Tree ring analysis was used to determine growth patterns within the arrays prior to the onset of CO2 treatment. The trees in three of the arrays have been exposed to elevated CO2 (ambient concentration + 150 ppm) during the growing seasons since 2017. Tree diameter was measured with manual dendrometers, and dry mass of oak trees was calculated using an allometric equation determined by terrestrial laser scan of the trees within the arrays. Dry matter production of understory species and coarse roots was calculated using allometric equations from the literature. Leaf production was calculated from mass of leaf litter collected in litter baskets. Fine-root production was measured in ingrowth cores and scaled to 1-meter depth based on fine-root biomass in deep cores. Exudation rates were scaled up to a full growing season and total fine-root mass.

Synaptic vesicle glycoprotein 2C enhances vesicular storage of dopamine and counters dopaminergic toxicity

Dopaminergic neurons of the substantia nigra exist in a persistent state of vulnerability resulting from high baseline oxidative stress, high energy demand, and broad unmyelinated axonal arborizations. Impairments in the storage of dopamine compound this stress due to cytosolic reactions that transform the vital neurotransmitter into an endogenous neurotoxicant, and this toxicity is thought to contribute to the dopamine neuron degeneration that occurs Parkinson's disease. We have previously identified synaptic vesicle glycoprotein 2C (SV2C) as a modifier of vesicular dopamine function, demonstrating that genetic ablation of SV2C in mice results in decreased dopamine content and evoked dopamine release in the striatum. Here, we adapted a previously published in vitro assay utilizing false fluorescent neurotransmitter 206 (FFN206) to visualize how SV2C regulates vesicular dopamine dynamics and identified that SV2C promotes the uptake and retention of FFN206 within vesicles. In addition, we present data indicating that SV2C enhances the retention of dopamine in the vesicular compartment with radiolabeled dopamine in vesicles isolated from immortalized cells and from mouse brain. Further, we demonstrate that SV2C enhances the ability of vesicles to store the neurotoxicant 1-methyl-4-phenylpyridinium (MPP+) and that genetic ablation of SV2C results in enhanced 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced vulnerability in mice. Together, these findings establish that SV2C functions to enhance storage of dopamine and toxicants and helps maintain the integrity of dopaminergic neurons.

Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity

The 1858C>T allele of the tyrosine phosphatase PTPN22 is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influence PTPN22 and its pro-autoimmune allele have in anti-viral immunity remains poorly defined. Here, we use single-cell RNA-sequencing and functional studies to interrogate the impact of this pro-autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP-619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8a- cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell-intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele of Ptpn22 drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection.