Find research datasets worth reusing

opencc-zeroNov 2020View details →

Habitat filtering differentially modulates phylogenetic and functional diversity relationships between predatory arthropods

Mechanisms underlying biological diversities at different scales have received significant attention over the last decades. The hypothesis whether local abiotic factors, driving functional and phylogenetic diversities, can differ among taxa of arthropods remains under-investigated. In this study, we compared correlations and drivers of functional (FD) and phylogenetic (PD) diversities between spiders and carabids, two dominant taxa of ground-dwelling arthropods in salt marshes. Both taxa exhibited high correlation between FD and PD; the correlation was even higher in carabids, probably due to their lower species richness. Analyses highlight that FD and PD were positively linked to taxonomic diversity in both taxa; however, abiotic factors driving the FD and PD differed between spiders and carabid. Salinity particularly drove the taxonomic diversity of carabids, but not that of spiders, suggesting that spiders are phenotypically more plastic and less selected by this factor. Conversely, phylogenetic diversity was influenced by salinity in spiders, but not in carabids. This result can be attributed to the different evolutionary history and colonisation process of salt marshes between the two model taxa. Finally, our study highlights that, in taxa occupying the same niche in a constrained habitat, functional and phylogenetic diversities can have different drivers, showing different filtering mechanisms.

opencc-by-4.0Oct 2020View details →

An incandescent metasurface for quasimonochromatic polarized Mid-Wave Infrared emission modulated beyond 10 MHz

README =============================== DESCRIPTION : This repository contains all datasets and MATLAB codes used in the following paper : Wojszvzyk, Léo, Anne Nguyen, Anne-Lise Coutrot, Cheng Zhang, Benjamin Vest, et Jean-Jacques Greffet. « An Incandescent Metasurface for Quasimonochromatic Polarized Mid-Wave Infrared Emission Modulated beyond 10 MHz ». Nature Communications 12, no 1 (5 mars 2021): 1492. <a href="https://doi.org/10.1038/s41467-021-21752-w">https://doi.org/10.1038/s41467-021-21752-w</a>. In order to run some of the scripts, users need to download the RETICOLO library available at doi : 10.5281/zenodo.3610175 Light-in-complex-nanostrucutres/RETICOLO and subsequently add this library to their MATLAB search path. 4 folders can be found: <ul> <li>EM_simulations: contains scripts to reproduce the electromagnetic simulations presented in the paper. The codes use functions in the RETICOLO library (therefore, please make sure that the folder containing all RETICOLO functions (RETICOLO_V8/reticolo_allege) are known to the MATLAB search path).</li> <li>PolarizedFreqResponse: contains raw datasets and ready-to-use analysis scripts to reproduce frequency response curves of the device presented in the paper. The main script to be run is "main.m".</li> <li>EmissivitySpectra: contains raw datasets and ready-to-use analysis scripts to reproduce the emissivity spectrum of the device presented in the paper.</li> <li>Response_to_pulse_simulation: contains raw datasets and ready-to-use analysis scripts to reproduce the pulse response of the device presented in the paper.</li> </ul> =============================== PAPER ABSTRACT: Incandescent sources such as hot membranes and globars are widely used for mid infrared spectroscopic applications. The emission properties of these sources can be tailored by means of resonant metasurfaces: control of the spectrum, polarization and directivity has been reported. For detection or communication applications, fast temperature modulation is desirable but is still a challenge due to thermal inertia. Reducing thermal inertia can be achieved using nanoscale structures at the expense of a low absorption and emission cross section. Here, we introduce a metasurface that combines nanoscale heaters to ensure fast thermal response and nanophotonic resonances to provide large monochromatic and polarized emissivity. The metasurface is based on platinum and silicon nitride and can sustain high temperatures. We report a peak emissivity of 0.8 and an operation up to 20 MHz, six orders of magnitude faster than commercially available hot membranes.

opencc-zeroDec 2020View details →

Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation

Condensed neural and behavioral data, included secondary results from model fits and analyses. This dataset contains all information required to recreate figures from the paper.

opencc-zeroDec 2020View details →

Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae

Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.

opencc-by-3.0Aug 2020View details →

Cochlear activity in silent cue-target intervals shows a theta-rhythmic pattern and is correlated to attentional alpha and theta modulations

Preprocessed data and analysis-scripts needed to reproduce the figures and statistics of the paper "Cochlear activity in silent cue-target intervals shows a theta-rhythmic pattern and is correlated to attentional alpha and theta modulations".

opencc-by-4.0Jan 2021View details →

Data associated with "Modulation of intercolumnar synchronization by endogenous electric fields in cerebral cortex"

These is data associated with the article  "Modulation of intercolumnar synchronization by endogenous electric fields in cerebral cortex" in Science Advances 2021, by the same authors.

opencc-zeroJan 2021View details →

A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease

Background: Chagas disease caused by Trypanosoma cruzi (T. cruzi) affects approximately six million individuals worldwide. Clinical manifestations are expected to occur due to the parasite persistence and host immune response. Herein we investigated potential associations between IL1B, IL6, IL17A or IL18 polymorphism profiles and cardiomyopathy or T. cruzi parasitemia, as well as the impact of HIV infection on cardiopathy. Methods: 206 patients and 90 control individuals were analyzed. IL1B rs1143627 T>C, IL6 rs1800795 C>G, IL17A rs2275913 G>A, IL18 rs187238 C>G, and IL18 rs1946518 C>A SNVs were analyzed by real-time PCR and T. cruzi parasitemia by PCR. Results: Our data revealed association between a cytokine gene polymorphism and parasitemia never previously reported. The IL6 rs1800795 CG genotype lowered the risk of positive parasitemia (OR=0.45, 95% CI 0.24–0.86, P=0.015). Original findings included associations between IL17A rs2275913 AA and IL18 s1946518 AA genotypes with decreased risk of developing cardiomyopathy (OR=0.27, 95% CI 0.07-0.97, P=0.044; and OR=0.35, 95% CI 0.14-0.87, P=0.023, respectively). IL18 rs1946518 AA and IL1B rs1143627 TC were associated with reduced risk for cardiomyopathy severity, including NYHA (New York Heart Association) class≥ 2 (OR=0.21, 95% CI 0.06-0.68, P=0.009; and OR=0.48, 95% CI 0.24-0.95, P=0.036, respectively) and LVEF (Left Ventricular Ejection Fraction) <45% for IL18 rs1946518 AA (OR=0.22, 95% CI 0.05-0.89, P=0.034). A novel, unexpected protective effect of HIV infection against development/progression of cardiomyopathy was identified, based on a lower risk of developing cardiopathy (OR=0.48, 95% CI 0.23‐0.96, P=0.039), NYHA class≥2 (OR=0.15, 95% CI 0.06‐0.39, P<0.001) and LVEF<45% (OR=0.03, 95% CI 0.00‐0.25, P=0.001). Digestive involvement was negatively associated with NYHA ≥2 and LVEF<45% (OR=0.20, 95% CI 0.09‐0.47, P<0.001; and OR=0.24, 95% CI 0.09-0.62, P=0.004, respectively). Conclusions: Our data support a protective role of IL17A AA, IL18 AA and IL1B TC genotypes against development/progression of cardiomyopathy and a modulatory effect of the IL6 CG genotype on the risk of parasitemia in Chagas disease. Notably, HIV infection was shown to protect against development/progression of cardiopathy, potentially associated with a synergistic effect of HIV and HAART, attenuating a Th1-mediated response in the myocardium. This proposed hypothesis requires confirmation, however, in larger and more comprehensive future studies.

opencc-zeroJan 2021View details →

Spatial modulation of visual responses arises in cortex with active navigation

During navigation, the visual responses of neurons in mouse primary visual cortex (V1) are modulated by the animal's spatial position. Here we show that this spatial modulation is similarly present across multiple higher visual areas but negligible in the main thalamic pathway into V1. Similar to hippocampus, spatial modulation in visual cortex strengthens with experience and with active behavior. Active navigation in a familiar environment, therefore, enhances the spatial modulation of visual signals starting in the cortex.

opencc-zeroApr 2020View details →

Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.

opencc-by-4.0Jun 2021View details →

Radiative Forcing of Nitrate Aerosols from 1975 to 2010 as Simulated by MOSAIC Module in CESM2-MAM4

Netcdf outputs from CESM2 simulations for publication: Radiative Forcing of Nitrate Aerosols from 1975 to 2010 as Simulated by MOSAIC Module in CESM2-MAM4

opencc-zeroSep 2019View details →

Data from: From forest to city: Urbanization modulates relative abundance of anti-predator coloration

Increased urbanization has resulted in community changes including alteration of predator communities. Little is known, however, about how such changes affect morphological anti-predator traits. Given the importance of coloration in predator avoidance, this trait in particular is expected to be susceptible to novel selective environments in urban areas. Here we investigate the coloration pattern of a Neotropical anuran species, the túngara frog (Engystomops pustulosus), along an urbanization gradient. Túngara frogs have two distinct color patterns (unstriped and striped) which we found to occur at different frequencies along an urbanization gradient. Striped individuals increased in frequency with urbanization. To assess the strength of selection imposed by predators on the two color morphs, we deployed clay models of túngara frogs in forest and semi-urban populations. In addition, we examined microhabitat selection by individuals of the different morphs. We found higher predation rates associated with urbanization than forested areas. In particular, frogs from forested habitats had lower number of attacks by avian predators. Contrary to our predictions, however, predation rates were similar for both color morphs independent of urbanization. Also, coloration of the frogs did not affect their microhabitat preference. Overall, túngara frogs are more likely to have a striped coloration pattern in semi-urban areas where predation by birds is higher than in the forest. Our findings suggest that factors other than predation pressure shape the coloration pattern of urban frogs and emphasize the complex nature of effects that anthropogenic changes in habitat and predator communities may have on prey morphology.

opencc-zeroJan 2020View details →

The integration of sensory feedback in the modulation of anuran landing preparation

Controlled landing requires preparation. Mammals and bipedal birds vary how they prepare for landing by predicting the timing and magnitude of impact from the integration of visual and non-visual information. Here we explore how an animal that moves primarily through hopping, Rhinella marina, the cane toad, integrates sensory information to modulate landing preparation. Earlier work suggests toads may modulate landing preparation using predictions of impact timing and/or magnitude based on non-visual sensory feedback during takeoff rather than visual cues about the landing itself. Here we disentangled takeoff and landing conditions by hopping toads off platforms of different heights and measured electromyographic (EMG) activity of an elbow extensor, m. anconeus, and used high-speed motion capture to quantify whole body and forelimb kinematics to test how toads integrate visual and non-visual information in landing preparation. We asked two questions: 1) when they conflict, do toads correlate landing preparation with takeoff or landing conditions? And 2) for hops with the same takeoff conditions, does visual information alter the timing of landing preparation? We found that takeoff conditions are a better predictor of the onset of landing preparation than landing conditions, but that visual information is not ignored. When hopping off higher platforms, toads start to prepare for landing later when takeoff conditions are invariant. This suggests that, unlike mammals, toads prioritize non-visual sensory feedback about takeoff conditions to coordinate landing, but that they do integrate visual information to fine-tune landing preparation.

opencc-zeroDec 2016View details →

Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small-mammal density. We tested the effects of a diverse LMH community on small-mammal habitat use using 4 years of spatially explicit small-mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi-arid Kenyan savanna. Small-mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small-mammal density associated with LMH exclusion. Our results show that LMH indirectly affect small-mammal behaviour, and that these effects are influenced by climate and can arise via density-independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small-mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East Africa (as predicted in many recent climate-model simulations) may relax constraints on small-mammal distribution where LMH are rare or absent, whereas increased aridity and/or drought frequency may tighten them.

opencc-zeroDec 2017View details →

Data from: Arena size modulates functional responses via behavioral mechanisms

Laboratory-based functional response experiments, in which foraging rates are measured across a range of resource densities, are central for determining trophic interaction strength. Historically these experiments often are performed in arbitrarily sized arenas, with larger sized organisms generally used in larger arenas. However, arena size influences foraging rates and therefore also estimates of the functional response parameters, particularly space clearance rate (attack rate). We hypothesized that non-random movement within arenas by predators and prey may explain this effect. To test this hypothesis, we video-recorded Schizocosa ocreata wolf spiders (predators) and flightless Drosophila melanogaster prey in circular arenas of three different sizes to reveal thigmotactic behavior. We then estimated foraging rates and space clearance rates from feeding trials performed at a single, low prey density in three differently-size arenas in either annular (ring-shaped) or circular arenas. Annular arenas mitigated the effects of predator and prey aggregation and thus controlled the experienced prey density near arena edges. Unlike the circular arenas, annular arenas produced similar foraging rates and space clearance rate estimates across arena sizes, confirming that it is the increased density of prey along edges that generates the previously observed arena size effect. Our results provide a key insight into how animal behavior and experimental design must be considered for the accurate interpretation of foraging rates, both when considering standalone functional responses and when making comparisons across experiments.

opencc-byOct 2021View details →

Digital Heritage Module - Skull Model

Photogrammetry model of skull from UCL Digital Heritage Module (Prof Gai Jorayev; Students: Alison G, Runqi W, Yuexi Y, Che W, Emma R) Source: Objaverse 1.0 / Sketchfab

opencc-zeroFeb 2015View details →

Module Data for the Empirical Investigation of Subsumption Test Hardness in Description Logic Classification

This dataset contains 224 modules of 14 distinct ontologies for the submission "Empirical Investigation of Subsumption Test Hardness in Description Logic Classification" to CADE, 2015. The submitted version with the dataset description can be found here: http://owl.cs.manchester.ac.uk/publications/supporting-material/subtest-hardness-in-classification/ The ontologies in this set are BioPortal ontologies from the snapshot provided at http://dx.doi.org/10.5281/zenodo.15667.  The following ontologies are in the set:  MFOEM - Emotion Ontology BT - Biotop Ontology NEMO - Neural Electromagnetic Ontology NTDO - Neglected Tropical Disease Ontology OBI - Ontology for Biomedical Investigations OGSF - Ontology for Genetic Susceptibility Factor ONL-MSA - Mental State Assemssment VSO - Vital Sign Ontology CAO - Clusters of Orthologous Groups Cog Analysis Ontology  ICO - Informed Consent Ontology OMRSE - Ontology of Medically Related Social Entities STATO - Statistics Ontology NPO - Nanoparticle Ontology OBCS - Ontology of Biological and Clinical Statistics

Module-based classification of OWL ontologies - Experiment 1+2 Dataset (Benign Module Conjecture)

The results of Experiment 1+2 (Chapter 5) in PhD Thesis "Module-based classification of OWL ontologies", both results for Benign Module Conjecture and Revised Benign Module Conjecture.

Module-based classification of OWL ontologies - Experiment 5 Dataset

The results of Experiment 5 (Chapter 7) in PhD Thesis "Module-based classification of OWL ontologies - Experiment 5 Dataset", both Experiment runs (K1, K2).

Module-based classification of OWL ontologies - Experiment 3 Dataset (Subsumption Test Hardness Survey BioPortal)

The results of Experiment 3 (Chapter 6) in PhD Thesis "Module-based classification of OWL ontologies", results of the subsumption test survey across BioPortal. Contains only the final data tables and the analysis scripts (not the raw data and intermediate states).

Module-based classification of OWL ontologies - Experiment 4 Dataset (Subsumption Test Hardness under Modularity)

The results of Experiment 4 (Chapter 6) in PhD Thesis "Module-based classification of OWL ontologies", results of the survey exploring subsumption test under modularity. Contains only the final data tables and the analysis scripts (not the raw data and intermediate states).