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Datasets of recordings of electrical activity of substrates colonised by oyster fungi P. ostreatus and P. djamor.

Datasets of recordings of electrical activity of substrates colonised by oyster fungi P. ostreatus and P. djamor.

Enhancement of cloud-to-ground lightning activity caused by the urban effect: a case study in the Beijing metropolitan area

The dataset here includes land-surface temperature, wind field, precipitation, UV aerosol index, and lightning information analyzed in the paper "Enhancement of cloud-to-ground lightning activity caused by the urban effect: a case study in the Beijing metropolitan area".

Replication package: Does the duration of rapid release cycles affect the bug handling activity?

Replication package for the paper: "Does the duration of rapid release cycles affect the bug handling activity?"

Output data from: From land productivity trends to land degradation assessment in Mozambique: Effects of climate, human activities and stakeholder definitions

This repository includes output data from the following article: Montfort, F., Bégué, A., Leroux, L., Blanc, L., Gond, V., Cambule, A.H., Remane, I.A.D., Grinand, C., 2020. From land productivity trends to land degradation assessment in Mozambique: Effects of climate, human activities and stakeholder definitions. Land Degrad Dev.; 32: 49– 65. <a href="https://doi.org/10.1002/ldr.3704">https://doi.org/10.1002/ldr.3704</a> This study aimed at characterizing and mapping the underlying factors (human or climatic) in land productivity changes over the 2000-2016 period, in order to assess land degradation in Mozambique. The methodology is based on remote sensing methodology. Land productivity change were first analyzed using MODIS NDVI time-series (2000–2016), and a two-step framework was then used to understand the main factors of these productivity changes, using climate times series (CHIRPS data for rainfall and CRU data for temperature), Land Use and Land Cover Change (LULCC) maps (Laurel project LULCC map), and ground knowledge. This repository includes raster data of annual land productivity change over the 2000-2016 period, annual land productivity climate factors, potential land productivity decrease factors and potential productivity increase factors. Data are available as GeoTIFF raster files at 250 m resolution in the UTM 37S projection (EPSG: 32737).

Multiple sequence alignments of full-length L1 elements with evidence of retrotransposition activity.

DNA sequences for full-length L1 elements showing evidence of retrotransposition activity were aligned using MUSCLE v3.8 with default number of iterations. Manual inspection of the multiple alignments was performed with Jalview v2.11 in order to remove upstream and downstream spurious sequences. <ul> <li>selected_active_L1sOK_aligned_trimmed.fa  file includes aligned DNA sequences for 86 full-length L1Hs with medium-high activity and for 1 active L1Pt (outgroup).</li> <li> all_active_L1sOK_aligned_trimmed.fa  file includes aligned DNA sequences for 143 active L1Hs and for 1 active L1Pt (outgroup).</li> </ul>

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.

Kinesin-1 activity recorded in living cells with a precipitating dye FIB-SEM data 1

Kinesin-1 activity recorded in living cells with a precipitating dye FIB-SEM dataset 1 - QPDTf precipitating dye with HeLa cells

opencc-zeroJan 2021View details →

Human activities with videos, inertial units and ambient sensors

Worldwide demographic projections point to a progressively older population. This fact has fostered research on Ambient Assisted Living, which includes developments on smart homes and social robots. To endow such environments with truly autonomous behaviours, algorithms must extract semantically meaningful information from whichever sensor data is available. Human activity recognition is one of the most active fields of research within this context. Proposed approaches vary according to the input modality and the environments considered. Different from others, this paper addresses the problem of recognising heterogeneous activities of daily living centred in home environments considering simultaneously data from videos, wearable IMUs and ambient sensors. For this, two contributions are presented. The first is the creation of the Heriot-Watt University/University of Sao Paulo (HWU-USP) activities dataset, which was recorded at the Robotic Assisted Living Testbed at Heriot-Watt University. This dataset differs from other multimodal datasets due to the fact that it consists of daily living activities with either periodical patterns or long-term dependencies, which are captured in a very rich and heterogeneous sensing environment. In particular, this dataset combines data from a humanoid robot's RGBD (RGB + depth) camera, with inertial sensors from wearable devices, and ambient sensors from a smart home. The second contribution is the proposal of a Deep Learning (DL) framework, which provides multimodal activity recognition based on videos, inertial sensors and ambient sensors from the smart home, on their own or fused to each other. The classification DL framework has also validated on our dataset and on the University of Texas at Dallas Multimodal Human Activities Dataset (UTD-MHAD), a widely used benchmark for activity recognition based on videos and inertial sensors, providing a comparative analysis between the results on the two datasets considered. Results demonstrate that the introduction of data from ambient sensors expressively improved the accuracy results.

opencc-zeroNov 2019View details →

Extreme variation in testes size in an insect is linked to recent mating activity

Ample sperm production is essential for successful male reproduction in many species. The amount of sperm a male can produce is typically constrained by the size of his testes, which can be energetically expensive to grow and maintain. Whilst the economics of ejaculate allocation has been the focus of much theoretical and empirical literature, relatively little attention has been paid to individual adult variation and plasticity at the source of sperm production, the testes themselves. We experimentally address this issue using the insect Narnia femorata Stål (Hemiptera: Coreidae). We established the metabolic cost of testicular tissue, then quantified variation in individual testes mass in response to multiple mate quality and quantity treatments. We uncovered extreme variation across individuals and considerable short-term effects of mating activity on testes dry mass. Importantly, the observed variation in testes mass was associated with notable fitness consequences; females paired with males with larger testes had greater hatching success. Overall, pairing with a female resulted in a 11% reduction in dry testes mass. Despite this apparent considerable mating investment, we found no evidence of strategic allocation to higher quality females or longer-term changes in testes mass. The dynamic nature of testes mass and its metabolic cost is vital to consider in the context of re-mating rates, polyandry benefits and general mating system dynamics both in this species and more broadly.

opencc-zeroDec 2019View details →

Data from: Canine sense of quantity: evidence for numerical ratio-dependent activation in parietotemporal cortex

The approximate number system (ANS), which supports the rapid estimation of quantity, emerges early in human development and is widespread across species. Neural evidence from both human and non-human primates suggests the parietal cortex as a primary locus of numerical estimation, but it is unclear whether the numerical competencies observed across non-primate species are subserved by similar neural mechanisms. Moreover, because studies with non-human animals typically involve extensive training, little is known about the spontaneous numerical capacities of non-human animals. To address these questions, we examined the neural underpinnings of number perception using awake canine functional magnetic resonance imaging. Dogs passively viewed dot arrays that varied in ratio and, critically, received no task-relevant training or exposure prior to testing. We found evidence of ratio-dependent activation, which is a key feature of the ANS, in canine parietotemporal cortex in the majority of dogs tested. This finding is suggestive of a neural mechanism for quantity perception that has been conserved across mammalian evolution.

opencc-zeroOct 2019View details →

Short neuropeptide F regulates the starvation mediated enhanced locomotor activity in Drosophila

The circadian clock regulates various behavioral, metabolic and physiological processes to occur at the most suitable time of the day. Internal energy stores and nutrient availability modulates the most apparent circadian clock mediated locmotor activity rhythm in Drosophila. Although previous studies unraveled the role of circadian clock in metabolism and activity rest rhythm, the precise pathway through which the circadian neuropeptidergic signaling regulates internal energy storage and the starvation-mediated increase in activity resembling foraging remains largely unclear. This study was aimed to elucidate the role of circadian neuropeptide, short neuropeptide F (sNPF) in triglyceride metabolism, starvation resistance and starvation-mediated increased locomotor activity in Drosophila. The results showed that snpf transcripts exhibits significant rhythmicity in wild type flies under 12:12 hour light-dark cycles (LD) and constant darkness (DD) whereas snpf transcript level in period null flies did not exhibit any significant rhythmicity under LD. Knockdown of sNPF in circadian clock neurons reduced the triglyceride level, starvation resistance and increased the starvation-mediated hyperactivity response after 24 hour of starvation. Further studies showed that knock down of sNPF receptors (sNPFR) expressed in insulin producing cells (IPC) increased the starvation resistance and reduced starvation-induced hyperactivity response after 24 hour of starvation. Collectively, our results suggest that transcriptional oscillation of snpf mRNA is endogenously controlled by the circadian clock and elucidate the role of sNPF in modulating locomotor activity in accordance with the nutrient availability in Drosophila.

opencc-by-4.0Jun 2021View details →

A dataset for tracking the activity and abundance of Bogong moths at Ken Green Bogong, near South Ram's Head, NSW in the austral summer of 2019-2020

This dataset contains images captured using wildlife cameras outside two Bogong moth aestivation caves on Ken Green Bogong, near South Ram's Head, NSW in the austral summer of 2019-2020. The images contain motion blurs from insects (predominantly Bogong moths Agrotis infusa) flying past the cameras, allowing for the measurement of Bogong moth wingbeat frequency, activity, and abundance using the Camfi software (<a href="https://github.com/J-Wall/camfi">https://github.com/J-Wall/camfi</a>).

opencc-zeroDec 2018View details →

Data from: Forest succession and climate variability interacted to control fire activity over the last four centuries in an Alaskan boreal landscape

Context: The boreal forest is globally important for its influence on Earth's energy balance, and its sensitivity to climate change. Ecosystem functioning in boreal forests is shaped by fire activity, so anticipating the impacts of climate change requires understanding the precedence for, and consequences of, climatically induced changes in fire regimes. Long-term records of climate, fire, and vegetation are critical for gaining this understanding. Objectives: We investigated the relative importance of climate and landscape flammability as drivers of fire activity in boreal forests by developing high-resolution records of fire history, and characterizing their centennial-scale relationships to temperature and vegetation dynamics. Methods: We reconstructed the timing of fire activity in interior Alaska, USA, using seven lake-sediment charcoal records spanning CE 1550–2015. We developed individual and composite records of fire activity, and used correlations and qualitative comparisons to assess relationships with existing records of vegetation and climate. Results: Our records document a dynamic relationship between climate and fire. Fire activity and temperature showed stronger coupling after ca. 1900 than in the preceding 350 yr. Biomass burning and temperatures increased concurrently during the second half of the twentieth century, to their highest point in the record. Fire activity followed pulses in black spruce establishment. Conclusions: Fire activity was facilitated by warm temperatures and landscape-scale dominance of highly flammable mature black spruce, with a notable increase in temperature and fire activity during the twenty-first century. The results suggest that widespread burning at landscape scales is controlled by a combination of climate and vegetation dynamics that together drive flammability.

opencc-zeroSep 2019View details →

Data from: Effects of the colour of photophase light on locomotor activity in a nocturnal and a diurnal South African rodent

Many physiological and behavioural responses to varying qualities of light, particularly during the night (scotophase) have been well documented in rodents. We used varying wavelengths of daytime (photophase) lighting to assess daily responses in locomotor activity in the nocturnal Namaqua rock mouse (Micaelamys namaquensis) and diurnal four-striped field mouse (Rhabdomys pumilio). Animals were exposed to three light-dark cycle regimes: a short-wavelength- (SWLC), a medium-wavelength- (MWLC) and a long-wavelength light-dark cycle (LWLC). Overall, daily locomotor activity of both species changed according to different wavelengths of light, the diurnal species displayed most activity under SWLC and the nocturnal species exhibited the highest levels of activity under LWLC. Both species showed an increase in diurnal activity and a decrease in nocturnal activity under LWLC. These results indicate an attenuated responsiveness to long wavelength light in the nocturnal species, but this does not appear to be true for the diurnal species. These results emphasize that the effect of light on the locomotor activity of animals depends on both the properties of the light and the temporal organization of activity of a species.

opencc-zeroFeb 2020View details →

Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence

Neosinocalamus affinis, a type of cluster bamboo, is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the N. affinis transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the N. affinis transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle Cyrtotrachelus buqueti, and develop low-cost chemical feedstock from bamboo.

opencc-by-4.0Jun 2021View details →

Characterisation of protease activity duringSARS-CoV-2 infection identifies novel viralcleavage sites and cellular targets withtherapeutic potential

Virus infections in siRNA-based cellular protein knockdowns - imaging dataset for cell viability Host proteins were knocked-down in A549-Ace2 cells using specific dsiRNAs from IDT. Briefly, A549-Ace2 cells seeded at 1x10$^{4}$ cells/well in 96-well plates. After 24 hours, each well was transfected with 5 pmol of individual dsiRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions. 24 hours post transfection, the cell culture supernatant was removed and replaced with virus inoculum (MOI of 0.1 PFU/cell). Following a 1 hour adsorption at 37°C, the virus inoculum was removed and replaced with fresh 2\% FBS/DMEM media. Cells were incubated at 37°C for 3 days before supernatants were harvested. Samples were either heat-inactivated at 80°C for 20 min and viral RNA was quantified by RT-qPCR, using previously published SARS-CoV-2 specific primers targeting the N gene \cite{ChuClinChem}. RT-qPCR was performed using the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler, using the following cycling conditions: 55 °C for 10 min, 95 °C for 1 min, and 40 cycles of 95 °C for 10 sec, followed by 60 °C for 1 min. The quantity of viral genomes is expressed as PFU equivalents, and was calculated by performing a standard curve with RNA derived from a viral stock with a known viral titer. Alternatively, infectious virus titers were quantified using plaque assays as described above. To quantify siRNA-based cellular protein knockdowns, A549-Ace2 cells were seeded and transfected with individual dsiRNAs as described above. After 24 hours incubation at 37 °C cells were lysed and RNA was extracted using Trizol (ThermoFisher Scientific) followed by purification using the Direct-zol-96 RNA extraction kit (Zymo) following the manufacturer’s instructions. RNA levels of target proteins were subsequently quantified by using RT-with the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler using gene-specific primers. Expression levels were compared to scrambled dsiRNA-transfected cells und normalized to expression of human beta-actin. Knockdown efficiencies were calculated using ΔΔCt in Matlab.  To assess cell viability after siRNA knockdowns, cells were seeded and transfected as described above. 24 hours after transfection cell viability was measured using alamarBlue reagent (ThermoFisher Scientific),  media was removed and replaced with alamarBlue and incubated for 1h at 37 °C and fluorescence measured in a Tecan Infinite M200 Pro plate reader. Percentage viability was calculated relative to untreated cells (100\% viability) and cells lysed with 20\% ethanol (0\% viability), included in each plate. For cell counting to determine cell numbers, cells were fixed in formalin to deactivate virus. The fixed cells were stained with 5µg/ml of Hoechst 33258 (Sigma). The assay plates were imaged on an IX-83 automated inverted microscope (Olympus) using a 10x objective. The DAPI settings (Ex UV 377/50, Em 415–480) were used to image Hoechst 33258. The acquisition setup was configured to image 4 sites per well. The nuclei were identified using the object detection module in the ScanR analysis software.   Data provided in two zip files. Sample layout/key within the plates is provided within the zip files.

opencc-zeroMar 2020View details →

Neural ensemble reactivation in REM and SWS coordinate with muscle activity to promote rapid motor skill learning

Neural activity patterns of recent experiences are reactivated during sleep in structures critical for memory storage, including hippocampus and neocortex. This reactivation process is thought to aid memory consolidation. Although synaptic rearrangement dynamics following learning involve an interplay between slow-wave sleep (SWS) and rapid eye movement sleep (REM), most physiological evidence implicates SWS directly following experience as a preferred window for reactivation. Here we show that reactivation occurs in both REM and SWS, and that coordination of REM and SWS activation on the same day is associated with rapid learning of a motor skill. We performed 6-hour recordings from cells in rats' motor cortex as they were trained daily on a skilled reaching task. In addition to SWS following training, reactivation occurred in REM, primarily during the pre-task rest period, and REM and SWS reactivation occurred on the same day in rats that acquired the skill rapidly. Both pre-task REM and posttask SWS activation were coordinated with muscle activity during sleep, suggesting a functional role for reactivation in skill learning. Our results provide the first demonstration that reactivation in REM sleep occurs during motor skill learning, and that coordinated reactivation in both sleep states on the same day, although at different times, is beneficial for skill learning.

opencc-by-4.0Jun 2021View details →

A dataset for tracking the activity and abundance of Bogong moths at Ken Green Bogong, near South Ram's Head, NSW in the austral summer of 2020-2021

This dataset contains images captured using wildlife cameras outside two Bogong moth aestivation caves on Ken Green Bogong, near South Ram's Head, NSW in the austral summer of 2020-2021. The images contain motion blurs from insects (predominantly Bogong moths Agrotis infusa) flying past the cameras, allowing for the measurement of Bogong moth wingbeat frequency, activity, and abundance using the Camfi software (<a href="https://github.com/J-Wall/camfi">https://github.com/J-Wall/camfi</a>).

opencc-zeroDec 2015View details →

Data from: Testosterone activates sexual dimorphism including male-typical carotenoid but not melanin plumage pigmentation in a female bird

In males it is frequently testosterone (T) that activates the expression of sexually selected morphological and behavioral displays, but the role of T in regulating similar traits in females is less clear. Here we combine correlational data with results from T and gonadotropin-releasing hormone (GnRH) manipulations in both sexes to assess the role of T in mediating sexually dimorphic coloration and morphology in the red-backed fairy-wren (Malurus melanocephalus). We show that (1) natural variation in female expression of ornamental traits (darkened bills and red back feathers) are positively associated with age and circulating androgen titres, (2) females have the capacity to express most male-typical traits in response to exogenous T, including carotenoid-pigmented body plumage, shorter feathers, darkened bill, and enlarged cloacal protuberance, but (3) appear constrained in production of male-typical melanin-pigmented plumage, and (4) low androgen levels during the pre-nuptial molt, probably due to low ovarian capacity for steroid production (or LH-sensitivity), prevent females from developing male-like ornamentation. Thus, females appear to retain molecular mechanism for hormonally regulated male-typical ornamentation, although these are rarely activated because of insufficient production of the hormonal signal.