Find research datasets worth reusing

opencc-zeroJul 2021View details →

Long-term stability of cortical ensembles

Neuronal ensembles, coactive groups of neurons found in spontaneous and evoked cortical activity, are causally related to memories and perception, but it still unknown how stable or flexible they are over time. We used two-photon multiplane calcium imaging to track over weeks the activity of the same pyramidal neurons in layer 2/3 of the visual cortex from awake mice and recorded their spontaneous and visually evoked responses. Less than half of the neurons were commonly active across any two imaging sessions. These "common neurons" formed stable ensembles lasting weeks, but some ensembles were also transient and appeared only in one single session. Stable ensembles preserved ~68 % of their neurons up to 46 days, our longest imaged period, and these "core" cells had stronger functional connectivity. Our results demonstrate that neuronal ensembles can last for weeks and could, in principle, serve as a substrate for long-lasting representation of perceptual states or memories.

opencc-by-4.0Jul 2021View details →

Functionally distinct tree species support long-term productivity in extreme environments

Dataset used for the article "Functionally distinct tree species support long-term productivity in extreme environments", submitted to Proceedings of the Royal society B. Contains raw output of simulations performed with the ForCEEPS forest gap model (http://capsis.cirad.fr/capsis/help_en/forceeps). For a description of the simulations performed and the dataset, see the associated GitHub (https://github.com/LDelalandre/Project-1_Distinct-sp_BEF) and the article. Simulations are grouped in 11 folders corresponding to the 11 environmental conditions used for simulating community dynamics. Subfolders group outputs by species richness gradients (30 random orders, plus "decreasing" order, which is from the most functionally distinct to the least functioonally distinct species, and "increasing, which is the other way around, and monocultures). For each species richness level (from 1: all the species, to 30, the last species of the richness gradient), four different files were generated: - biomass data: 'complete' (every individual); 'mean' (aggregated at the community level each year); - productivity data: productivity (every individual); productitity_scene (aggregated at the species level each year).

opencc-by-4.0Aug 2021View details →

Long-term time series of mussel and scallop abundances in the Bay of Seine (Normandy, France).

In Normandy (France), and particularly in the Bay of Seine, the great scallop Pecten maximus and the blue mussel Mytilus edulis are the main bivalve molluscs species harvested by the local fishing fleet. In this area, the scallop stock is one of the most important in Europe and appears to be growing since a few years. Its exploitation actually sustains an important economic activity (with a landed volume of 15.000 tons per year). However, population growth is not monotonous and yearly recruitment of young scallops seems to be very variable. For mussels, a fleet of nearly 40 boats exploited the natural banks in the subtidal area, with a landed volume ranging between 1.000 and 5.000 tons, exceptionally reaching 30.000 tons per year depending of the yearly fluctuations of the juvenile mussels’ settlement. Since 2014, however, the yearly prospective campaigns have pointed a dramatic decline of the recruitment throughout the area. Long-term data series on bivalve settlement usually show strongly fluctuating patterns, due to the environmental sensitivity of mollusk-recruitment process. While scallop and mussel stocks historically presented strong fluctuations of abundance, yearly monitoring programs were required to estimate annual abundance, and to adjust the fishing effort in line with the available resources. In accordance with stakeholders and fishermen, Ifremer (the French Research Institute for Exploitation of the Sea) and the Regional Fisheries Committee conducted these campaigns since 1992 for scallops and 1982 for mussels. Here, we present the dataset synthetizing the results of these campaigns in order to extend the reuse potential of these data. Particularly, database may help to quantify the effects of environmental variations on recruitment of two marine bivalve species and forecast simulations of recruitment under climate change scenario For scallops, a various number of one nautical mile squares were sampled each year in the southern part of the Bay of Seine (approximately south of 49°35 north latitude). This number was determined following the results of the campaigns conducted in the previous years, to ensure the representativeness of the abundance estimators. In each sampling unit, the fisher boat hauled 2 survey dredges with a 2 meters wide aperture. Harvested individuals were then classified by age-class, and numbered. Later, we calculated back an abundance index per age-class and per surface unit covered by the dredges. For mussels, 5 small banks located in the south-western part of the Bay of Seine were prospected each year. Grandcamp bank is approximately located between 1°07’ W and 0°56’ W, and 49°26’ N. and 49°23’ N. Ravenoville bank boundaries are 1°16’ W-1°07’ W, and 49°32’ N-49°25’N. Réville bank boundaries are 1°15’ W and 1°10’ W, and 49°37’ N and 49°34’ N. Moulard bank boundaries are 1°15’ W and 1°10’ W, and 49°41’ N and 49°38’ N. Barfleur bank boundaries are 1°21’ W and 1°10’ W, and 49°48’ N and 49°40’ N. During the annual campaigns, chartered fishermen vessels prospected the different banks by dredging, following a sampling design adapted to the mussel distribution and divided by a various number of one mile squares. Each year and for each bank, they realized one haul in the sampling squares located in the periphery of the bank to determine the mussel coverage. Once the boundaries of the bank delimited, the sampling effort was uniformly distributed within the area. In any one haul, the mussels were weighted and a subsample of the harvested individuals were numbered, measured and weighted individually. Later, we estimated the mean individual mass per size-class, and deduced the number of mussel per size-class and per sampling unit. In this case, the abundance index consists in an index of dredging-yield, expressed in kilograms per minute of hauling one dredge. This index was calculated for the commercial-sized mussels (> 40 mm) only, because of the reduced catchability of smaller mussels. The dataset contains 4 columns and 186 rows. The columns are ‘year’, ‘species’, ‘area’, ‘index’.

opencc-zeroAug 2021View details →

Temporal and regional trends of antibiotic use in long-term aged care facilities across 39 countries, 1985-2019: systematic review and meta-analysis

Background Antibiotic misuse is a key contributor to antimicrobial resistance and a concern in long-term aged care facilities (LTCFs). Our objectives were to: i) summarise key indicators of systemic antibiotic use and appropriateness of use, and ii) examine temporal and regional variations in antibiotic use, in LTCFs (PROSPERO registration CRD42018107125). Methods & Findings Medline and EMBASE were searched for studies published between 1990-2021 reporting antibiotic use rates in LTCFs. Random effects meta-analysis provided pooled estimates of antibiotic use rates (percentage of residents on an antibiotic on a single day [point prevalence] and over 12 months [period prevalence]; percentage of appropriate prescriptions). Meta-regression examined associations between antibiotic use, year of measurement and region. A total of 90 articles representing 78 studies from 39 countries with data between 1985-2019 were included. Pooled estimates of point prevalence and 12-month period prevalence were 5.2% (95% CI: 3.3-7.9; n=523,171) and 62.0% (95% CI: 54.0-69.3; n=946,127), respectively. Point prevalence varied significantly between regions (Q=224.1, df=7, p<0.001), and ranged from 2.4% (95% CI: 1.7-2.7) in Eastern Europe to 9.0% in the British Isles (95% CI: 7.6-10.5) and Northern Europe (95% CI: 7.7-10.5). Twelve-month period prevalence varied significantly between region (Q=15.1, df-3, p=0.002) and ranged from 53.9% (95% CI: 48.3-59.4) in the British Isles to 68.3% (95% CI: 63.6-72.7) in Australia. Meta-regression found no association between year of measurement and antibiotic use prevalence. The pooled estimate of the percentage of appropriate antibiotic prescriptions was 28.5% (95% CI: 10.3-58.0; n=17,245) as assessed by the McGeer criteria. Year of measurement was associated with decreasing appropriateness of antibiotic use over time (OR: 0.78, 95% CI: 0.67-0.91). The most frequently used antibiotic classes were penicillins (n=44 studies), cephalosporins (n=36), sulphonamides/trimethoprim (n=31), and quinolones (n=28). Conclusions Coordinated efforts focusing on LTCFs are required to address antibiotic misuse in LTCFs. Our analysis provides overall baseline and regional estimates for future monitoring of antibiotic use in LTCFs.

opencc-zeroSep 2021View details →

Why cannot long-term cascade be predicted? Exploring temporal dynamics in information diffusion processes

Predicting information cascade plays a crucial role in various applications such as advertising campaigns, emergency management, and infodemic controlling. However, predicting the scale of an information cascade in a long-term could be difficult. In this study, we take Weibo, a Twitter-like online social platform, as an example, exhaustively extract predictive features from the data, and use a conventional machine learning algorithm to predict the information cascade scales. Specifically, we compare the predictive power (and the loss of it) of different categories of features in short-term and long-term prediction tasks. Among the features that describe the follower-followee network, retweet network, tweet content, and early diffusion dynamics, we find that early diffusion dynamics are the most predictive ones in short-term prediction tasks but lose most of their predictive power in long-term tasks. In-depth analyses reveal two possible causes of such failure: the bursty nature of information diffusion and feature temporal drift over time. Our findings further enhance the comprehension to information diffusion process and may assist in the control of such process.

opencc-zeroOct 2021View details →

Local canopy disturbance as an explanation for long-term increases in liana abundance

Canopy disturbance explains liana abundance and distribution within tropical forests and thus may also explain the widespread pattern of increasing liana abundance; however, this hypothesis remains untested. We used a 10-year study (2007 – 2017) of 117,100 rooted lianas in an old-growth Panamanian forest to test whether local canopy disturbance explains increasing liana abundance. We found that liana density increased 29.2% and basal area 12.5%. The vast majority of these increases were associated with clonal stem proliferation following canopy disturbance, particularly in liana-dense, low-canopy gaps, which had far greater liana increases than did undisturbed forest. Lianas may be ecological niche constructors; arresting tree regeneration in gaps and thus creating a high-light environment that favors sustained liana proliferation. Our findings demonstrate that liana abundance is increasing rapidly and their ability to proliferate via copious clonal stem production in canopy gaps explains much of their increase in this and possibly other tropical forests.

opencc-zeroOct 2021View details →

Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies

Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing "superorganisms" – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.

opencc-zeroOct 2022View details →

Data From: Long-term winter food supplementation shows no significant impact on reproductive performance in Mountain Chickadees in the Sierra Nevada Mountains

Supplemental feeding of wild animal populations is popular across many areas of the world and has long been considered beneficial, especially to avian taxa. Over four billion dollars are spent by hobby bird feeders in the United States each year alone. However, there is mixed evidence whether wildlife feeding is beneficial, including when it is implemented as a conservation management tool, a targeted experimental design, or an avocation. Much of the current evidence suggests that providing supplemental food is advantageous to the reproductive output and general survival of focal taxa. However, many of these studies are limited in scope and duration, leaving possible negative impacts unaddressed. This is particularly true regarding passive backyard feeding, which describes the majority of supplemental feeding, including the immense effort of millions of public enthusiasts. Here we show that winter supplemental feeding prior to reproduction had no significant impact on a range of reproductive parameters in a resident, montane passerine species, the Mountain Chickadee (Poecile gambeli). This population resides in an intact natural environment with no exposure to supplemental food beyond our experimental treatments, and individual birds were tracked across six years using radio frequency identification technology. Our results add to the growing evidence that supplemental feeding alone, isolated from the effects of urban environments, may have little to no impact on the population dynamics of some avian taxa.

opencc-zeroOct 2022View details →

Long-term fire and vegetation change in northwestern Amazonia

Amazonian forest plots are used to quantify biodiversity and carbon sequestration, and provide the foundation for much of what is known about tropical ecology. Many plots are assumed to be undisturbed, but recent work suggests that past fire, forest openings, and cultivation created vegetation changes that have persisted for decades to centuries (ecological legacies). The Yasuní Forest Dynamics plot is one of the most biodiverse places on earth, yet its human history remains unknown. Here, we use charcoal and phytolith analysis to investigate the fire and vegetation history of the Yasuní forest plot, and compare results with nearby forest plots in Colombia (Amacayacu) and Peru (Medio Putumayo-Algodón (MPA)) to explore the spatial variability of past disturbances and ecological legacies in northwestern Amazonia. Three 14C dated charcoal fragments provided evidence for a modern (1956 CE) and a past fire event ca. 750 years ago at Yasuní, compared with fire ages of 1000-1600 years ago documented at Amacayacu and MPA. Small-scale disturbances and localized canopy-openings also occurred in the Yasuní plot. Phytolith assemblages from Yasuní and Amacayacu showed more variability in past vegetation change than MPA. Low-intensity, non-continuous disturbances occurred at all three plots in the past, and our results highlight the variability of past human activities both in space and time in northwestern Amazonia. Our data also suggest that post-Columbian human disturbances from the Rubber Boom (AD 1850-1920) and subsequent oil exploration have likely left stronger ecological legacies than those left by pre-Columbian peoples in our studied regions.

opencc-by-4.0Oct 2022View details →

Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening

We uploaded the image of the mansucript Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening accepted on Biology.

opencc-zeroOct 2022View details →

Resistance of termite mounds to variation in long-term fire regimes across semi-arid African savannas

1. Fire regimes are expected to change with climate change, resulting in a crucial need to understand the specific ways in which variable fire regimes impact important contributors to ecosystem functioning, such as mound-building termites. Termite mounds and fire are both important agents of savanna ecosystem heterogeneity and functioning, but there is little understanding of how they interact across savanna types. 2. We used very high-resolution LiDAR remote sensing to measure the size, density, and distribution of termite mounds across approximately 1,300 ha of experimental burn plots in four South African savanna landscapes representing a wide range of fire treatments differing in seasonality and frequency of burning. 3. In nutrient-poor granitic savannas, fire had no impact on termite mound size, densities, and spatial distributions. In nutrient-rich basaltic savannas with high mammalian herbivore abundance and intermediate rainfall, very frequent fires caused a decrease in termite mound size, whereas in arid nutrient-rich basaltic savannas, fires that occurred at intermediate frequencies and in transitional seasons (i.e., late dry season and late wet season) decreased the degree of spatial overdispersal exhibited by mounds. 4. Overall, our results suggest that termite mounds are resistant to variation in fire seasonality and frequency, likely indicating that ecosystem services provided by mound-building termites will be unaffected by changing fire regimes. However, consideration of changes to termite mound size and distribution could be necessary for land managers in specific savanna types, such as nutrient-rich soils with high mammalian herbivore abundance.

Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X

Dynamic Ca2+ signals reflect acute changes in membrane excitability and also mediate signaling cascades in chronic processes. In both cases, chronic Ca2+ imaging is often desired but challenged by the cytotoxicity intrinsic to calmodulin (CaM)-based GCaMP, a series of genetically-encoded Ca2+ indicators that have been widely applied. Here, we demonstrate the performance of GCaMP-X in chronic Ca2+ imaging of cortical neurons, where GCaMP-X by design is to eliminate the unwanted interactions between the conventional GCaMP and endogenous (apo)CaM-binding proteins. By expressing in adult mice at high levels over an extended time frame, GCaMP-X showed less damage and improved performance in two-photon imaging of sensory (whisker-deflection) responses or spontaneous Ca2+ fluctuations, in comparison with GCaMP. Chronic Ca2+ imaging of one month or longer was conducted for cultured cortical neurons expressing GCaMP-X, unveiling that spontaneous/local Ca2+ transients progressively developed into autonomous/global Ca2+ oscillations. Along with the morphological indices of neurite length and soma size, the major metrics of oscillatory Ca2+, including rate, amplitude and synchrony were also examined. Dysregulations of both neuritogenesis and Ca2+ oscillations became discernible around 2–3 weeks after virus injection or drug induction to express GCaMP in newborn or mature neurons, which were exacerbated by stronger or prolonged expression of GCaMP. In contrast, neurons expressing GCaMP-X were significantly less damaged or perturbed, altogether highlighting the unique importance of oscillatory Ca2+ to neural development and neuronal health. In summary, GCaMP-X provides a viable solution for Ca2+ imaging applications involving long-time and/or high-level expression of Ca2+ probes.

Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas

Tropical savannas are characterised by high primary productivity and high fire frequency, such that much of the carbon captured by vegetation is rapidly returned to the atmosphere. Hence, there have been suggestions that management-driven reductions in savanna fire frequency and/or severity could significantly reduce greenhouse gas emissions and sequester carbon in tree biomass. However, a key knowledge gap is the extent to which savanna tree biomass will respond to modest shifts in fire regimes due to plausible, large-scale management interventions. Here, we: (1) characterise relationships between the frequency and severity of fires and key demographic rates of savanna trees, based on long-term observations in vegetation monitoring plots across northern Australia; (2) use these relationships to develop a process-explicit demographic model describing the effects of fire on savanna tree populations; and (3) use the demographic model to address the question: to what extent is it feasible, through the strategic application of prescribed burning, to increase tree biomass in Australian tropical savannas? Our long-term tree monitoring dataset included observations of 12,344 tagged trees in 236 plots, monitored for between 3 and 24 years. Analysis of this dataset showed that frequent high-severity fires significantly reduced savanna tree recruitment, survival and growth. Our demographic model suggested that: (1) despite the negative effects of frequent high-severity fires on demographic rates, savanna tree biomass appears to be suppressed by only a relatively small amount by contemporary fire regimes, characterised by a mix of low- to high-severity fires; and (2) plausible, management-driven reductions in the frequency of high-severity fires are likely to lead to increases in tree biomass of about 11.0 t DM ha–1 (95% confidence interval: -1.2–20.8) over a century. Accounting for this increase in carbon storage could generate significant carbon credits, worth on average three times those generated annually by current greenhouse gas (methane and nitrous oxide) abatement projects, and has the potential to significantly increase the economic viability of fire/carbon projects, thereby promoting ecologically sustainable management of tropical savannas in Australia and elsewhere. This growing industry has the potential to bring much-needed economic activity to savanna landscapes, without compromising important natural and cultural values.

Data for: Grazing effects of wintering geese on grassland yield: A long-term study from NW-Germany

Conflicts between grassland farming and wintering geese stimulated a long-term study on goose-dependent yield losses. In the period 1996-2018 the loss of dry biomass of the first harvest increased from ca. 15 % to 50 % which corresponds with changes in the number and migratory behaviour of the barnacle goose. In contrast we found no decline in grassland yields with increasing number of greater white-fronted geese. The second harvest was not affected by wintering geese. The present study forms the basis for a fair and comprehensible system of compensation payments fo affected farmers.

opencc-by-4.0Nov 2022View details →

Supporting data for the manuscript entitled: Long-term biodegradation of oil under Arctic Conditions: the Baffin Island Oil Spill (BIOS) revisited after almost four decades.

The potential of an unintentional oil spill from ships or upcoming oil development is rising as the Arctic warms up more. It is crucial to understand how oil behaves in this setting and what influences oil biodegradation in the Arctic. On Baffin Island in the Canadian High Arctic, the Baffin Island Oil Spill (BIOS) project staged a number of simulated oil spills on the backshore zone of beaches in the 1980s. Two BIOS sites were revisited in 2019, about 40 years after the first oil pollution, providing a unique chance to research the long-term weathering of crude oil in Arctic conditions. Here, we demonstrate that even after over 40 years, residual oil is still detectable at these locations. Oil at both locations seems to deteriorate relatively slowly, with estimated loss rates ranging from 1.8 to 2.7% annually and appearing to vary across the two locations. We also demonstrate how the locations' sediment microbial communities are still severely impacted by leftover oil, as seen by a decline in diversity, variations in microbial load, and an enrichment of reported oil-degrading bacteria in contaminated sediments. The most enriched putative oil degraders were found in non-oiled control sediments as well, indicating that these degraders are a normal component of the Arctic sediment microbiome even in the absence of oil. Reconstructed genomes of putative oil degraders indicate that only a portion of these degraders have unique adaptations for growth in psychrothermic environments. This study's findings taken together demonstrate that oil spills in the Arctic can linger and have a lasting, major impact on the environment for decades.

opencc-by-4.0Dec 2022View details →

Global long-term (2010-2020) daily seamless fused XCO2 and XCH4 from GOSAT, OCO-2, and CAMS-EGG4

A novel spatiotemporally self-supervised fusion method is proposed to establish long-term daily seamless XCO2 and XCH4 products from 2010 to 2020 over the globe at grids of 0.25°. More details are provided in https://doi.org/10.5194/essd-2023-28.

Long-term spatially-replicated data show no physical cost to a benefactor species in a facilitative plant-plant interaction

Facilitation is an interaction where one species (the benefactor) positively impacts another (the beneficiary). However, the reciprocal effects of beneficiaries on their benefactors are typically only documented using short-term datasets. We use Azorella selago, a cushion plant species and benefactor, and a co-occurring grass species, Agrostis magellanica, on sub-Antarctic Marion Island, comparing cushion plants and the grasses growing on them over a 13-year period using a correlative approach. We additionally compare the feedback effect of A. magellanica on A. selago identified using our long-term dataset with data collected from a single time period. We hypothesized that A. selago size and vitality would be negatively affected by A. magellanica cover and that the effect of A. magellanica on A. selago would become more negative with increasing beneficiary cover and abiotic-severity, due to, e.g., more intense competition for resources. We additionally hypothesized that A. magellanica cover would increase more on cushion plants with greater dead stem cover, since dead stems do not inhibit grass colonization or growth. The relationship between A. magellanica cover and A. selago size and vitality was not significant in the long-term dataset, and the feedback effect of A. magellanica on A. selago did not vary significantly with altitude or aspect; however, data from a single time period did not consistently identify this same lack of correlation. Moreover, A. selago dead stem cover was not significantly related to an increase in A. magellanica cover over the long term; however, we observed contrasting results from short-term datasets. Long-term datasets may, therefore, be more robust (and practical) for assessing beneficiary feedback effects than conventional approaches, particularly when benefactors are slow-growing. For the first time using a long-term dataset, we show a lack of physical cost to a benefactor species in a facilitative interaction, in contrast to the majority of short-term studies.

opencc-zeroDec 2022View details →

Wild kangaroos become more social when caring for young and may maintain long-term affiliations with popular individuals

Kangaroos are an iconic group of Australian fauna. Despite considerable research on kangaroo behaviour, key gaps remain in our understanding of their social organization in the wild. In particular, it remains largely unknown whether kangaroos form long-term social bonds and what factors might prompt individuals to associate or dissociate from one another. Over 6 years, we monitored the social affiliations of individually identified eastern grey kangaroos, Macropus giganteus, in a large wild population. We investigated the short-term and long-term relationships of kangaroos and the extent those relationships varied with age, sex and reproductive state. We found evidence that long-term relationships among eastern grey kangaroos are possible, especially between adult females. Those individuals that were more sociable within years were also more likely to establish affiliations across years. Contrary to previous studies, we observed females actively associating with other mothers in the years in which they had young. These data suggest that the fission-fusion dynamics of eastern grey kangaroo social behaviour allow females to modulate their social position with conspecifics according to their current reproductive state. We highlight the adaptive implications of the formation of long-term bonds and the changes in social behaviour observed in females.

opencc-zeroDec 2022View details →

Simulated data for: Long-term persistence of exaggerated ornaments under Fisherian runaway despite costly mate search

This repository contains simulated datasets relating to: Anna Waffender, Jonathan M. Henshaw "Long-term persistence of exaggerated ornaments under Fisherian runaway despite costly mate search" We simulate the evolution of male ornaments and female preferences under Fisherian runaway. We include costly mate search effort, reducing female fecundity. Datasets are organized into CSV files named after the corresponding figure in the publication. For further information see the publication and the file README.md in this repository.