Find research datasets worth reusing

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.

opencc-by-4.0Mar 2022View details →

Agile and the Long Crisis of Software (Audio Recording)

From <a href="https://logicmag.io/clouds/agile-and-the-long-crisis-of-software/">the article</a>: "I  began to explore the history of Agile. What I discovered was a long-running wrestling match between what managers want software development to be and what it really is, as practiced by the workers who write the code. Time and again, organizations have sought to contain software’s most troublesome tendencies—its habit of sprawling beyond timelines and measurable goals—by introducing new management styles. And for a time, it looked as though companies had found in Agile the solution to keeping developers happily on task while also working at a feverish pace. Recently, though, some signs are emerging that Agile’s power may be fading. A new moment of reckoning is in the making, one that may end up knocking Agile off its perch."

Data for: Long-term clade-wide shifts in trilobite segment number and allocation during the Palaeozoic

Arthropods are characterized by having an exoskeleton, paired jointed appendages, and segmented body. The number and shape of those segments varies dramatically and unravelling the evolution of segmentation is fundamental to our understanding of arthropod diversification. Because trilobites added segments to the body post-hatching which were expressed and preserved in biomineralized exoskeletal sclerites, their fossil record provides an excellent system for understanding the early evolution of segmentation in arthropods. Over the last 200 years, palaeontologists have hypothesized trends in segment number and allocation in the trilobite body, but they have never been rigorously tested. We tabulated the number of segments in the post-cephalic body for over 1500 species, selected to maximize taxonomic, geographic, and temporal representation. Analysis reveals long-term shifts in segment number and allocation over the 250-million-year evolutionary history of the clade. For most of the Palaeozoic, the median number of segments in the body did not change significantly. Instead, the total range decreased over time and there was long-term increase in the proportion of segments allocated to the fused terminal sclerite relative to the articulated thoracic region. There was also increased conservation of thoracic segment number within families. Neither taxonomic turnover nor trends in functionally-relevant defensive behaviour sufficiently explain these patterns.

opencc-by-4.0Aug 2022View details →

Long document similarity dataset, Wikipedia excerptions for movies collections

Movies-related articles extracted from Wikipedia. For all articles, the figures and tables have been filtered out, as well as the categories and "see also" sections. The article structure, and particularly the sub-titles and paragraphs are kept in these datasets   Movies The Wikipedia Movies dataset consists of 100,371 articles describing various movies. Each article may consist of text passages describing the plot, cast, production, reception, soundtrack, and more.

opencc-by-4.0Dec 2022View details →

URInary peptidomic patterns of Long-COVID syndrome "UriCoV"

Post acute sequelae of SARS-CoV-2 infection (PASC), also referred to as long COVID, is the most frequent, yet poorly characterized sequelae of COVID-19. It has tremendous, unpredictable consequences on personal health and socioeconomic status of affected individuals, and on global economic issues. UriCov is a multidisciplinary, comprehensive project with the aim to investigate in depth the molecular phenotype(s) of individual patients previously infected by SARS-CoV-2 and identify patients at risk of PASC. This will be achieved through multi-disciplinary research based on omics and clinical data in a bioinformatics framework, based on the hypothesis that endothelial damage is a key event in PASC. The developed molecular tools may allow patient stratification to initiate personalized treatment for prevention of PASC prior to symptoms and to decrease the PASC incidence. UriCoV will also provide missing fundamental knowledge on the molecular pathophysiology of PASC.

Wind effects on the long-distance migration of GPS-tracked adult ospreys (Pandion haliaetus) from Germany

Birds that repeatedly visit distinct places along their migratory routes in consecutive years must be able to navigate to these places and respond appropriately to unfavourable wind conditions. This study analysed the migratory routes, repeatedly-visited areas, and responses to sidewinds of 15 GPS-tracked adult ospreys (Pandion haliaetus) from northeast Germany migrating to their wintering sites in Africa and back. We determined stopovers and intermediate goal areas and performed repeatability estimations on timing and migratory paths in four regions. The orientation behaviour of the ospreys was analysed with regard to perpendicular wind components at each GPS point during autumn and spring migrations. Generalised linear mixed models were used to test the dependence of orientation behaviour on region and the distance to the next goal. The findings showed that ospreys demonstrate high fidelity to migratory paths in autumn and spring, as well as to the timing of migration in autumn; and sidewinds are predominantly compensated, especially when sidewinds are strong. Furthermore, during autumn migration, the proportion of compensation increases in most regions with decreasing distances to the next goal; however, during spring migration, drift behaviour was detected more often at smaller distances to the next goal than at higher distances in the regions of Mediterranean and Central Europe. In general, ospreys compensate for unfavourable sidewinds and utilise supporting tailwinds on their journeys to the wintering sites in Africa and back to Central Europe.

NDVI-based monitoring of long-term vegetation dynamics and responses to multi-time scales droughts in Inner Mongolia

The characteristics of vegetation and drought for different seasons between 1982 and 2015 in Inner Mongolia were studied based on the Normalized Difference Vegetation Index (NDVI) and the Standardized Precipitation Evapotranspiration Index (SPEI). The response of vegetation to drought over various time scales for different seasons and vegetation types was investigated using the maximum Pearson correlation, allowing a discussion about the possible causes of any changes. The results indicate that the vegetation NDVI in Inner Mongolia showed an increasing trend in different seasons, with spring vegetation NDVI (April to May) having the largest significant increasing rate, followed by the growing season (April to October), autumn (September to October), and summer (June to August). Accordingly, the proportion of stations with decreasing SPEI was, in descending order, summer, growing season, autumn, and spring. Additionally, the magnitude of the SPEI decrease was greater in eastern Inner Mongolia. NDVI and SPEI were positively correlated in most regions of Inner Mongolia, indicating that changes in vegetation in most parts of this region were affected by the spatial and temporal characteristics of drought, the correlation being them being strongest in the growing season, followed by summer, then spring and autumn. Considering the different types of vegetation, forests were less affected by drought, with broadleaf forests more affected than coniferous forests. The meadow steppes and typical steppes were more affected by 12-month droughts in the growing season and summer, 6-month droughts in spring, and 3-month droughts in autumn, with desert steppes mainly affected by 3-month droughts. The shrubs, sandy vegetation, and cropland were mostly affected by droughts in summer, and show a greater response to 3-month droughts in autumn. Finally, the water balance was found to be the most important factor affecting the response of vegetation to drought in Inner Mongolia.

openother-openDec 2022View details →

dmurraystoker/OGC-biomass: Long-term comparison of invertebrate communities in a blackwater river reveals taxon-specific biomass change

Data, metadata, and R code for "Long-term comparison of invertebrate communities in a blackwater river reveals taxon-specific biomass change." Abstract 1. Around the world, researchers are reporting declines in insect fauna. Though uncommonly evaluated in high-profile studies of insect declines, the community context of population trends can facilitate interpretation of the causes and consequences of such losses. Here, we aimed to explore the shifts in a well-studied invertebrate community of a blackwater river and identify potential catalysts of such change. 2. We compared the density, biomass, and community structure of freshwater invertebrate assemblages separated by more than 30 years in the Ogeechee River, in the southeastern US, and found biomass declines. We also evaluated long-term trends in river discharge, water temperature, and precipitation. 3. Overall, the biomass in the 2010s was approximately 60% of the total in the 1980s. Community analyses indicated that this decline was driven by reduced densities of large-bodied, filter-feeding insects, particularly Hydropsychidae caddisflies (Trichoptera). Conversely, predators and small-bodied primary consumers increased in density, though their contributions to overall biomass were minimal and their increased density was not sufficient to compensate for biomass declines. Seasonal shifts in both invertebrate populations and environmental parameters were evident, especially when focusing on discharge and dissolved organic carbon. 4. Through a combination of direct analysis and the use of established research on the metabolic dynamics of the study site, we determined that the overall decline of freshwater invertebrate biomass may be driven by climate-related changes in flood dynamics: seasonal flooding that facilitates delivery of floodplain carbon to filter-feeding consumers has decreased over several decades. Water temperature had also increased and has likely had effects on the invertebrate assemblages. 5. Whole-community evaluations such as this one, in contrast to single-taxon and abundance-based studies, provide critical information to elucidate the dynamics of freshwater impairment and insect loss in the Anthropocene.

Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters

Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of Daphnia magna to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that Daphnia are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.

opencc-by-4.0Feb 2022View details →

Data for LEELO-LA (Long-term Energy Expansion Linear Optimization - Latin America)

This repository contains the data for LEELO-LA (Long-term Energy Expansion Linear Optimization - Latin America)

Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and Rps2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.

Data from: Range reexpansion after long stasis: Italian otters (Lutra lutra) at their northern edge

Species range shifts and expansion are subjects of primary research interest in the context of climate warming and biological invasions. Few studies have focused on reexpansion of species that suffered severe declines. Here, we focused on population recovery of Eurasian otters (Lutra lutra) in Italy, first detected in 2003 after a southward range contraction. We modelled the rate of range expansion and occupancy at the northern expanding front (central Italy), to gain insights into the progress of recovery and mechanisms of reexpansion. We performed a field survey in 2021, which redefined the northern limit of distribution further north, in close proximity to the Gran Sasso National Park. Then we analyzed a time series (1985–2021) of distances of northernmost occurrences from the centre of the 1985 range. Using segmented regression, we were able to identify a prolonged stasis of the northern range edge and a simultaneous increase in occupancy from 0.151 to 0.4. A breakpoint was estimated in 2006, after which the range expanded northwards at an average rate of 5.48 km/year. From 2006 to 2021, the overall northward shift was about 80 km. Occupancy continued to increase until 2019 and abruptly declined in 2021. These patterns suggest that the reexpansion of the range can be limited by low occupancy at the expanding front. As occupancy increases, long-distance dispersal increases and then range expands. The low occupancy at the current distribution limit of otters may reflect a higher anthropogenic pressure on northern habitats, which could slow down the reexpansion process.

Does long-term soil warming affect microbial element limitation? A test by short-term assays of microbial growth responses to labile C, N and P additions

Increasing global temperatures have been reported to accelerate soil carbon (C) cycling but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0–10, 10–20 cm) in control and warmed (>14 yrs warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 hours. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration – though easy and cheap to measure – is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

Raising offspring increases ageing: Differences in senescence among three populations of a long-lived seabird, the Atlantic puffin

1. Actuarial senescence, the decline of survival with age, is well documented in the wild. Rates of senescence vary widely between taxa, to some extent also between sexes, with the fastest life histories showing the highest rates of senescence. Few studies have investigated differences in senescence among populations of the same species, although such variation is expected from population-level differences in environmental conditions, leading to differences in vital rates and thus life histories. 2. We predict that, within species, populations differing in productivity (suggesting different paces of life) should experience different rates of senescence, but with little or no sexual difference in senescence within populations of monogamous, monomorphic species where the sexes share breeding duties. 3. We compared rates of actuarial senescence among three contrasting populations of the Atlantic puffin Fratercula arctica. The data set comprised 31 years (1990–2020) of parallel capture-mark-recapture data from three breeding colonies, Isle of May (North Sea), Røst (Norwegian Sea) and Hornøya (Barents Sea), showing contrasting productivities (i.e. annual breeding success) and population trends. We used time elapsed since first capture (TFC) as a proxy for bird age, and productivity and the winter North Atlantic Oscillation Index (wNAO) as proxies for the environmental conditions experienced by the populations within and outside the breeding season, respectively. 4. In accordance with our predictions, we found that senescence rates differed among the study populations, with no evidence for sexual differences. There was no evidence for an effect of wNAO, but the population with the lowest productivity, Røst, showed the lowest rate of senescence. As a consequence, the negative effect of senescence on the population growth rate (λ) was up to 3–5 times smaller on Røst (Δλ = -0.009) than on the two other colonies. 5. Our findings suggest that environmentally induced differences in senescence rates among populations of a species should be accounted for when predicting effects of climate variation and change on species persistence. There is thus a need for more detailed information on how both actuarial and reproductive senescence influence vital rates of populations of the same species, calling for large-scale comparative studies.

Global expansion of a solitary-social tropical spitting spider shaped by multiple long-distance dispersals

The spitting spider Scytodes fusca is well known species complex for its unusual hunting technique which involves spitting a venomous sticky silken substance over its prey. Previous studies supposed that S. fusca was native to Central and Southern America but had been expanded to the tropics of almost every continent. We aimed to test the hypothesis of a Neotropical origin for this spider followed by a secondary dispersal to other regions, and to discuss how population expansion occurred in the tropics was driven. We investigated the population structure and spatiotemporal biogeography of the species complex through a culmination of a 22-year comprehensive global sampling using the mitochondrial and nuclear loci (COI, 16S, 18S, 28S, H3 and ITS2). The S. fusca species complex is divided into two clades. One clade comprises the haplotypes from Australasian regions and a haplotype from Baja Peninsula, Mexico. The other is composed of the haplotypes from all analyzed regions including Asia, Australia, the Americas and Madagascar. The Americas and Madagascar populations exhibit a lower genetic diversity compared with the Australasian population, and both have different population demographic histories. The initial divergence within the species complex started during the early Miocene. Diversifications of both clades occurred during the late Miocene. One haplotype was recently and widely dispersed into Southeast Asia, South Asia, Australia, the Americas and Madagascar. Our results elucidate the global spread history of the S. fusca species complex, suggesting a Malay Archipelago origin, two expansion routes, and its multiple dispersals into the Americas that stem from a common native source population, as well as from Australia, Fiji, French Polynesia, or Turks and Caicos bridgeheads. Our data support that the expansion of the S. fusca species complex from Australasia to America and Madagascar was facilitated by long-distance jump dispersal events.

Why do parents produce small broods of offspring that have lower body mass, survival, and lifetime reproductive success? A case study in a long-lived bird

Numerous studies have examined the correlation between offspring quantity and quality, and many have found that the most common brood size is often smaller than broods with the highest offspring quality or production. However, the reasons why these small broods with lower offspring quality are produced, are still poorly explained. Using data spanning 29 years, we investigated the effects of brood size on nestlings' body mass and the lifetime fitness for those offspring as adults (as proxies of offspring quality) in the Crested Ibis (Nipponia nippon). We also examined the temporal variation of brood size. We found that overall offspring quality increases with brood size and that individuals from broods of three had the highest quality, as quantified by larger body mass, higher adult survival, and lifetime reproductive success. Furthermore, brood size of an individual pair significantly varied across years, and the proportion of broods containing two offspring increased while broods of three decreased after 2000 when the population dispersed to low-quality habitat. These findings indicate that spatiotemporal variation in resources may impact variation in brood size and subsequent fitness consequences, and that small broods are more common in resource-poor years or low-quality habitats. In contrast, parents with access to high-quality resources produce larger broods of nestlings that achieve higher body mass and subsequently experience higher adult survival and lifetime fitness. This study highlights how variation in life history traits can be influenced by resource condition, and provides an insight into particular habitat that need conservation for Crested Ibis.

Long-term responses to large-scale disturbances: Spatiotemporal variation in gastropod populations and communities

The Anthropocene is characterized by complex, primarily human-generated, disturbance regimes that include combinations of long-term press (e.g. climate change, pollution) and episodic pulse (e.g. cyclonic storms, floods, wildfires, land use change) disturbances. Within any regime, disturbances occur at multiple spatial and temporal scales, creating complex and varied interactions that influence spatiotemporal dynamics in the abundance, distribution, and biodiversity of organisms. Moreover, responses to disturbance are context-dependent, with the legacies of previous disturbances affecting responses to ensuing perturbations. We use three decades of annual data to evaluate the effects of repeated pulse disturbances and global warming on gastropod populations and communities in Puerto Rico at multiple spatial scales. More specifically, we quantify (1) the relative importance of large-scale and small-scale aspects of disturbance on variation in abundance, biodiversity, and species composition; and (2) the spatial scales at which populations and communities integrate information in the spatially heterogenous environments created by disturbances. Gastropods do not exhibit consistent decreases in abundance or biodiversity in association with global warming: abundance for many species has increased over time and species richness does not evince a temporal trend. Nonetheless, gastropods are sensitive to hurricane severity, spatial environmental variation, and successional trajectories of the flora. In addition, they exhibit context-dependent (i.e. legacy effects) responses that are scale-dependent. The Puerto Rican biota has evolved in a disturbance-mediated system. This historical exposure to repeated, severe hurricane-induced disturbances has imbued the biota with high resistance and resilience to the current disturbance regime, resulting in an ability to persist or thrive under current environmental conditions. Nonetheless, these ecosystems may yet be threatened by worsening direct and indirect effects of climate change. In particular, more frequent and severe hurricanes may prevent the establishment of closed-canopy forests, negatively impacting populations and communities that rely on these habitats.

opencc-by-4.0Jul 2022View details →

Measurement of the fumarole temperature of the north eastern crater rim of Vesuvius -----Long-term variations of fumarole temperature of the north eastern crater rim of Vesuvius (Italy)

<pre>Measurements of the fumarole temperature of the north eastern edge of Vesuvius have been carried out since 1995. The temperature is measured at a depth of 10 cm using a K-type thermocouple. The coordinate of the fumarole is 33T 451833.1m E - 4519224.8m N.</pre> <pre>The monitored fumarole is the one at the highest altitude present on Vesuvius </pre> The fumarole is characterized by low temperatures (59.5 - 75.6 ˚C) and discharge a mixture of air (46% -72%), steam (25% -45%) and CO2 (0.2% -2%). The air is the main component of fumarole, is most likely included in the upper fluids part of the fumarolic ducts found in the highly permeable products of the Vesuvian cone.

Immediate and long-term genetic consequences of linear transport infrastructure: Can fauna crossing mitigate its cost?

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare, and to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic dataset collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12–69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of 8 koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.