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Fig. 4 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 4. Diversification of Analges through time. A, dated maximum clade credibility tree revealed by BEAST analysis from concatenated COI, 16S and 28S sequences for Analges species and their outgroups. Intensity of node colouration designates PP of Bayesian analysis. The chronostratigraphic scale is given with absolute geological ages (MYA, million years ago). The node bars indicate credibility intervals (± 95% highest posterior densities HPD). Two columns of coloured squares on the right designate two taxonomic hypotheses of intrageneric groupings. The category 'ungrouped' describe male Analges without both chelate legs III and finger-like processes on tarsi III. B, lineages through time (LTT) plot for Analges. The upturn around 23 Mya reflects an acceleration in the rate of speciation which coincides with the origin of the crown in the Analges clade.

Fig. 3 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 3. Phylogenetic conflict in the BI post-burnin trees reconstructed from concatenated sequences of COI, 16S and 28S as shown by consensus network analyses for threshold values 0.3 (A) and 0.012 (B). The hypothesized Analges corvinus–A. sturninus clade is depicted in red, the hypothesized Analges sp.n. 6–A. sturninus clade is depicted in blue. The numbers near splits are confidence values for alternate hypotheses.

Fig. 1 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 1. Morphological characteristics applied in two different intrageneric groupings in the Analges genus. A, general view of male, Analges corvinus, ventral side; B, hypertrophied leg III in males of the passerinus species group, A. passerinus, dorsal side; C, hypertrophied leg III in males of the chelopus species group, A. spiniger, ventral side; D, male tarsus III with ventral finger-like process bearing seta w in Analgopsis subgenus, A. poppei, dorsal side; E, male tarsus III lacking the ventral process in Analges subgenus, A. corvinus, ventral side.

Fig. 2 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 2. Neighbour-joining tree with sequence groups of putative Analges species recovered by automatic barcode gap discovery from COI barcode sequences.

opencc-by-4.0Dec 2021View details →

Long-term health-related quality of life, healthcare utilisation and back-to-work activities in Intensive Care Unit survivors: prospective confirmatory study from the Frisian Aftercare Cohort

More substantial information on recovery after Intensive Care Unit (ICU) admission is urgently needed. In a previous retrospective study, the proportion of non-recovery patients was 44%. The aim of this prospective follow-up study was to evaluate changes Health-Related Quality of Life (HRQoL) in the first year after ICU-admission. Long-stay adult ICU-patients (≥ 48 hours) were included. HRQoL was evaluated with the Dutch translation of the RAND-36 item Health Survey (RAND-36) at baseline via proxy measurement, and at three, six, and twelve months after ICU admission. Subsequently, the relation between  physical functioning, healthcare utilisation, and work activities was explored.

opencc-zeroJun 2022View details →

Biological and physiological responses of Bradysia odoriphaga 4th instar larvae to long-term constant and fluctuating mild heat stress

Global climate change can expose insects to high-temperature stress, including extreme and mild heat stress. For soil insects, mild heat stress is more common than extreme heat stress. High summer temperature is a key barrier for Bradysia odoriphaga (Diptera: Sciaridae), a devastating soil pest of vegetables in China. The 4th instar larvae possess the strongest thermal tolerance to high temperatures. To determine whether the 4th instar larvae of B. odoriphaga possess other adaptations to summer mild heat stress besides thermal plasticity, we evaluated the biological performance of 4th instar larvae under constant and fluctuating long-term mild heat stress. The physiological responses were studied including energy storage, hormone level, and expression of related genes. Bioassay results indicated that 4th instar larvae survived, without pupation, for more than 40 days under long-term mild heat stress (34°C). Combined with constant and fluctuating treatment, mild heat stress delayed larval development, reduced longevity, and reduced fecundity. However, a summer diapause-like phenomenon was observed, including larval development stasis under mild heat stress and a prolonged recovery time after mild heat stress. Protective physiological responses were involved in regulating the larval stage including accumulating fat and glycogen, a high level of juvenile hormone, and a low level of molting hormone. Also, high expression levels of hsp70 and hsp90 were detected. The delayed development of B. odoriphaga 4th instar larvae appears to be a special adaptation strategy to withstand mild heat stress in summer, and it is regulated by complex physiological processes.

opencc-by-4.0Jun 2022View details →

Long-term observation of the wastewater from the Parisian conurbation

Wastewater contains a wide range of biological and chemical markers related to human activity. The collection and analysis of these markers in the effluents (wastewater and sludge) allow make it possible to qualify the public health of the population and to evaluate the impact of the chemicals used in daily life on the environment. In line with these studies, the Innovation Department of SIAAP and its scientific partners (ISA and LEESU) have created an Observatory of the city with the objectives of: • Monitoring the long-term dynamics of known and/or potential pollutants according to French regulations. • Contributing to studies aimed at a better understanding of anthropogenic activities. • Structuring and centralizing data (wastewater and end-of-treatment sludge), ensuring their storage for 10 years. • Providing technical and scientific knowledge by publishing every two years the data generated by the Observatory of the city via the open platform Zenodo. Regarding the pre-treated wastewater, the Clichy pretreatment plant has been chosen as a strategic location because it collects wastewater from the Paris catchment area (2.7 million inhabitants). Data on the wastewater quality during dry weather and on rain events (biological and physicochemical global quality parameters, metals, polycyclic aromatic hydrocarbons – PAHs and polychlorinated biphenyls – PCBs) is available since 2000 (for dry weather) and from 2005 (for rain events).   Dataset description The dataset “Dataset _Clichy-SEC-Inlet.xlsx” includes the monthly analysis of various micro pollutants (trace metals, PAHs and PCBs) and usual physico-chemical parameters. The oldest analyses date back to 2000. The dataset “Dataset _Clichy-CSO.xlsx” includes the monthly quantified analysis of various micro pollutants (trace metals, PAHs and PCBs) and usual physico-chemical parameters for samples collected during 384 rain events. The oldest analyses date back to 2005. Details on each analysis are provided in the “Dataset_analyticalmethods_Clichy.xlsx”   The following files are available: <ul> <li>Dataset _Clichy-SEC-Inlet.xlsx</li> <li>Dataset _Clichy-CSO.xlsx</li> <li>Dataset_analyticalmethods_Clichy.xlsx</li> </ul>

opencc-by-4.0Jul 2022View details →

The long-term monthly discharge data of hydrological stations in the Pearl River during 1994-2018

This dataset contains the monthly discharge data of hydrological stations (i.e., Gaoyao, Shijiao, and Boluo) in the Pearl River during 1994-2018. The total discharge means the sum of discharges of Gaoyao, Shijiao, and Boluo.

opencc-by-4.0Aug 2022View details →

Long-term (2003-2020) hourly 0.25° global PM2.5 dataset (DeepCAMS) Part-2: 2012-2020

This is part II (2012-2020) of our DeepCAMS. Part I (2003-2011) can be found at: https://doi.org/10.5281/zenodo.6967082 Usage: The raw data -- (scaling factor: 0.1) --> the true PM2.5 concentration Paper title: Generating a Long-term (2003-2020) hourly 0.25° global PM2.5 dataset via spatiotemporal downscaling of CAMS with deep learning (DeepCAMS) Paper doi: <a href="https://doi.org/10.1016/j.scitotenv.2022.157747">https://doi.org/10.1016/j.scitotenv.2022.157747</a> <pre>If you find our work helpful, please cite it. Thank you very much!</pre>

opencc-by-4.0Aug 2022View details →

Machine Learning Constructs Color Features to Accelerate Development of Long-Term Continuous Water Quality Monitoring

This is a machine learning method for predicting the concentration of colored pollutants based on RGB and kmeans methods. This dataset includes raw images of pollutants as well as characteristic data of pollutants, as well as code for the model. You can see the contents of the zip file for details.

opencc-by-4.0Aug 2022View details →

Replication Package for "Long-term and Intergenerational Effects of Education: Evidence from School Construction in Indonesia"

Replication package for: Akresh, Richard, Daniel Halim, and Marieke Kleemans. 2023. "Long-term and Intergenerational Effects of Education: Evidence from School Construction in Indonesia" Economic Journal, forthcoming.

opencc-by-4.0Sep 2022View details →

Replication Package for Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects"

This replication package can be used for replicating results in the paper. It contains 1) a dataset of 290,255 repositories; and 2) Python scripts for training and interpreting models.  We recommend manually setup the required environment in a commodity Linux machine with at least 1 CPU Core, 8GB Memory and 100GB empty storage space. We conduct development and execute all our experiments on a Ubuntu 20.04 server with two Intel Xeon Gold CPUs, 320GB memory, and 36TB RAID 5 Storage. We use GHTorrent to restore historical states of 290,255 repositories with more than 57 commits, 4 PRs, 1 issue, 1 fork and 2 stars. The raw data of repositories are stored in `Replication Package/data/prodata.pkl`, and the contribution of features resulting from LIME model is stored in `Replication Package/data/limeres_m2_k1.pkl`. We sort items by the order in `Replication Package/data/randind.npy`, which can be used to reproduce the same results as in the paper.  `Replication Package/data/X_test_m2_k1.pkl` and `Replication Package/data/y_test_m2_k1.pkl` store the test dataset for the LIME model. You can run `Replication Package/fitdata.py` to get the results in Table III and IV, run `Replication Package/draw_compare_variable.py` to get Figure 2 and run `Replication Package/allvari_statistics.py` to get Table II. In `Replication Package/Variable_comparison_with_different_parameter.pdf`, we show the LIME results under different parameters. In `Replication Package/sample_pros.csv`, we also provide the list of randomly selected repositories in Section III.B.

opencc-by-4.0Sep 2022View details →

Replication Package for Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects"

opencc-by-4.0Sep 2022View details →

Experimental data for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels

Experimental data set for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels. Provides all raw data needed to reproduce experimental graphs presented within the paper.

opencc-zeroSep 2022View details →

Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long-term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two lab and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2-, 3-, 4- and 5-strains for hundreds of generations and asked which fitness related phenotypes – maximum growth rate or relative competitive fitness – would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long-term co-existence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multi-genotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long-term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.

opencc-zeroDec 2021View details →

Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

The coastal wetland is easily invaded by alien species due to its location in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to community restoration and species diversity protection. To reveal the long-term S. alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariquete, ruderal and unvegetated site) and soil depths (0–5 cm and 5–10 cm) in the Chongming island coastal salt marsh wetland. The results showed that the soil seed bank richness and species density under different vegetation types were higher than aboveground vegetation, and those of 0–5 cm seed banks were higher than 5–10 cm, except for the unvegetated site. The species richness and the S. alterniflora seed proportion in the seed banks under the S. alterniflora communities (S.AS) were lower and larger, respectively, than other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0–5 cm and 5–10 cm depths were interpreted 3.03% and 2.25% by aboveground communities, while 4.92% and 5.55% were interpreted by soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks' richness at the 0–5 cm depth and 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks' species density at the 0–5 cm depth and 5–10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0–5 cm seed banks' richness and species density, while its height and biomass only affected the 5–10 cm seed banks' species density. The microbial biomass of the 0–10 cm soil depth indirectly affected the richness and species density of the 0-5 cm seed bank, and only affected the richness of the 5–10 cm seed bank. Soil physical and chemical properties only indirectly affected the 0–5 cm seed banks' species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China and guidance for the protection and restoration of the native plant communities.

opencc-zeroOct 2022View details →

Data for: Estimating density dependence, environmental variance and long-term selection on a stage-structured life history

We model growth of a density-dependent stage-structured population undergoing small or moderate fluctuations around a deterministically stable equilibrium in a stochastic environment, assuming that a weighted sum of stage abundances, N, exerts density dependence on the stage-specific vital rates of survival and reproduction. We approximate the dynamics of N as a onedimensional stochastic process with three key parameters: the density-independent growth rate and the net density dependence and environmental variance in the life history. Comparisons of populations and species with different life histories are facilitated using the key parameters, which we show how to estimate from long-term demographic data on fluctuations in the vital rates. We also show that life history evolution is a stochastic maximization of a simple function of the key parameters. Elements in the long-term selection gradient acting on the life history can be expressed as sensitivities of this function with respect to density-independent, density-dependent, and stochastic components of the vital rates. Using years of demographic data on a great tit population, we estimate the key demographic parameters, which accurately predict the observed mean, coefficient of variation, and fluctuation rate of N, and also evaluate the long-term selection gradient on the population.

opencc-by-4.0Dec 2016View details →

Supplementary material 1 from: Pyšková K, Storch D, Horáček I, Kauzál O, Pyšek P (2016) Golden jackal (Canis aureus) in the Czech Republic: the first record of a live animal and its long-term persistence in the colonized habitat. ZooKeys 641: 151-163. https://doi.org/10.3897/zookeys.641.10946

Goledn jackal's howling record : Explanation note: Recording of an individual howling back to the recording of golden jackal. Recorded on 15 September 2015 around midnight.

opennotspecifiedOct 2017View details →

Figure 5 in Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

Figure 5. The Wallich Catalogue. Screenshot of Wallich Catalogue hosted by Royal Botanic Garden Edinburgh showing popup for stable URI containing information hosted at Botanic Garden and Botanical Museum Berlin-Dahlem.