Find research datasets worth reusing

opencc-by-4.0Oct 2021View details →

Figure 1 in Enhancing survival of Demodex folliculorum (Acari: Demodecidae) under in vitro condition: Effect of temperature and culture media

Figure 1. Photograph of the eyelids of a patient with cylindrical dandruff attached to the eyelid margin and around the eyelash base.

opencc-by-4.0Oct 2021View details →

Figure 3 in Sublethal effects of cyflumetofen and spirodiclofen on biological parameters of citrus red mite, Panonychus citri McGregor (Acari: Tetranychidae)

Figure 3. Age-stage life expectancy (exj) of offspring from P. citri females treated with LC20 sublethal concentration of cyflumetofen and spirodiclofen compared with untreated females.

opencc-by-4.0Oct 2021View details →

"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.

Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data 3D ED data sets of 5 compounds and JANA refinement files of 12 compounds Relevant tools: <ul> <li>PETS2: data reduction and analysis of electron diffraction patterns <ul> <li>Download program and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst. B75, 512–522 (2019). <a href="https://doi.org/10.1107/S2052520619007534">DOI: 10.1107/S2052520619007534</a></li> </ul> </li> <li>JANA2006: crystal structure model refinement program <ul> <li>Download program from <a href="http://jana.fzu.cz/">http://jana.fzu.cz/</a> and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Results here were obtained with JANA2006. We recommend using JANA2020.</li> <li>Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. Z. Kristallogr. 229, 345–352 (2014). <a href="https://doi.org/10.1515/zkri-2014-1737">DOI: 10.1515/zkri-2014-1737</a></li> </ul> </li> <li>DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives <ul> <li>Program automatically included in JANA2006/JANA2020</li> <li>Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Cryst. A71, 235–244 (2015). <a href="https://doi.org/10.1107/S2053273315001266">DOI: 10.1107/S2053273315001266</a></li> </ul> </li> </ul> 3D ED data sets: STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a>. <ul> <li>α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)</li> <li>abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)</li> <li>STW_HPM-1, continuous-rotation (1 data set, room temperature)</li> <li>STW_HPM-1, continuous-rotation (1 data set, T = 100 K, cryotransfer)</li> </ul> JANA refinement and CIF files: CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details. JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included. <ul> <li>α-quartz</li> <li>albite</li> <li>mordenite</li> <li>natrolite</li> <li>STW_HPM-1</li> <li>cobalt aluminophosphate (CAP)</li> <li>CAU-36</li> <li>α-glycine</li> <li>carbamazepine</li> <li>(+)-limaspermidine</li> <li>abiraterone acetate</li> <li>MBBF4</li> </ul> For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files. Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.

opencc-by-4.0Aug 2022View details →

Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster: scripts and files

Pipeline and analysis scripts as well as final data files

Evolutionary effects of nitrogen are not easily predicted from ecological responses

Anthropogenic nitrogen (N) addition might alter the evolutionary trajectories of plant populations, in part because it alters the abiotic and biotic environment by increasing aboveground primary productivity, light asymmetry, and herbivory intensity, and reducing plant species diversity. Such evolutionary impacts could be caused by N altering patterns of natural selection (i.e., trait-fitness relationships) and the opportunity for selection (i.e., variance in relative fitness). Because at the community level N addition favors species with light acquisition strategies (e.g., tall species), we predict that N would also increase selection favoring those same traits. We also hypothesize that N could alter the opportunity for selection via its effects on mean fitness and/or competitive asymmetries.To investigate these evolutionary consequences of N, we quantified the strength of selection and the opportunity for selection in replicated populations of the annual grass Setaria faberi Herrm. (giant foxtail) growing in a long-term N addition experiment. We also correlated our measures of selection and opportunity for selection with light asymmetry, diversity, and herbivory intensity to identify the proximate causes of any N effects on evolutionary processes. N addition increased aboveground productivity, light asymmetry, and reduced species diversity. Contrary to expectations, N addition did not strengthen selection for trait values associated with higher light acquisition such as greater height and specific leaf area (SLA); rather, it strengthened selection favoring lower SLA. Increased light asymmetry was associated with stronger selection for lower SLA and lower species diversity was associated with stronger selection for greater height and lower SLA, suggesting a role for these factors in driving N-mediated selection. The opportunity for selection was not influenced by N addition (despite increased mean fitness) but was negatively associated with species diversity. Our results indicate that anthropogenic N enrichment can affect evolutionary processes, but that evolutionary changes in plant traits within populations are unlikely to parallel the shifts in plant traits observed at the community level.

opencc-by-4.0Feb 2022View details →

Ungulates mitigate the effects of drought and shrub encroachment on the fire hazard of Mediterranean oak woodlands

Dataset included:  Shrub density; Shrub biomass; Fuel load of Cistus ladanifer; Fuel load herbs; Fuel load litter

Data from: Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs

Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, i.e. resistance, resilience and elasticity, using a tritrophic ---and thus more realistic---plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift towards a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and potentially elasticity as functional diversity declines.

Figure S1. Mediation analysis on the effect of insulin resistance on intraocular pressure. Figure S2. Forest plot showing the OR (95% CI) for EIOP of ALD versus NAFLD and the OR (95% CI) for EIOP of drinkers versus non-drinkers. Abbreviations: OR, odds ratio; CI, confidence interval; ALD, alcoholic liver disease; NAFLD, non-alcoholic fatty liver disease.

Figure S1. Mediation analysis on the effect of insulin resistance on intraocular pressure. Figure S2. Forest plot showing the OR (95% CI) for EIOP of ALD versus NAFLD and the OR (95% CI) for EIOP of drinkers versus non-drinkers. Abbreviations: OR, odds ratio; CI, confidence interval; ALD, alcoholic liver disease; NAFLD, non-alcoholic fatty liver disease.

opencc-by-4.0May 2022View details →

Effect of iron content on thermal conductivity of ferropericlase: implications for planetary mantle dynamics

Dataset for the article "Effect of iron content on thermal conductivity of ferropericlase: implications for planetary mantle dynamics". by Youyue Zhang, Takashi Yoshino, Masahiro Osako, submitted to Journal of Geophysical Research: Solid Earth.

Data from: Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird

Parental age can have considerable effects on offspring phenotypes and health. However, intergenerational effects may also have longer-term effects on offspring fitness. Few studies have investigated parental age effects on offspring fitness in natural populations while also testing for sex- and environment-specific effects. Further, longitudinal parental age effects may be masked by population-level processes such as the selective disappearance of poor-quality individuals. Here, we used multi-generational data collected on individually marked Seychelles warblers (Acrocephalus sechellensis) to investigate the impact of maternal and paternal age on offspring lifespan and lifetime reproductive success. We found negative effects of maternal age on female offspring lifespan and lifetime reproductive success, which were driven by within-mother effects. There was no difference in annual reproductive output of females born to older versus younger mothers, suggesting that the differences in offspring lifetime reproductive success were driven by effects on offspring lifespan. In contrast, there was no association between paternal age and female offspring lifespan or either maternal or paternal age and male offspring lifespan. Lifetime reproductive success, but not annual reproductive success, of male offspring increased with maternal age, but this was driven by between-mother effects. No paternal age effects were found on female offspring's lifetime reproductive success but there was a positive between-father effect on male offspring's lifetime reproductive success. We did not find strong evidence for environment-dependent parental age effects. Our study provides evidence for parental age effects on the lifetime fitness of offspring and shows that such effects can be sex-dependent. These results add to the growing literature indicating the importance of intergenerational effects on long-term offspring performance and highlight that these effects can be an important driver of variation in longevity and fitness in the wild.

The Missing Link Between Black Holes in High-Mass X-ray Binaries and Gravitational-Wave Sources: Observational Selection Effects

Data tables containing the calculated binary parameters used to acquire all results in <a href="https://arxiv.org/abs/2210.01825v1">arXiv:2210.01825v1</a>. The file "xrb_params_illustris_z0.05_sample.csv" contains data for the z<0.05 sampled population and the file xrb_params_illustris_z20_sample.csv contains data for the z<20 sampled population.

Development and evaluation of E3SM-MOSAIC: Spatial distributions and radiative effects of nitrate aerosol

FC20TR-MOZ_NUG_PD_V2beta4_ANN_200501_201412_climo.nc  10-yr mean for MZT_PD FC20TR-MOZ_MOSAIC_AIKDST_NUG_PD_V2beta4_ANN_200501_201412_climo.nc 10-yr mean for MTC_SLOW_PD FC20TR-MOZ_MOSAIC_AIKDST_MTC_NUG_PD_V2beta4_ANN_200501_201412_climo.nc 10-yr mean for MTC_WGT_PD FC20TR-MOZ_MOSAIC_AIKDST_MTC-SPLC_NUG_PD_V2beta4_ANN_200501_201412_climo.nc 10-yr mean for MTC_SPLC_PD   NO3_TM_2005-2014.nc 10-yr mean nitrate burden NO3_AQCH_GAEX_2005-2014.nc 10-yr mean for nitrate chemistry production NO3_DRF_2005-2014.nc 10-yr mean nitrate direct forcing between PD and PI NO3_INDRF_2005-2014.nc 10-yr mean nitrate indirect forcing between PD and PI   NH4_TM_2005-2014.nc 10-yr mean for ammonium burden NH4_DRF_2005-2014.nc 10-yr mean ammonium direct forcing between PD and PI   SO4_TM_2005-2014.nc 10-yr mean for sulfate burden SO4_DRF_2005-2014.nc 10-yr mean sulfate direct forcing between PD and PI   CCN3_1850.nc Cloud condensation nuclei number concentrations at 0.1% super saturation at PI CCN3_2005-2014.nc CCN3 at PD CCN3_NONO3_1850.nc CCN3 at PI without nitrate formation CCN3_NONO3_2005-2014.nc CCN3 at PD without nitrate formation   CDNC_*.nc cloud droplet number concentrations CLDFRC_*.nc cloud fraction CWP_*.nc cloud liquid water path

Raw data accompanying the manuscript "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse"

These are the raw datasets used to generate the figures for the manuscript entitled "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse". The data files are 3D image stacks of a custom-built wide field deconvolution fluorescence microscope (.tif) and super-resolution structured illumination microscopy data (.dv) of Jurkat T cells transferring HIV-1 virus particles to previously uninfected primary T cells.

Measuring protected-area effectiveness using vertebrate distributions from leech iDNA

Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas.

Species-specific effects and the ecological role of Programmed cell Death in the microalgae Ankistrodesmus (Sphaeropleales, Selenastraceae)

Reports of programmed cell death (PCD) in phytoplankton raise questions about the ecological evolutionary role of cell death in these organisms. We induced PCD by nitrogen deprivation and unregulated cell death (non-PCD) in one strain of the green microalga Ankistrodesmus densus and investigated the effects of the cell death supernatants on phylogenetically related co-occurring organisms using growth rates and maximum biomass as proxies of fitness. PCD-released materials from A. densus CCMA-UFSCar-3 significantly increased growth rates of two conspecific strains compared to healthy culture (HC) supernatants and improved the maximum biomass of all A. densus strains compared to related species. Although growth rates of non-A. densus with PCD supernatants were not statistically different from HC treatment, biomass gain was significantly reduced. Thus, the organic substances released by PCD, possibly nitrogenous compounds, could promote conspecific growth. These results support the argument that PCD may differentiate species or subtypes and increases inclusive fitness in this model unicellular chlorophyte. Further research, however, is needed to identify the responsible molecules and how they interact with cells to provide the PCD benefits.

A general approach for quantifying microbial effects on plant competition

Purpose A growing perspective in plant ecology highlights the ways that microbial interactions can promote or hinder plant coexistence. Towards this aim, recently-proposed approaches provide ways to empirically quantify how microbes affect the outcome of competition between plants. One such approach experimentally measures competition coefficients by comparing biomass performance of plants growing individually or with competitors, then quantifies microbial effects by comparing with a sterilization treatment. Nonetheless, the complexity of plant-microbe interactions presents general challenges when linking observations of microbial effects to underlying models. Results We show how the implementation of a density gradient design can help quantify potential nonlinearities and facilitative interactions in plant-soil microbe interactions, which are properties once thought to hinder the quantification of the microbial impact of plant competitive outcome. We provide guidelines for setting up the experiment and accurately interpreting the results. Conclusion We argue that future studies should aim to parameterize suitable demographic models to characterize the contribution of soil microbes to plant coexistence.

Data for: Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought, and their interactions on plants, aphids, and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by a previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that historical climate warming-induced plant latitudinal range expansion and extreme drought contingencies can be contained as soil 'memories' that influence plant performance and aboveground community interactions in the next growing season.

Dataset supplementing "Low-high-low or high-low-high? Pattern effects on sequential auditory scene analysis."

These data supplement the paper Thomassen, S., Hartung, K., Einhäuser, W., & Bendixen, A. (2022). Low-high-low or high-low-high? Pattern effects on sequential auditory scene analysis. Journal of the Acoustical Society of America, 152(5), 2758-2768.<a href="https://doi.org/10.1121/10.0015054"> https://doi.org/10.1121/10.0015054</a> figure2.m, figure3.m and figure4.m reproduce the respective figures of the paper, using the data of dataExp1.mat, dataExp2.mat and dataExp3.mat, respectively (Figure 1 is not a Results figure). Please note that the legend command may throw a warning or an error in some matlab versions, when interpreting the underscore (_) as command character. These warnings can be ignored or the legend command commented out. The mat-files contain the following data: dataExp1.mat: The 18 x 4 x 3 (subjects x Delta f x pattern) cell arrays   time_buttonPress_integrated           time_buttonPress_segregated           time_buttonRelease_integrated         time_buttonRelease_segregated       contain the time points (in ms relative to block onset) at which the button for integrated / segregated percept is pressed / released. These matrices are already sorted by condition (in Delta f and pattern), and the buttons organized by reported percept.   The 18 x 4 x 3 (subjects x Delta f x pattern) matrix   time_blockEnd contains the timepoint (in ms after onset) of the end of each block. The 18 x 4 x 3 (subjects x Delta f x pattern) matrix     originalBlockNum                 contains the serial order of the block of this condition during the experiment. The 1 x 4 vector    Df contains the Delta f levels used (in order as used in the matrices' and cells' second dimension). The 1 x 3 cell     patternLabel                         contains the patterns used (in order as used in the matrices' and cells' third dimension). see figure2.m for an example   dataExp2.mat: The 18 x 2 x 2 x 2 x 20 cell   buttonTimes contains the times (in ms relative to trial onset) at which the button status changed. The 18 x 2 x 2 x 2 x 20 cell   buttonStates contains the new state of the button at the corresponding time in buttonTimes. The dimensions of both cell arrays are (in order):  subject (18 levels)  convergence (2 levels: divergent, convergent)  pattern (2 levels: HLH_, LHL_)  duration (2 levels: short/fast [10s], long/slow [15s])  instance (20 repetitions). see figure3.m for an example   dataExp3.mat The 20 x 2 x 4 x 30 (subjects x pattern x Delta f x repetition) cell arrays  time_buttonPress_integrated          time_buttonPress_segregated    contain the time points (in s relative to block onset) at which the button for integrated / segregated percept is pressed. The 1 x 2 cell   patternLabel                         contains the patterns used (in order as used in the cells' second dimension). The 1 x 4 vector   Df contains the Delta f levels used (in order as used in the cells' third dimension). Note that the order of dimensions and of patterns deviates between the three experiments, but is consistent within each experiment.

Air temperature and humidity effects on the performance of conservation detection dogs

This is the dataset which underlies the submitted manuscript entitled " Air temperature and humidity effects on the performance of conservation detection dogs". The uploaded data contain an xlsx file,which includes the data, as well as a txt readme file, which explains the header information in the data file.