Find research datasets worth reusing

FIGURE 8 in Differentiating convergent pathologies in turtle shells using computed tomographic scanning of modern and fossil bone

FIGURE 8. Characteristic examples of shell disease and bite marks in modern and fossil turtle shells. Modern shell disease on the plastron of Trachemys scripta, specimen UTK 2317 (A). Modern bite marks (bisected punctures) on the plastron of Trachemys scripta, specimen SAAF unnumbered (B). Fossil shell disease on a fragment of turtle shell, specimen DMNH 2013-07-0563 (C). Fossil bite marks (four scores and one pit) on a fragment of turtle shell, specimen DMNH 2013-07-1319 (D). Scale bars equal 10 mm.

FIGURE 3 in Differentiating convergent pathologies in turtle shells using computed tomographic scanning of modern and fossil bone

FIGURE 3. Fossil turtle shell fragment (DMNH 2013-07-0567) with putative bite marks. Photograph (A) and orthographic model based on µCT data (B) shown in external view. Frames on the photograph and model highlight specific areas with bite marks as both direct µCT data (C, E) and heatmapped slices illustrating bone density changes (D, F). In the heatmapped cross sections, colors range from purple (lowest density), to orange (medium density), to white (highest density). Specific bite marks are indicated with purple arrows. Scale bars in A and B equal 2 cm. Scale bars in C and E equal 5 mm.

FIGURE 5 in Differentiating convergent pathologies in turtle shells using computed tomographic scanning of modern and fossil bone

FIGURE 5. Modern Trachemys scripta plastron and partial carapace elements (UTK 1844) with shell disease. Photograph (A) and orthographic model based on µCT data (B) shown in ventral view. Frames on the photograph and model highlight specific areas of shell disease, shown on the right as both direct µCT data (C, E, G) and heatmapped slices illustrating bone density changes (D, F, H). In the heatmapped cross sections, colors range from purple (lowest density), to orange (medium density), to white (highest density). Patches of shell disease are indicated with purple arrows. Scale bars in A and B equal 5 cm. Scale bars in C, E, and G equal 5 mm.

opencc-by-4.0Feb 2024View details →

Alberta Differential Magnetometer Measurement (DMM) Data from 2021

This data product consists of a magnetometer dataset from the augmented differential magnetometer measurement (DMM) study conducted in Alberta, Canada in 2021 and GIC data from a nearby transformer substation. This data was analyzed and presented in the paper "Using a Differential Magneoter Measurement to Infer Geomagnetically Induced Currents: An Augmented Approach." Specifically, these datasets were used to create Figures 3,  4, 5, 6, 7, 9 and 10 in this paper. The data files available here are from two magnetometers (USB4 and USB5) on a magnetically quiet day, September 26th, 2021, and a magnetically active day, October, 12th, 2021. USB4 data is from the underline sensor and USB5 is from the remote sensor. Each DMM data file includes the time in UT and magnetic field measurements in the x, y, and z components, where Bx is magnetic north and By is magnetic east. The GIC data file includes the local time (Mountain Daylight Time = GMT-6) and the transformer neutral-to-ground current at the Ellerslie substation (89S) in both transformers (T1 and T2) during the magnetic storm on October 12th, 2021. The magnetic data has a resolution of 1 Hz. The GIC data has a resolution of 0.5 Hz.

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R code for differential gene expression and enrichment analyses

The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperatures. Temperature decrease to 18°C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28°C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection on males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has the potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.

opencc-zeroMay 2024View details →

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Differential impacts of land use change on multiple components of common Milkweed (Asclepias syriaca) pollination success

Land-use change is one the greatest threats to biodiversity and is projected to increase in magnitude in the coming years, stressing the importance of better understanding how land-use change may affect vital ecosystem services, such as pollination. Past studies on the impact of land-use change have largely focused on only one aspect of the pollination process (e.g. pollinator composition, pollinator visitation, pollen transfer), potentially misrepresenting the full complexity of land-use effects on pollination services. Evaluating the impacts across multiple components of the pollination process can also help pinpoint the underlying mechanisms driving land-use change effects. This study evaluates how land-use change affects multiple aspects of the pollination process in common milkweed populations, including pollinator community composition, pollinator visitation rate, pollen removal, and pollen deposition. Overall, land-use change altered floral visitor composition, with small bees having a larger presence in developed areas. Insect visitation rate and pollen removal were also higher in more developed areas, perhaps suggesting a positive impact of land-use change. However, pollen deposition did not differ between developed and undeveloped sites. Our findings highlight the complexity evaluating land-use change effects on pollination, as these likely depend on the specific aspect of pollination evaluated and on the of the intensity of disturbance. Our study stresses the importance of evaluating multiple components of the pollination process in order to fully understand overall effects and mechanisms underlying land-use change effects on this vital ecosystem service.

opencc-zeroMay 2024View details →

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Data from: Species richness and evenness of European bird communities show differentiated responses to measures of productivity

Understanding patterns of species diversity is crucial for ecological research and conservation, and this understanding may be improved by studying patterns in the two components of species diversity, species richness and evenness of abundance of species. Variation in species richness and evenness has previously been linked to variation in total abundance of communities as well as productivity gradients. Exploring both components of species diversity is essential because these components could be unrelated or driven by different mechanisms. The aim of this study was to investigate the relationship between species richness and evenness in European bird communities along an extensive latitudinal gradient. We examined their relationships with latitude and Net Primary Productivity, which determines energy and matter availability for heterotrophs, as well as their responses to territory densities (i.e., the number of territories per area) and community biomass (i.e., the bird biomass per area). We applied a multivariate Poisson log-normal distribution to unique long-term, high-quality time-series data, allowing us to estimate species richness of the community as well as the variance of this distribution, which acts as an inverse measure of evenness. Evenness in the distribution of abundance of species in the community was independent of species richness. Species richness increased with increasing community biomass, as well as with increasing density. Since both measures of abundance were explained by NPP, species richness was partially explained by energy-diversity theory (i.e., the more energy, the more species sustained by the ecosystem). However, species richness did not increase linearly with NPP but rather showed a unimodal relationship. Evenness was not explained either by productivity nor by any of the aspects of community abundance. This study highlights the importance of considering both richness and evenness to gain a better understanding of variation in species diversity. We encourage the study of both components of species diversity in future studies, as well as use of simulation studies to verify observed patterns between richness and evenness.

opencc-zeroMay 2024View details →

opencc-by-4.0May 2024View details →

Electrophysiological data of the paper 'Serotonergic and dopaminergic neurons in the dorsal raphe are differentially altered in a mouse model for parkinsonism'

This excel data set contains the electrophysiological data presented in the paper including figure 1I, 1J, figure 3, figure 5, suppl. figure 2A, suppl. figure 3, suppl. figure 6E, 6G, 6L & 6N.   More information about how the data was extracted can be found in the materials and methods section of the paper.

Fig. 1 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 1 Schematic diagram illustrating the origin (a) and beginning of differentiation (b) of the oncospheral tegument and hook region membrane in the preoncospheral stage of embryonic development of Echinococcus multilocularis. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. Two red arrows show direction of progressive sinking or migration of the binucleate subtegumental perikaryon which sunk deep into the central region of differentiating oncosphere. HFC hook-forming cell or oncoblast, HP hook primordium, HRC hook region cavity, IE inner envelope, m mitochondria, N1, N2 two nuclei of the binucleate complex primordium, N nucleus of hook-forming cell, PBC binucleate complex primordium, V vesicles in the outer cytoplasm, undergoing progressive fusion

Fig. 6 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 6 TEM micrographs of mature eggs of Echinococcus multilocularis. a Part of the oncosphere showing the high concentration of beta-glycogen particles (β-gl) in the musculature of oncospheral hooks (HM) as indicated by the cytochemical test of Thiéry. b Low-power electron micrograph illustrating the general topography of mature intrauterine egg. Note: (1) a bilateral symmetry of the oncosphere (white interrupted line) and (2) position of hook region membrane and oncospheral tegument at one pole of the hexacanth. The hook region is marked by a frame composed of interrupted black lines. EmB embryophoric blocks, GC germinative cells, GL granular layer, HRM hook region membrane, IE inner envelope, LH lateral hooks, MH median hooks, OE outer envelope, OM oncospheral membrane, PG penetration glands, SC somatic cells

Fig. 5 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 5 High-power TEM micrographs showing ultrastructural details of the oncospheral tegument and hook region membrane. a Note two oblique sections of blades of the oncospheral hooks (HBl), surrounded by numerous long microvilli (Mv) which protrude into large cavity situated under the hook region membrane (HRM) and oncospheral membrane (OM). b Oblique section through the hook region membrane showing hook blade exit and oncospheral tegument with numerous long microvilli at its surface. DR desmosome rings, HM hook musculature, IE inner envelope

Fig. 4 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 4 Consecutive stages of a tegumental perikaryon migration. a Part of an embryo in the early preoncospheral stage of development showing much infolded oncospheral membrane and the binucleate perikaryon (BSP) of the oncospheral tegument in the early stage of its migration, sunken already below the peripheral layers of oncospheral musculature. b Part of the late stage of preoncospheral differentiation showing the binucleate perikaryon of oncospheral tegument sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. H oncospheral hooks, HCF hook forming cell, HRM hook region membrane, IE inner envelope, N1, N2, nucleus, OE outer envelope, OM oncospheral membrane, SC somatic cells

Fig. 3 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 3 Comparison of an early and advanced preoncospheral stage of embryonic development in Echinococcus multilocularis. a Ultrastructure of an embryo in the early preoncospheral stage of embryonic development. Note the binucleate complex primordium (PBC), which appears as a syncytial cap or "calotte" situated beneath the inner envelope (IE) at one pole of the developing embryo; two thick arrows mark the direction of progressive migration of both nuclei (N1, N2) surrounded by a thin layer of common cytoplasm and become transformed into the binucleate subtegumental perikaryon. b Part of the embryo in the advanced stage of preoncosphere showing the binucleate subtegumental perikaryon (BSP) of the tegumental syncytium sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. Bl blastomere, C vitelline capsule, EmB embryophoric blocks, GL granular layer, H oncospheral hooks, HM hook muscles, HRM hook region membrane, KI keratin-like protein islands, MeN mesomere nucleus, OE outer envelope, OM oncospheral membrane, PG penetration gland, UW uterine wall

Fig. 2 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 2 Schematic diagram illustrating the general topography of the oncospheral tegument and hook region membrane in relation to the oncospheral hooks, penetration gland arms and glandular exits in the mature intrauterine eggs. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. BSP binucleate subtegumental perikaryon, HRM hook region membrane, IE inner envelope LH lateral hooks, MH median hooks, Mv microvilli, N1, N2 nucleus, OT oncospheral tegument, PGA penetration glands arms

opencc-by-4.0Jun 2024View details →

Figure 4 in Investigation the effects of vitreous humor on proliferation and dedifferentiation of differentiated NTERA2 cells

Figure 4. Western blot analysis show that the NT2 cells are known as perfectly positive cells for OCT4 protein expression.

opencc-by-4.0Jun 2024View details →

Figure 2 in Investigation the effects of vitreous humor on proliferation and dedifferentiation of differentiated NTERA2 cells

Figure 2. Cell cycle analysis of NT2-RA cells after treatment with different amounts of VH at (A) 3 days and (B) 6 days post-treatment. After treatment with RA the number of cells at S phase decreased. These numbers were recovered after three and six days treatment with different amounts of VH.

Fig 1 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions

Fig 1: Relative gene expression in tambaqui juveniles farmed in two Brazilian regions: Northern (Balbina; BA) and Southeast (Brumado; BRU). Different letters represent statistical differences between populations. The graphs show expression of A) hif-1α (p = 0.137), B) hsp-70 (p = 0.465), C) mstn (p = 0.907), D) ube3a (p = 0.205), E) ras (p = 0.041), F) cry-1 (p = 0.001), G) per-1 (p = 0.001), H) ogt (p = 0.001) and I) acly (p = 0.025).

Fig 3 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions

Fig 3: IBR analyses of relative gene expression in Balbina (BA) and Brumado (BRU) populations. The IBR values are 42.7 (Balbina) and 6.79 (Brumado).

Fig 2 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions

Fig 2: Heatmap of relative expression in Balbina (BA) and Brumado (BRU) populations. The colour scale ranges from blue (low transcript levels) to red (high transcript levels).