Find research datasets worth reusing

Fig. 5 in The generic affinities of the Indo-West Pacific species assigned to Rochinia A. Milne-Edwards, 1875 (Crustacea: Brachyura: Majoidea: Epialtidae)

Fig. 5. Laubierinia globulifera (Wood-Mason, in Wood-Mason & Alcock, 1891) new combination. A–C, lectotype female (11.0 × 6.7 mm) (NHM 96.5.14.2), Andaman; D–F, male (9.2 × 6.0 mm) (AM P.34652), Indonesia. A, D, overall dorsal view; B, E, overall ventral view; C, F, lateral view of carapace.

Fig. 4. Left G1. A–C in The generic affinities of the Indo-West Pacific species assigned to Rochinia A. Milne-Edwards, 1875 (Crustacea: Brachyura: Majoidea: Epialtidae)

Fig. 4. Left G1. A–C, Samadinia longispina Ng & Richer de Forges, 2013, holotype male (25.3 × 17.9 mm) (MNHN-IU-2011-4190) (after Ng & Richer de Forges, 2007: fig. 4A–D); D–G, S. moluccensis (Griffin & Tranter, 1986) new combination, paratype male (11.5 × 6.9 mm) (RMNH De:103.737), Java Sea; H, I, S. granulosa (Ng & Richer de Forges, 2013) new combination, paratype male (6.5 × 4.6 mm) (MNHN-IU-2011-2944b), Papua New Guinea; J–M, S. debilis (Rathbun, 1932) new combination, male (27.0 × 19.2 mm) (NSMT-Cr 12139), Japan. A, D, H, J, ventral view; B, E, K, ventral view of distal portion; C, G, M, dorsal view of distal portion; F, I, L, dorsal view. Scale bar = 1 mm.

Fig. 3 in The generic affinities of the Indo-West Pacific species assigned to Rochinia A. Milne-Edwards, 1875 (Crustacea: Brachyura: Majoidea: Epialtidae)

Fig. 3. Lateral view of carapace. A, Samadinia longispina Ng & Richer de Forges, 2013, holotype male (25.3 × 17.9 mm) (MNHN- IU-2011-4190), Polynesia; B, S. suluensis (Griffin & Tranter, 1986) new combination, holotype male (7.8 × 5.0 mm) (RMNH De:103.921), Bougainville Strait; C, S. granulosa (Ng & Richer de Forges, 2013) new combination, holotype female (9.2 × 6.9 mm) (MNHN-IU-2011- 2944a), Papua New Guinea; D, S. debilis (Rathbun, 1932) new combination, holotype female (10.8 × 7.0 mm) (USNM 49572), Japan.

Fig. 8. A–C in The generic affinities of the Indo-West Pacific species assigned to Rochinia A. Milne-Edwards, 1875 (Crustacea: Brachyura: Majoidea: Epialtidae)

Fig. 8. A–C, Siderochinia kagoshimensis (Rathbun, 1932) new combination, holotype male (11.2 × 6.8 mm) (USNM 48253), Japan; D–F, S. aglaos, new species, holotype male (10.7 × 6.9 mm) (ZRC 2016.0549), South China Sea. A, D, side view of cardiac spine; B, E, dorsal view of intestinal spine along lateral carapace margin; C, F, dorsal view of P5.

opencc-by-4.0Dec 2017View details →

Figs 30‒36 in Revision of type and non-type material assigned to the genus Orthocladius by Goetghebuer (1940-1950), deposited in the Royal Belgian Institute of Natural Sciences (Diptera: Chironomidae)

Figs 30‒36. Orthocladius (Orthocladius) mitisi Goetghebuer, 1938: 30 ‒ eyes, 31 ‒ thorax, 32 ‒ palps, 33 ‒ anal point, 34 ‒ superior volsella, 35 ‒ inferior volsella, 36 ‒ gonostylus.

opencc-by-4.0Dec 2017View details →

Figs 24‒29 in Revision of type and non-type material assigned to the genus Orthocladius by Goetghebuer (1940-1950), deposited in the Royal Belgian Institute of Natural Sciences (Diptera: Chironomidae)

Figs 24‒29. Orthocladius (Orthocladius) glabripennis (Goetghebuer, 1921). 24 ‒ antenna, 25 ‒ wing, 26 ‒ palps, 27 ‒ hypopygium, 28 ‒ inferior volsella, 29 ‒ superior volsella.

opencc-by-4.0Nov 2020View details →

Text-fig. 2. Scatter diagram of the length/width ratio of the upper fourth premolar (P4) of Chalicomys jaegeri from Grytsiv as compared to those of C. jaegeri only (a) and additionally of Euroxenomys minutus rhenanus (E. min rhen), Euroxenomys minutus (Eurex min) (b) from other localities. Abbreviations for localities: Cana – Çanakkale (probably MN 8/9 after Sen 2016; data from Ünay 1974), DornD – Dorn-Dürkheim 1 (MN 11; data from Franzen and Storch (1975) for both C. jaegeri and E. minutus rhenanus), Epp – Eppelsheim (MN 9; Stefen 2009), Kücük – Küçükçekmece (probably MN 8/9; Sen 2016), and Sansan (MN 6 after Sen 1997; data from Hugueney and Duranthon 2012). A single specimen from Grytsiv (G) – NMNHU-P 22/218 is tentatively assigned to Euroxenomys minutus based on its size. in Beavers (Castoridae, Rodentia) From The Late Miocene (Mn 9) Locality Grytsiv In Ukraine

Text-fig. 2. Scatter diagram of the length/width ratio of the upper fourth premolar (P4) of Chalicomys jaegeri from Grytsiv as compared to those of C. jaegeri only (a) and additionally of Euroxenomys minutus rhenanus (E. min rhen), Euroxenomys minutus (Eurex min) (b) from other localities. Abbreviations for localities: Cana – Çanakkale (probably MN 8/9 after Sen 2016; data from Ünay 1974), DornD – Dorn-Dürkheim 1 (MN 11; data from Franzen and Storch (1975) for both C. jaegeri and E. minutus rhenanus), Epp – Eppelsheim (MN 9; Stefen 2009), Kücük – Küçükçekmece (probably MN 8/9; Sen 2016), and Sansan (MN 6 after Sen 1997; data from Hugueney and Duranthon 2012). A single specimen from Grytsiv (G) – NMNHU-P 22/218 is tentatively assigned to Euroxenomys minutus based on its size.

opencc-by-4.0Nov 2019View details →

Text-fig. 11. Scanning electron microscope (SEM) images of seeds assigned to the BEG group (a–d) and associated pollen grains (e–i); Torres Vedras locality, Portugal. a) Seed of Tomcatia taylorii showing the four horns formed by extensions of the envelope and the central projection of the envelope that surrounds to the micropylar tube; b, c) Seeds of Quadrispermum parvum in lateral (b) and apical (c) views showing the transverse ribs and the central projection of the envelope that surrounds the micropylar tube; d–f) Seeds of Ephedrispermum lusitanicum showing the four-angled seed envelope (d), the micropylar tube surrounded by the tissues of the integument (e), and ephedroid pollen grains on the seed surface (f); g) Apex of seed of Quadrispermum parvum showing simple in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community

Text-fig. 11. Scanning electron microscope (SEM) images of seeds assigned to the BEG group (a–d) and associated pollen grains (e–i); Torres Vedras locality, Portugal. a) Seed of Tomcatia taylorii showing the four horns formed by extensions of the envelope and the central projection of the envelope that surrounds to the micropylar tube; b, c) Seeds of Quadrispermum parvum in lateral (b) and apical (c) views showing the transverse ribs and the central projection of the envelope that surrounds the micropylar tube; d–f) Seeds of Ephedrispermum lusitanicum showing the four-angled seed envelope (d), the micropylar tube surrounded by the tissues of the integument (e), and ephedroid pollen grains on the seed surface (f); g) Apex of seed of Quadrispermum parvum showing simple

Figure 5 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 5. Frontal view of AM M.39811, male, paratype of N. holtorum sp. nov. showing enlarged dorsal snout mound posterior to the noseleaf. Scale 5 mm.

Figure 4 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 4. Relatively greater inflation of the braincase of left, the holotype of N. holtorum sp. nov. (WAM M.64188), compared with N. gouldi (AM M.51228). Both are adult males with equal GSL.

Figure 2 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 2. Specimen scores on the first two axes of a PCA based on a correlation matrix of nine cranial characters of adult male N. holtorum sp. nov. (squares, n = 6) and N. gouldi sensu stricto (circles, n = 79): (a) PCA scores grouped by species, and (b) same plot with N. gouldi coded by four geographic localities: montane and subcoastal NSW and far southeastern Qld (closed circles); southern and eastern Victorian montane regions (closed diamonds); inland and northern Qld (open circles) and inland NSW and northern Victoria (triangles).

Figure 3 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 3. Bivariate plots (mm) showing overlap in measurements of adult N. holtorum sp. nov. (squares, polygons) and adult N. gouldi sensu stricto (circles). Solid symbols are females, open symbols male: (a), condylo-basal skull length (CON) vs. least inter-temporal breadth (INT); (b) CON vs. mastoid breadth (MASB); (c), CON vs. braincase height (BRH); (d) forearm length (FA) vs. greatest skull length (GSL), and (e) FA vs. length from canine to upper rear molar (CM3).

Figure 6 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 6. Distributional records of N. holtorum sp. nov. based on AM and WAM voucher specimens examined (n = 26 localities) and bioregional boundaries of the Interim Biological Regionalization Scheme (IBRS version 7; DSEWPAC, 2012). Regions are: AVW, Avon Wheatbelt; JAF, Jarrah Forests; SWA, Swan Coastal Plain and WAR, Warren.

Figure 1 in A New Bat Species from Southwestern Western Australia, Previously Assigned to Gould's Long-eared Bat Nyctophilus gouldi Tomes, 1858

Figure 1. Highest maximum likelihood tree of relationships amongst Nyctophilus using: (a) 28 COI haplotypes, and (b) 21 CytB haplotypes. Bootstrap support (%) is shown at branch nodes. All M numbers refer to AM specimens except where indicated.

opencc-zeroNov 2022View details →

dryad40/100

Insights into natal origins of migratory Nearctic hover flies (Diptera: Syrphidae): New evidence from stable isotope (δ2H) assignment analyses

Hover flies (Diptera: Syrphidae) are an important group of insects that provide a multitude of key ecosystem services including pollination and biological control, yet many of their major life history traits are not understood. Some Palearctic hover fly species are known to migrate in response to changing seasonal conditions, yet this behavior is almost entirely unrecognized in Nearctic species. At least one species, Eupeodes americanus (Wiedemann 1830), is partially migratory during autumn while Allograpta obliqua may be non-migratory, but it is unknown where these insects originate and how far they may travel. We examined natal origins of two Nearctic hover fly species, Allograpta obliqua and Eupeodes americanus, using stable hydrogen isotope (δ2H) measurements of metabolically inactive tissues (wings and legs) to derive a hover fly δ2H isoscape. While Allograpta obliqua was mostly of local origin, several Eupeodes americanus were sourced from northern latitudes in the Midwestern United States and Canada, representing travel distances of up to 3,000 km likely using seasonally favorable air currents. This phenomenon is expected to have major ecological and economic ramifications, especially in the realm of plant pollination ecology and biological control.

opencc-by-4.0Nov 2022View details →

Calculation of overlaps between assignments of Research Areas and SDGs

This collection of MS Excel sheets contains tables (matrices) with Jaccard similarity values between research areas (RAs) and sustainable development goals (SDGs) as declared by the United Nations. The underlying taxonomy of RAs is based on one used in Web of Science (WoS). For each pair of RA1 x RA2 or SDG1 x SDG2 or SDG1 x RA1, the corresponding matrix entry is calculated as the quotient of the number of projects that have both items assigend (numerator) and the number of projects that have at least one of the items assigend (denominator). We interpret this Jaccard index as a measure of similarity or "overlap". The assignment of RAs to projects is based on the computational method of ESA ("Explicit Semantic Analysis"). For SDGs, also hand-coded assignments (SDG_Man) are available in addition to automatically calculated ESA-based values. In two versions, the RAs and SDGs included are limited to those that have at least been assigned to 5 projects overall (min5 version) or 10 projects overall (min10 version). The calculations are based on a sample of 208 projects extracted from the CS Track database.

opencc-by-4.0Jan 2022View details →

The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data

In our work, we implemented the ABC-model and could show that one assay for measuring the openness of enhancers is sufficient. Further, we propose a generalised calculation of the ABC-score, which describes enhancer activity in a gene-specific manner, and which includes all TSS, without requiring any additional data. We combined our implementation of the ABC-score with an approach to quantify TF binding affinity into STARE: a framework to derive TF affinities to genes. STARE was also designed for potential application on single-cell data. You can find the code in our <a href="https://github.com/schulzlab/stare">GitHub repository</a> and more details in our <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtad062">publication</a>. We provide the data for the validation of our ABC-implementation on two CRISPR-screens. We also provide the results of our analysis of single-cell data of the human heart with STARE. All data is in hg19. Content: <ul> <li>CRISPRi_screens: One file for each CRISPRi-screen with interactions that were used to plot precision-recall curves, containing columns for different ABC scoring versions.</li> <li>Enformer: Similar to the CRISPRi_screens, but containing columns for different calculations for Enformer's predicted expression change upon in silico mutagenesis of the enhancer region.</li> <li>K562_CandidateEnhancer: K562 enhancer with the 4th column for enhancer activity, one file for each activity representation that was measured.</li> <li>K562_ABC_Predictions: Regular ABC-scores and generalised ABC-scores for each activity measurement. The files contain all scored interactions for a 10MB window, without any cut-off. We also included the results of the implementation of the ABC-score of Fulco et al. (2019).</li> <li>STARE_Hocker_*: Whole STARE output for human heart single-cell data, one for regular ABC, generalised ABC, generalised ABC with average Hi-C matrix and one based on co-accessibility analysis. All approaches were run with a 5 MB window (except for GeneralisedABC500kb), the ABC-based runs with a score cut-off of 0.02. Each folder contains two subdirectories, one for the ABC-scoring and one for the Gene-TF affinity matrices. The 'ABC_output' also contains a GeneInfo file for each cell type, summarising different attributes per gene.</li> <li>INVOKE_Hocker_*: Folder with the input and output of INVOKE (see https://github.com/schulzlab/tepic), based on the STARE runs. CS genes stands for cell type-specific genes, defined as genes with a z-score across cell types of ≥ 2 and TPM ≥ 0.5. The INVOKE commands were as follows: <ul> <li>Rscript INVOKE.R --dataDir=<TF-Gene matrix> --outDir=<out_path> --response=Expression --regularization=E --performance=TRUE --outerCV=10 --seed=1234</li> </ul> </li> </ul> Importantly, the results are based on data from the following publications: <ul> <li>CRISPRi-screens: <ul> <li>Gasperini, Molly, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D. Zhang, Dana Jackson, et al. “A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.” Cell 176, no. 1–2 (January 2019): 377-390.e19. https://doi.org/10.1016/j.cell.2018.11.029.</li> <li> Schraivogel, Daniel, Andreas R. Gschwind, Jennifer H. Milbank, Daniel R. Leonce, Petra Jakob, Lukas Mathur, Jan O. Korbel, Christoph A. Merten, Lars Velten, and Lars M. Steinmetz. “Targeted Perturb-Seq Enables Genome-Scale Genetic Screens in Single Cells.” Nature Methods 17, no. 6 (June 2020): 629–35. https://doi.org/10.1038/s41592-020-0837-5. </li> <li> Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” Nature Genetics 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0. </li> </ul> </li> <li>Enformer model: Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R. Ledsam, Agnieszka Grabska-Barwinska, Kyle R. Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R. Kelley. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” Nature Methods 18, no. 10 (October 2021): 1196–1203. https://doi.org/10.1038/s41592-021-01252-x.</li> <li>K562 predictions and average Hi-C matrix: Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” Nature Genetics 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</li> <li>Hi-C matrix for K562 predictions: Rao, S. et al. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell, 159(7), 1665–1680</li> <li>STARE and INVOKE runs: Hocker, J. D. et al. (2021). Cardiac cell type–specific gene regulatory programs and disease risk association. Science Advances, 7(20), eabf1444</li> <li>H3K27ac HiChIP for STARE runs: Anene-Nzelu, C. G. et al. (2020). Assigning Distal Genomic Enhancers to Cardiac Disease–Causing Genes. Circulation, 142(9), 910–912</li> <li>INVOKE software: Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction Schmidt et al., Nucleic Acids Research 2016; doi: 10.1093/nar/gkw1061</li> </ul>

opencc-by-4.0Dec 2022View details →

Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h).

opencc-by-4.0Mar 2023View details →

Solid-state NMR assignment data of TasA filaments

Raw and processed solid-state NMR data of the main biofilm protein TasA from Bacillus subtilis. The CCPN 2.4.2 assignment project is contained which includes all data deposited in the BMRB under accession code 51785. Talos+ output is included as well. The results are presented in the publication Roske, Y., Lindemann, F., Diehl, A. et al. TapA acts as specific chaperone in TasA filament formation by strand complementation. Proc. Natl. Acad. Sci. USA 17, 120 (2023). https://doi.org/10.1073/pnas.2217070120 and my thesis "A Structural View on Mechanisms of Bacterial Communal Life and Toxicity" submitted to the Free University Berlin (<a href="http://dx.doi.org/10.17169/refubium-41725">http://dx.doi.org/10.17169/refubium-41725</a>). <h2>Notes</h2>