Find research datasets worth reusing

opencc-by-4.0Aug 2022View details →

Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision

Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g).

opencc-by-4.0Sep 2022View details →

Datasets for "Resolving the microscopic hydrodynamics at the moving contact line"

Datasets for the article: "Resolving the microscopic hydrodynamics at the moving contact line"  Amal K. Giri, Paolo Malgaretti, Dirk Peschka, and Marcello Sega Phys. Rev. Fluids 7, L102001 DOI: 10.1103/PhysRevFluids.7.L102001 Includes: <ol> <li>GROMACS input files</li> <li>Modifications to the GROMACS source code thermostat as described in the article</li> <li>Instructions on how to invoke the patched version of GROMACS with decoupled directions</li> <li>Matlab datafiles with FE solutions and scripts to analyse and compare them to MD velocity field (also included)</li> </ol>   See also:  https://github.com/Marcello-Sega/pytim https://github.com/dpeschka/stokes-free-boundary

Fig. 3 in Tannic acid-modified silver nanoparticles enhance the anti-ACanthamoeba activity of three multipurpose contact lens solutions without increasing their cytotoxicity

Fig. 3 Anti-Acanthamoeba activity of AgTANPs conjugated with ReNu MultiPlus contact lens solution after 6 h of incubation in relation to cytotoxicity

Fig. 5 a–d Acanthamoeba trophozoites after 6 h in Tannic acid-modified silver nanoparticles enhance the anti-ACanthamoeba activity of three multipurpose contact lens solutions without increasing their cytotoxicity

Fig. 5 a–d Acanthamoeba trophozoites after 6 h of incubation. a Control culture in PYG medium. b Incubation with AgTANPs. c Incubation with SCA. d Incubation with AgTANPs conjugated with SCA.The arrow shows a rounded form. All images (× 40) represent the population of treated amoebae and were taken under a live cell imaging microscope (EVOS FLoid Cell Imaging Station). For abbreviations, see Figs. 1 and 2

Fig. 2 in Tannic acid-modified silver nanoparticles enhance the anti-ACanthamoeba activity of three multipurpose contact lens solutions without increasing their cytotoxicity

Fig. 2 Anti-Acanthamoeba activity of AgTANPs conjugated with Solo Care Aqua (SCA) contact lens solution after 6 h of incubation in relation to cytotoxicity

Fig. 4 in Tannic acid-modified silver nanoparticles enhance the anti-ACanthamoeba activity of three multipurpose contact lens solutions without increasing their cytotoxicity

Fig. 4 Anti-Acanthamoeba activity of AgTANPs conjugated with Opti-Free contact lens solution after 6 h of incubation in relation to cytotoxicity

Fig. 1 in Tannic acid-modified silver nanoparticles enhance the anti-ACanthamoeba activity of three multipurpose contact lens solutions without increasing their cytotoxicity

Fig. 1 High-resolution scanning transmission electron microscopy image of the distribution and diameters of the tannic acid-modified silver nanoparticles (AgTANPs)

opencc-by-4.0Jun 2024View details →

Switchable Contact Model (SCM) Research Data

This is the research data of the article describing the implementation of the Switchable Contact Model (SCM), link: https://github.com/DamlaSerper/Switchable_Contact_Model-SCM.

opencc-by-4.0Jun 2024View details →

Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species' range

Files required to run analyses related to the journal article:" Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species’ range." Code which utilizes these data are found at: https://github.com/k-lamb/Campanula-range-history DOI code link: https://doi.org/10.5281/zenodo.12097775

opencc-by-4.0Jun 2024View details →

Supplementary Simulation Data for "A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch"

Additional simulation data for "A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch" Content: 'clusters_foldswitch': Contains representative structures in PDB format of the refolding landscape of RfaH using all-atom structure-based models. The QA and QB values indicated in each filename correspond to the fraction of native contacts contain in the representative structure in comparison to the total number of contacts in the structure of the autoinhibited ⍺-folded (A) and active β-folded (B) states of the C-terminal domain of RfaH. 'input_one_fs': Contains a trajectory of RfaH refolding from the ⍺-folded to the β-folded state, with each frame contained into a separate PDB file, totalling 400 PDB files. These files can be used with the frustration-based windowing method  scripts and Colab notebook made available at https://github.com/pb3lab/RfaH-frustration 'input_many_fs': Contains several trajectory of RfaH reversible refolding between the ⍺-folded and β-folded states, with each frame contained into a separate PDB file, totalling 11,999 PDB files. These files can be used with the frustration-based windowing method  scripts and Colab notebook made available at https://github.com/pb3lab/RfaH-frustration 'output_one_fs': Contains output results from the analysis of local energetic frustration dynamics of the 400 frames contained in 'input_one_fs' using the windowing method available in the Colab notebook at https://github.com/pb3lab/RfaH-frustration. 'output_many_fs': Contains output results from the analysis of local energetic frustration dynamics of the 11,999 frames contained in 'input_many_fs' using the windowing method available in the Python script at https://github.com/pb3lab/RfaH-frustration.

opencc-by-4.0May 2024View details →

syncomat: Synthetic Contact Matrices for 200 UN Countries

<h2>What's Changed</h2> <ul> <li>Fixed bugs and general improvements :)</li> <li>Updated <code>renv</code> for better reproducibility</li> <li>Improved README for a better user experience</li> <li>A separate <a href="https://github.com/idem-lab/syncomat/blob/main/Methodology.md">Methodology page</a> is now available for a deeper dive into modifying syncomat for a user's specific needs.</li> </ul>

opencc-by-4.0Jul 2024View details →

Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species

Replicated secondary contact zones can provide insights on the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies of the genus Erebia using whole-genome re-sequencing data. We assessed the genomic relationships between populations and species and find hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between the contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont Wolbachia, which can cause reproductive isolation between its hosts, in all E. cassioides, while it appears to be fully or largely absent in contact zone populations of E. tyndarus. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.

opencc-by-4.0Dec 2023View details →

Рис. 6. Контактно-тревожная позывка «перекΛичка» птенцов I. sinensis (a) и гибриΑных птиц (b) Fig. 6. Contact-alarm call "roll call" of I. sinensis nestlings (a) and hybrid birds (b) in Call repertoire of Bitterns Ixobrychus in Russian Far East

Рис. 6. Контактно-тревожная позывка «перекΛичка» птенцов I. sinensis (a) и гибриΑных птиц (b) Fig. 6. Contact-alarm call "roll call" of I. sinensis nestlings (a) and hybrid birds (b)

opencc-by-4.0Dec 2023View details →

Рис. 5. Контактно-пищевая позывка «мяуканье» (1) и пищевое «шипение» (2) птенцов: a — I. eurythmus; b — I. sinensis; c — гибриΑных птиц Fig. 5. Contact-food "meow" call (1) and food "hissing" (2) of nestlings: a — I. eurythmus; b — I. sinensis; c — hybrid birds in Call repertoire of Bitterns Ixobrychus in Russian Far East

Рис. 5. Контактно-пищевая позывка «мяуканье» (1) и пищевое «шипение» (2) птенцов: a — I. eurythmus; b — I. sinensis; c — гибриΑных птиц Fig. 5. Contact-food "meow" call (1) and food "hissing" (2) of nestlings: a — I. eurythmus; b — I. sinensis; c — hybrid birds

opencc-by-4.0Jul 2021View details →

Fig. 2. Contact experiments with Terpios hoshinota sponge. a in Ophiomonas shinseimaruae Okanishi & Matsuo & Fujita 2021, sp. n.

Fig. 2. Contact experiments with Terpios hoshinota sponge. a, Two fragments from different individuals (N1 × N2) in the direct contact assay (at day 0). b, Boundary zone (arrow heads) between two individuals (N4 × N5) in the growing-edge contact assay (at day 19). c, Enlarged view of b. d, Colony of Montipora coral (81 cm in diameter) which was covered by sponge patches of N4 and N5 in Nakijin.

Fig. 11 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 11 Rates of chatter calls in different magpie populations and individuals. a Each mark represents average chattering rate for a single bird from five populations indicated by colours. Figures are numbers for the outliers: 1, 2—jankowskii from the mixed population of Argun'; 3, 4, 5—hybrid birds from the hybridogeneous population of Kerulen. b Each mark represents average chattering rate for a series of chatterings of one selected individual representing jankowskii, leucoptera, and hybrid birds, respectively. Green mark—pair #6 jankowskii from Vladivostok; gray—pair #43 leucoptera from Tsasuchei, Transbaikalia; blue—pair #24 hybrids from Kerulen, eastern Mongolia. X-axis—number of elements per second in a total series of chattering; Y-axis— number of elements per second in a series of 5 elements of chattering

Fig. 12 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 12 Violin plot diagram of the chatter call speed (elements per second) of Eurasian magpie populations across regions. X-axis presents a set of populations; Y-axis—elements per second. Box outlines the interquantile range (25%, 75%), whiskers represent range without outliers, central bar is the median, red dot is the mean, and figure shape is the probability density. The brackets on the top denote statistically significant pairwise differences (GamesHowell test, p<0.05)

Fig. 9 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 9 Population genetic structure based on unlinked SNP markers. Scatter plots of principal component analysis (PCA) show individual variation in components one and two (a) and three and four (b). The amount of variance explained by each PC is shown in parentheses. I—leucoptera,

Fig. 7 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 7 Bayesian skyline plots (BSPs) for effective female population sizes for haplogroups, subspecies, and populations of Pica pica. a Comparison of 6 haplogroups, depicted in the network Fig. 4. b Comparison of 6 subspecies. c Comparison of 4 populations of P. p. jankowskii. d Comparison of 3 populations of P. p. leucoptera.

Fig. 6 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 6 Mismatch distribution of nucleotide differences in populations representing different haplogroups as at Figs. 4 and 5. X-axis— number of nucleotide differences; Y-axis—proportion (frequency). Solid lines—expected distributions (under expectation of population growth); dashed lines—observed distributions. a Haplogroup 1: