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Supplementary material 1 from: Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA (2022) Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. Metabarcoding and Metagenomics 6: e78128. https://doi.org/10.3897/mbmg.6.78128
Figures S1–S4
Supplementary material 2 from: Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA (2022) Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. Metabarcoding and Metagenomics 6: e78128. https://doi.org/10.3897/mbmg.6.78128
Table S1
Lean mass dynamics in hibernating bats and implications for energy and water budgets
<p>Hibernation requires balancing energy and water demands over several months with no food intake for many species. Many studies have considered the importance of fat for hibernation energy budgets because it is energy dense and can be stored in large quantities. However, protein catabolism in hibernation has received less attention and whole animal changes in lean mass have not previously been considered. We used quantitative magnetic resonance body composition analysis to measure fat and lean mass in two systems of hibernating bats, emphasizing the importance of lean mass for energy and water budgets. For cave myotis ( Myotis velifer ), lean mass represented 38 and 25% (male and female respectively) of pre-hibernation mass gain. In Townsend's big-eared bats ( Corynorhinus townsendii ), lean mass accounted for 18 – 35% of mass change during hibernation, but lean only contributed 3 – 7% of the energy budget. Water is produced from the catabolism of both fat and lean, but net water production is much less than gross water production when accounting for the water required to excrete urea. Although most mammals can't rely on protein catabolism for metabolic water production due to the water cost of excreting urea, we propose a variation on the protein-for-water strategy whereby hibernators could temporally compartmentalize the benefits of protein catabolism to periods of torpor, and the water cost to periodic arousals when free drinking water is typically available. Combined, our analyses demonstrate that lean mass is dynamic in hibernation, with important functional consequences for both energy and water budgets. </p>
Data for 'Phase Stability of Al-bearing Dense Hydrous Magnesium Silicates at Topmost Lower Mantle Condition: Implication for Water Transport in the Mantle '
<p>1 dataset for the phase diagram in Figure 2</p> <p>1 dataset for the unin-cell parameters for Figure3</p>
Figure 9 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 9 Predicted structural elements in the control regions of Challia fletcheri, Euborellia arcanum, Eudohrnia metallica, and Paratimomenus flavocapitatus.
Figure 4 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 4 Evolutionary rates of PCGs in six species of earwigs. The bar indicates each gene's Ka/Ks value.
Figure 5 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 5 Secondary structures of tRNA genes in the mitogenome of Apachyus feae. Mismatched base pairs are indicated by red circles; reduced arms are indicated by red arrowheads.
Figure 6 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 6 Secondary structures of tRNA genes in the mitogenome of Diplatys flavicollis. Mismatched base pairs are indicated by red circles; reduced arms are indicated by red arrowheads.
Figure 1 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 1 Mitochondrial maps of Apachyus feae and Diplatys flavicollis. Genes outside the map are transcribed clockwise, whereas those inside the map are transcribed counterclockwise. Names and other details of the genes are listed in Tables 2 and 3. The inside circles show the GC content and the GC skew. GC content and GC skew are plotted as the deviation from the average value of the entire sequence.
Figure 10 from: Chen Z-T (2022) Comparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys 1087: 105-122. https://doi.org/10.3897/zookeys.1087.78998
Figure 10 Phylogenetic relationships within Dermaptera inferred by Bayesian inference and maximum likelihood analysis. Numbers at the nodes are posterior probabilities (left) and bootstrap values (right). The family names are listed after the species. Infraorders and parvorders are indicated below each family name.
Competing controls of fluid overpressurization and chloritization on strength and instability of faults in granite: Implications for seismicity triggered by fluid-injection
<p>Fluids injection for hydraulic stimulation and fracturing, typical in the development of enhanced geothermal systems (EGS) in granites, can reactivate deep faults and induce seismicity. Such faults typically contain chlorite coatings as an alteration product that may impact styles of deformation – aseismic through seismic. We performed shear experiments on simulated granite fault gouges under conditions typifying a geothermal reservoir at ~4 km depth with a confining pressure of 110 MPa, a temperature of 150℃, fluid pressures of 21-80 MPa, and chlorite contents of 0-100%, to investigate the influence of effective stress and mineral composition on fault strength and stability. Our results show a transition from velocity-strengthening to velocity-weakening behavior in simulated granite gouge when the fluid pressure was elevated from 21 to 80 MPa, characterized by a transition from fault compaction to dilation – as revealed by microstructural observations – with implications in enabling unstable failure. Conversely, increasing chlorite content stabilizes slip but reduces frictional strength. The microstructures of these mixed gouges exhibit shear localized on chlorite-enriched planes and promoting fault sliding. These results suggest that earthquake ruptures occurring during fluid injection can be facilitated by fluid overpressures. And that controlling fluid overpressures and being aware of the presence of alteration minerals are both important controls in mitigating such injection-induced seismic risks.</p>
Supplementary material 1 from: Din JU, Bari F, Ali H, Rehman E, Adli DSH, Abdullah NA, Norma-Rashid Y, Kabir M, Hameed S, Nawaz DA, Nawaz MA (2022) Drivers of snow leopard poaching and trade in Pakistan and implications for management. Nature Conservation 46: 49-62. https://doi.org/10.3897/natureconservation.46.76036
Questionnaire 1
High-Pressure Melting Curve of FeH: Implications for Eutectic Melting between Fe and Non-Magnetic FeH
<p><strong>Table 1</strong>. Experimental Results</p> <p><strong>Table 2</strong>. Physical properties</p>
Figure 2 in Filling Linnean shortfalls increases endemicity patterns: conservation and biogeographical implications for the extreme case of Liolaemus (Liolaemidae, Squamata) species
Figure 2. Histogram showing the extent of species distribution for each studied period.
Figure 6 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 6 Phylogenetic relationships of major synbranchiform lineages. Molecular phylogeny based on comparative mitochondrial PCGs from relevant available mitogenomes and the newly generated herein for O. infernale. Troglobitic cave-dwelling species are marked with an asterisk to distinguish them from surface-dwelling ones. Outgroup taxa not shown. Colored circles on nodes indicate degree of clade support as determined by bootstrap values.
Figure 3 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 3 Secondary structure of the 22 tRNA genes of the mitochondrial genome of O. infernale predicted by tRNAScan-SE 2.0.
Figure 4 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 4 Comparison (multiple sequence alignment) of the mtDNA control region of O. infernale with those of fellow teleosts Siniperca chuatsi and Cyprinion semiplotum. The alignment displays the three canonical domains distinguished by Termination Associated Sequences (TAS) of the upstream hypervariable region (in red), central conserved domain blocks (CSB-F, CSB-E, CSB-D) (in blue), and conserved sequence blocks of the downstream hypervariable region (CSB-1, CSB-2 and CSB-3) (in green).
Figure 5 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 5 Patterns of selection in mtDNA PCGs of synbranchiform fishes. Results from KA/KS ratio analysis on mitochondrial PCGs (x-axis) in synbranchiform fishes of the families Synbranchidae (a) and Mastacembelidae (b).
Figure 2 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 2 Results from analysis of Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of O. infernale. Codon families are plotted on the x-axis. The label for the 2, 4, or 6 codons that compose each family is shown in the boxes below the x-axis, and the colors correspond to those in the stacked columns. RSCU values are shown on the y-axis.
Figure 1 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 1 Annotated map of the mitochondrial circular genome of O. infernale. The outer ring corresponds to the H- (outermost) and L-strands, and depicts the location of PCGs (in black, except for ND6 which is encoded in the L-strand and is portrayed in red), the non-coding control region (in dark brown), tRNAs (in red), and rRNAs (in light brown). The inner ring (black sliding window) denotes GC content along the genome. Live specimen photograph taken in the Cenote Kancabchen (Homún, Yucatán), courtesy of cave diver Erick Sosa.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.