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3,878 results for “Molecular Data”
Raw data molecular dynamics and alphafold (Lemaire et al)
<p>Raw data molecular dynamics and alphafold for manuscript NCOMMS-24-29370</p>
Computational Data - Role of Molecular Orientation: Comparison of Nitrogenous Aromatic Small Molecule Inhibitors for Area-Selective Atomic Layer Deposition
<p><span><span>Area-selective atomic layer deposition (AS-ALD) shows great potential for meeting the stringent demands of the semiconductor industry for precision nanopatterning. Small molecule inhibitors (SMIs) have recently proven to be a promising, industry-compatible means of achieving AS-ALD. In this work, we compare three nitrogenous aromatic SMIs – aniline, pyrrole, and pyridine – for their ability to block Al</span></span><sub><span><span>2</span></span></sub><span><span>O</span></span><sub><span><span>3</span></span></sub><span><span> ALD on copper with (CuO</span></span><sub><span><span>x</span></span></sub><span><span>) and without (Cu) a native oxide. We find that pyrrole and aniline perform much better as inhibitors than does pyridine. Furthermore, when redosed on copper before every ALD cycle in an ABC scheme, pyrrole and aniline provide outstanding inhibition, facilitating the selective deposition of over 11 nm of Al</span></span><sub><span><span>2</span></span></sub><span><span>O</span></span><sub><span><span>3</span></span></sub><span><span> on an SiO</span></span><sub><span><span>2</span></span></sub><span><span> growth surface in the presence of Cu with 99.9% selectivity. By combining both theory and experiment, we provide new understanding of the mechanisms by which selectivity is prolonged and lost. First, we show that the CuO</span></span><sub><span><span>x</span></span></sub><span><span> surface is inherently more reactive than the Cu surface, leading to an eventual loss of selectivity, even when the inhibitor is redosed. Second, we find that whereas pyrrole and aniline adsorb in a planar bonding orientation, pyridine binds upright at the copper surface and we propose that the upright orientation is the origin of the ineffective inhibition of pyridine. Finally, we observe that redosing of aniline protects the copper surface from undesired oxidation, whereas the redosing of pyridine does not. As such, we posit that a likely benefit of redosing is preventing oxidation and thus reducing reactive site formation during ALD. Through this work, we demonstrate the capability of nitrogenous aromatics to serve as SMIs for AS-ALD, and we contribute valuable insights regarding the impact of ALD process parameters on selectivity. </span></span></p>
Figure 5 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000
Figure 5 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.
Figure 3 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000
Figure 3 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.
Figure 2 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000
Figure 2 Apanthura stocki. All scales represent 0.1 mm.
Figure 4 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000
Figure 4 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.
Figure 3 from: Sukhorukov AP, Nilova MV, Krinitsina AA, Zaika MA, Erst AS, Shepherd KA (2018) Molecular phylogenetic data and seed coat anatomy resolve the generic position of some critical Chenopodioideae (Chenopodiaceae – Amaranthaceae) with reduced perianth segments. PhytoKeys 109: 103-128. https://doi.org/10.3897/phytokeys.109.28956
Figure 3 Pericarp of Blitumantarcticum. Scale bar: 200 μm.
Figure 11 from: Chen K, Liu Q, Jin J, Zhang D (2019) Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae). ZooKeys 836: 113-133. https://doi.org/10.3897/zookeys.836.32796
Figure 11 Wing venation of Emphylicacrassihamata.
Figure 24 from: Chen K, Liu Q, Jin J, Zhang D (2019) Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae). ZooKeys 836: 113-133. https://doi.org/10.3897/zookeys.836.32796
Figure 24 Distribution map of Emphylica spp.
Data from: Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae)
The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15–25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.
Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations
Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
Data from: Grouping substitution types into different relaxed molecular clocks
Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure by analysing a 0.15 Mb intergenic region to infer divergence times relating eight primates. The different groupings of substitution types that we explore have little effect on the posterior means of divergence times, but the widths of the credibility intervals decrease as the number of groups increases.
Figure 45 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052
Figure 45 Mesembrius spp., habitus, lateral view. M. vockerothi sp. nov. (♀).
sulphate and molybdate incorporation at calcite-water interface - ab initio molecular dynamics data
<p>Provided here are ab initio molecular dynamics data files generated in CP2K, relating to the publication entitled<br> Sulphate and Molybdate Incorporation at the Calcite-Water Interface: Insights from Ab Initio Molecular Dynamics. By Scott D. Midgley, Devis Di Tommaso, Dominik Fleitmann, Ricardo Grau-Crespo.</p> <p>We have provided the CP2K input file (.inp), the CP2K energy file (.ener), and a single geometry snapshot from the simulation (.xyz).<br> It is not possible to share the fully dynamics trajectory, because each file is extremely large.</p> <p>N.B. for the sulphate ion in water, a corruption in the .ener file meant that it was not possible to share. Instead a list of MD energies are given as a .txt file, with energies in eV.<br> </p>
Molecular dynamic simulation data of liquid Al-Cu alloys
<p>This dataset contains all obtained data for molecular dynamics investigation of Al-Cu melts.</p>
Figure 9 from: Guayasamin J, Paez D, Yanez M (2011) A new species of Andean toad (Bufonidae, Osornophryne) discovered using molecular and morphological data, with a taxonomic key for the genus. ZooKeys 108: 73-97. https://doi.org/10.3897/zookeys.108.1129
Figure 9 - Distribution of Osornophryne simpsoni sp. n. (white circles) in Ecuador.
Figure 7 from: Guayasamin J, Paez D, Yanez M (2011) A new species of Andean toad (Bufonidae, Osornophryne) discovered using molecular and morphological data, with a taxonomic key for the genus. ZooKeys 108: 73-97. https://doi.org/10.3897/zookeys.108.1129
Figure 7 - Pectoral girdle of Osornophryne simpsoni sp. n. in ventral view; adult male, QCAZ 45899.
Figure 6 from: Guayasamin J, Paez D, Yanez M (2011) A new species of Andean toad (Bufonidae, Osornophryne) discovered using molecular and morphological data, with a taxonomic key for the genus. ZooKeys 108: 73-97. https://doi.org/10.3897/zookeys.108.1129
Figure 6 - Vertebral column of Osornophryne simpsoni sp. n. in dorsal view; adult male, QCAZ 45899.
Figure 2 from: Guayasamin J, Paez D, Yanez M (2011) A new species of Andean toad (Bufonidae, Osornophryne) discovered using molecular and morphological data, with a taxonomic key for the genus. ZooKeys 108: 73-97. https://doi.org/10.3897/zookeys.108.1129
Figure 2 - Osornophryne simpsoni sp. n. in life (male holotype, QCAZ 49774).
Figure 4 from: Andújar C, Hernando C, Ribera I (2011) A new species of endogean, anophthalmous Parazuphium Jeannel from Northern Morocco (Coleoptera: Carabidae), with new molecular data for the tribe Zuphiini. ZooKeys 103: 49-62. https://doi.org/10.3897/zookeys.103.1124
Figure 4 - Habitat of Parazuphium aguilerai sp. n.
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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)
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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.