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Data related to: "Molecular Interaction Properties of the 90-231 Segment of PrP-E200K: a Multilayered Computational Study"
<p>3D coordinates of all d1-d5 structures in the pdb file format</p>
Identification of Sclareol As a Natural Neuroprotective Cav1.3-Antagonist Using Synthetic Parkinson-Mimetic Gene Circuits and Computer-Aided Drug Discovery
<p>Data underlying the figures in the publication “Identification of Sclareol As a Natural Neuroprotective Ca<sub>v</sub>1.3-Antagonist Using Synthetic Parkinson-Mimetic Gene Circuits and Computer-Aided Drug Discovery”, published in <em>Adv. Sci.,</em> <strong>2022</strong>, 9, 2102855.</p> <p><a href="https://doi.org/10.1002/advs.202102855">https://doi.org/10.1002/advs.202102855</a></p> <p>Table of contents:</p> <p><strong>1. Figure 1-3.xlsx</strong>: Source data for <em>Figures 1-3</em>.</p> <p><strong>2. Figure 4-5</strong>: Source data for <em>Figures 4-5</em>.</p> <p><strong>3. Figure1-3.zip</strong>: .zip archive containing the raw data of <em>Figures 1-3 </em>in <em>.pzfx</em> format.</p> <p><strong>4. Movie S1,2</strong>: Movie s1 and S2.</p>
A computational study of steady and stagnating positive streamers in N$_2$-O$_2$ mixtures
<p>This dataset consists of files used to produce the data presented in the article "A computational study of steady and stagnating positive streamers in N$_2$-O$_2$ mixtures". This dataset includes 1) source code for the simulations; 2) transport data files, which contain a list of included reactions, their reaction rate coefficients, and transport coefficients; 3) configuration files for running the simulations and 4) outputted log files of the simulations.</p> <p>This dataset is for the revised paper.</p>
Data from: Computing the local field potential (LFP) from integrate-and-fire network models
Leaky integrate-and-fire (LIF) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli, tasks or dynamic network states. However, neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field potential (LFP). Given that LFPs are generated by spatially separated currents across the neuronal membrane, they cannot be computed directly from quantities defined in models of point-like LIF neurons. Here, we explore the best approximation for predicting the LFP based on standard output from point-neuron LIF networks. To search for this best "LFP proxy", we compared LFP predictions from candidate proxies based on LIF network output (e.g, firing rates, membrane potentials, synaptic currents) with "ground-truth" LFP obtained when the LIF network synaptic input currents were injected into an analogous three-dimensional (3D) network model of multi-compartmental neurons with realistic morphology, spatial distributions of somata and synapses. We found that a specific fixed linear combination of the LIF synaptic currents provided an accurate LFP proxy, accounting for most of the variance of the LFP time course observed in the 3D network for all recording locations. This proxy performed well over a broad set of conditions, including substantial variations of the neuronal morphologies. Our results provide a simple formula for estimating the time course of the LFP from LIF network simulations in cases where a single pyramidal population dominates the LFP generation, and thereby facilitate quantitative comparison between computational models and experimental LFP recordings in vivo.
Data from:A computational study of cancer hyperthermia based on vascular magnetic nanoconstructs
The application of hyperthermia to cancer treatment is studied using a novel model arising from the fundamental principles of flow, mass and heat transport in biological tissues. The model is defined at the scale of the tumour microenvironment and an advanced computational scheme called the embedded multiscale method is adopted to solve the governing equations. More precisely, this approach involves modelling capillaries as one-dimensional channels carrying flow, and special mathematical operators are used to model their interaction with the surrounding tissue. The proposed computational scheme is used to analyse hyperthermic treatment of cancer based on systemically injected vascular magnetic nanoconstructs carrying super-paramagnetic iron oxide nanoparticles. An alternating magnetic field is used to excite the nanoconstructs and generate localized heat within the tissue. The proposed model is particularly adequate for this application, since it has a unique capability of incorporating microvasculature configurations based on physiological data combined with coupled capillary flow, interstitial filtration and heat transfer. A virtual tumour model is initialized and the spatio-temporal distribution of nanoconstructs in the vascular network is analysed. In particular, for a reference iron oxide concentration, temperature maps of several different hypothesized treatments are generated in the virtual tumour model. The observations of the current study might in future guide the design of more efficient treatments for cancer hyperthermia.
Marked crosswalks in US transit-oriented station areas, 2007–2020: A computer vision approach using street view imagery
<p>This is the supplementary dataset for the article “Marked crosswalks in US transit-oriented station areas, 2007–2020: A computer vision approach using street view imagery” (<a href="https://journals.sagepub.com/doi/10.1177/23998083221112157">https://journals.sagepub.com/doi/10.1177/23998083221112157</a>) published on Environment and Planning B: Urban Analytics and City Science. The dataset contains comprehensive information of the presence of marked crosswalks (i.e., parallel-line and high-visibility) at each street intersection within a 250-meter buffer of all US TOD stations for each consecutive year between 2007 and 2020. We describe each field of the dataset below. Most of the column station variable names are taken directly from the National TOD Database from the <a href="https://toddata.cnt.org/">Center for Transit-Oriented Development</a>. </p> <ul> <li>intersecton_id: numeric, unique identifier of each intersection.</li> <li>tod_id: numeric, unique identifier of the associated TOD station. We retain all records of intersections that are associated with multiple TOD stations. </li> <li>year: numeric, one year between 2007 and 2020. </li> <li>plain: numeric, the number of presence of parallel-line crosswalks (bounding boxes) detected among the four 90-degree images at each intersection in that particular year. Zero for the years where GSV are not available. </li> <li>zebra: numeric, the number of presence of high-visibility crosswalks (bounding boxes) detected among the four 90-degree images at each intersection in that particular year. Zero for the years where GSV are not available. </li> <li>impute: binary, 1 if imputed; 0 otherwise. </li> <li>lon_intersection: longitude of each intersection obtained from OSM. </li> <li>lat_intersection: latitude of each intersection obtained from OSM. </li> <li>distance_intersection_to_tod: distance of each intersection from TOD station by meters. </li> <li>Agency: operating transit agency of the associated TOD station. </li> <li>Lines (s): transit lines of the associated TOD station. </li> <li>Station Name: station name of the associated TOD station. </li> <li>Year Opened: the year when the associated station opened. </li> <li>lat_tod: latitude of the associated TOD station obtained from the National TOD Database. </li> <li>lon_tod: longitude of the associated TOD station obtained from the Nation TOD Database. </li> <li>Both: numeric, the total number of marked (parallel-line + high-visibility) crosswalks detected among the four 90-degree images at each intersection in that particular year. </li> <li>plain_b: binary, 1 if presence of parallel-line crosswalk; 0 if otherwise. </li> <li>zebra_b: binary, 1 if presence of high-visibility crosswalk; 0 if otherwise. </li> <li>both_b: binary, 1 if presence of marked crosswalk; 0 if otherwise. </li> </ul>
Contrast solution properties and scan parameters influence the apparent diffusivity of computed tomography contrast agents in articular cartilage
<p>The inability to detect early degenerative changes to the articular cartilage surface that commonly precede bulk osteoarthritic degradation is an obstacle to early disease detection for research or clinical diagnosis. Leveraging a known artifact that blurs tissue boundaries in clinical arthrograms, contrast agent diffusivity can be derived from computed tomography arthrography (CTa) scans. We combined experimental and computational approaches to study protocol variations that may alter the CTa-derived apparent diffusivity. In experimental studies on bovine cartilage explants, we examined how contrast agent dilution and transport direction (absorption vs. desorption) influence the apparent diffusivity of untreated and enzymatically digested cartilage. Using multiphysics simulations, we examined mechanisms underlying experimental observations and the effects of image resolution, scan interval and early scan termination. The apparent diffusivity during absorption decreased with increasing contrast agent concentration by an amount similar to the increase induced by tissue digestion. Models indicated that osmotically induced fluid efflux strongly contributed to the concentration effect. Simulated changes to spatial resolution, scan spacing and total scan time all influenced the apparent diffusivity, indicating the importance of consistent protocols. With careful control of imaging protocols and interpretations guided by transport models, CTa-derived diffusivity offers promise as a biomarker for early degenerative changes.</p>
Computational Screening Data of Transition Metal-Doped CdS for Photocatalytic Hydrogen Production
<p>Data access for the paper publication.</p>
Screening and mechanism of novel angiotensin-I-converting enzyme inhibitory peptides in X. sorbifolium seed meal: A computer-assisted experimental study method
<p>本文档是补充材料</p>
Figure 9 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 9 - Comparative material, Carychium mexicanum Pilsbry, 1891 (AJC 2092) from Puebla, Mexico A, C, E, G, I, K and topotypic C. costaricanum E. von Martens, 1898 (AJC 2093) B, D, F, H, J, L; A–L CT scans showing columellar apparatus and configuration of the columellar lamella in both species A–L. Scale bar 1 mm.
Figure 8 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 8 - Comparative material, Carychium mexicanum Pilsbry, 1891 (AJC 2092) from Puebla, Mexico. A–L fresh shells collected proximal to topotypic locality (Orizaba, Mexico) A, I–J degrees of variation in apertural barriers. Scale bar 1 mm.
Figure 7 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 7 - Comparative material, Carychium floridanum Clapp, 1918 (CM 46540). A–F CT scans showing columellar apparatus and simple lamellar sinuosity of syntype C moderately thickened S-shaped lamella A, E zones of increased callus concentration on the peristome G umbilical view showing turned back rim of peristome. Scale bar 1 mm.
Figure 14 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 14 - Carychium zarzaae sp. n. A–D CT scans showing columellar apparatus of paratype (NMBE 549927/1) D–F prominent parietal denticle. Scale bar 1 mm.
Figure 10 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 10 - Type locality of Carychium hardiei sp. n., Indian Springs State Park, Flovilla, Georgia, USA. A collector A. Jochum; B Carychium hardiei in action on rotten leaf.
Figure 4 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 4 - Carychium hardiei sp. n. A–F holotype (NMBE 549920/1) G–L paratype shell (NMBE 549921/8). Scale bar 1 mm.
Figure 6 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 6 - Comparative material, Carychium floridanum Clapp, 1918 (CM 46540). A–H syntypes and specimen information; E peristome with thick parieto-columellar callus and prominent parietal denticle. Scale bar 1 mm.
Figure 12 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 12 - Carychium belizeense sp. n. A–L CT scans showing columellar apparatus of paratype (NMBE 549924/8) C–D two-tiered, tightly coiled columellar lamella and prominent parietal denticle I–J highly sinuate tongue-like primary lamella tightly arching over swollen secondary lamella. Scale bar 1 mm.
Figure 5 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 5 - Carychium hardiei sp. n. A–F CT scans showing columellar apparatus of paratype (NMBE 549921/8) G umbilical view H aerial view of protoconch and spire. Scale bar 1 mm.
Figure 2 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 2 - Comparative material, Carychium mexicanum Pilsbry, 1891 (RBINS 10591) (ex. Autor) S. N. & M. C. Rhoads Expedition, "Texolo Falls V. Cruz, Mexico Rhoads legit". A–E with Bynes degradation; Carychium costaricanum E. von Martens, 1898 (RBINS 10591) original type series F–I; F peristome thickly callused showing apertural barriers. Scale bar 1 mm.
Figure 3 from: Jochum A, Weigand AM, Bochud E, Inäbnit T, Dörge DD, Ruthensteiner B, Favre A, Martels G, Kampschulte M (2017) Three new species of Carychium O.F. Müller, 1773 from the Southeastern USA, Belize and Panama are described using computer tomography (CT) (Eupulmonata, Ellobioidea, Carychiidae). ZooKeys 675: 97-127. https://doi.org/10.3897/zookeys.675.12453
Figure 3 - Neighbor-Joining overview topology based on COI K2P-distances for all North and Central American evolutionary lineages accessed in Weigand et al. (2013) and the three newly described Carychium species. COI data for C. mexicanum and C. jardineanum are added. Numbers at the branches indicate bootstrap support for the lineages. BOLD-IDs: Carychium lineage C1, E / SE USA: BARCA014-10, BARCA015-10, BARCA019-10, BARCA020-10, BARCA021-10, BARCA022-10, BARCA025-10, BARCA026-10, BARCA027-10, BARCA028-10, BARCA029-10, BARCA030-10, BARCA127-12; C2 C. exiguum (Say 1822): BARCA041-10, BARCA042-10, BARCA043-10; C3 C. exile H.C. Lea, 1842: BARCA044-10, BARCA045-10, BARCA046-10, BARCA047-10, BARCA048-10, BARCA049-10, BARCA050-10, BARCA051-10; Carychium lineage C4, USA; Florida: BARCA128-12; C5 C. floridanum G.H. Clapp, 1918: BARCA032-10, BARCA033-10, BARCA034-10, BARCA035-10, BARCA037-10; C9 C. hardiei sp. n.: BARCA038-10, BARCA039-10, BARCA040-10; C10 C. belizeense sp. n.: BARCA135-12, BARCA136-12; C11 C. costaricanum E. von Martens, 1898: BARCA137-12, BARCA138-12, BARCA139-12, BARCA140-12, BARCA141-12; Carychium lineage C12, Panama: BARCA142-12, BARCA143-12, BARCA144-12; C13 C. zarzaae sp. n.: BARCA145-12, BARCA146-12, BARCA147-12, BARCA148-12; C14 C. minimum O.F. Müller, 1774: BARCA064-10, BARCA065-10, BARCA069-10; C15 C. nannodes G.H. Clapp, 1905: BARCA099-10, BARCA100-10, BARCA149-12; C20 C. occidentale Pilsbry, 1891: BARCA054-10, BARCA055-10, BARCA058-10, BARCA059-10, BARCA061-10; C23 C. tridentatum (Risso, 1826): BARCA075-10, BARCA079-10, BARCA081-10; C. mexicanum Pilsbry, 1891: BARCA221-17; C. jardineanum (Chitty, 1853): BARCA222-17; Z3 Zospeum exiguum Kuščer, 1932; BARCA116-10; Z4: Zospeum frauenfeldi (Freyer, 1855): BARCA107-10.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.