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Research data supporting: "Machine learning of microscopic structure-dynamics relationships in complex molecular systems"
<p>This repository contains the set of data and the code to reproduce the results shown in "Machine learning of microscopic structure-dynamics relationships in complex molecular systems" published on Machine Learning: Science and Technology (DOI: 10.1088/2632-2153/ad0fa5).</p>
Figure 17 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 17. Selected dentaries of Thylacinus showing differences in the diastemata between the premolars as the effect of increasing age. A, subadult (in labial view) with m3 erupted, but not m4. Only slight suggestions of diastemata are evident between the premolars; B (lingual view) and C (labial view), showing later stages of m4 eruption and the increase of diastemata in adults.
Figure 16 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 16. Later stages of early eruption in Thylacinus showing the presence and early loss of dp3 in the dentary. A, Part of the dentary (CU A6 7/10), redrawn from Moeller (1968), showing the erupted dp3, the unerupted successor p3 in its alveolar crypt, immediately anterior to dp3, and the erupting m1. The erupting dp1 and dp2 are also labeled; B, A slightly later stage of eruption in the dentary (USNM 115365) shows that the dp3 has been lost, and successor p3 is in early eruption. The m1 is now almost completely erupted. c indicates lower successional canine in B.
Figure 13 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 13. Computed tomography images from the supplementary data of Newton et al. (2018). A, section of the skull and dentition from TMAG A931, a thylacine pouch young of 35 - 37 days old; B, Section of the skull and dentition from TMAG A930, a thylacine pouch young of 66 - 67 days old. Scale bars are 5 mm. C, canine; dP1, deciduous first premolar; dP2, deciduous second premolar; dP3, deciduous third premolar; M1, first molar; P3, successional third premolar.
Figure 12 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 12. Section through dp3 and its successor p3. Only a small fragment of the lingual successional lamina is evident. Compare this single section with the camera lucida drawings in Figure 11. dp3, deciduous third premolar; lsl, lingual successional lamina; p3, successional third premolar.
Figure 10 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 10. Section through the level of the metacone on M1, with thick enamel on its apex and disrupted dentin; d, dentin; e, enamel; me, metacone apex.
Figure 11 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 11. Camera lucida drawings of dp3 and p3 in the dentary, at different planes of section. A, The lingual successional lamina is fragmented, but still largely intact, between the small dp3 and its larger successional p3; B, The small dp3 is evident with its dentin and enamel, and its primary dental lamina connection to the oral epithelium is fragmented but still evident. The section through the successor p3 is not central, but it shows the fragmented lingual successional lamina between the two teeth. A, ameloblasts; AB, alveolar bone; D, dentin; dp3, deciduous third premolar; E, enamel; O, odontoblasts; OE, oral epithelium; P, dental papilla; p3, successor third premolar; PL, primary dental lamina; SL, lingual successional lamina; SR, stellate reticulum.
Figure 6 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 6. Longitudinal section through dP2, with disrupted dentin and well - developed enamel. d, dentin; e, enamel.
Figure 9 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 9. Section of M1, at level of paracone. A, paracone with overlying epithelial nodule; B, paracone at more central level, lacking the epithelial nodule; en, epithelial nodule; pa, paracone apex.
Figure 3 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 3. Histological section of I1 in Thylacinus, in middle bell stage. dp, dental papilla; en, epithelial nodule; o, oral epithelium; pdl, primary dental lamina.
Figure 1 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 1. Thylacinus (71.1 mm Head Length) pouch young, with unerupted dentition; redrawn from Flower, 1867. C, upper and lower canine; dP3, upper and lower deciduous third premolar; M1, upper and lower first molar; P3, upper and lower successional third premolar.
Figure 5 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 5. Longitudinal section through large successional upper canine, with disrupted dentin and well -developed enamel. d, dentin; e, enamel.
Figure 8. Late bell stage successor P3 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 8. Late bell stage successor P3. This tooth lies anterior to dP3 and it lacks dentin and enamel. lsl, short segment of lingual successional lamina; t, tongue.
Figure 2. Sibling pouch young thylacines. A, NMV C5754 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 2. Sibling pouch young thylacines. A, NMV C5754, male specimen sectioned for histology images; B, NMV C 5757, female specimen, used by Feigin et al. (2018) for genomic analysis.
Figure 14 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 14. Images of the head, skull, and dentition of the thylacine pouch young from the Australian Museum (AM P 762). A, X-ray of the skull, showing deciduous and successional teeth in varying stages of development and early eruption; B, Head and upper body of the pouch young, prior to X-ray analysis; C, Higher magnification of a portion of the X-ray shown in figure A, with emphasis on the erupted lower dp3, and the unerupted but larger successional p3 immediately anterior to it.
Supplementary material for: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.
<h1>Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.</h1> <h2>Supplementary material</h2> <p>This deposition contains supplementary material for a paper on coordinate system calibration in 4D STEM. A preprint of the paper is available at <a href="https://arxiv.org/abs/2403.08538">https://arxiv.org/abs/2403.08538</a>.</p> <h2>Contents</h2> <div> <div><code>20221025_154811.zip</code>: Overfocused 4D STEM test dataset</div> <div> </div> <div><code>overfocus.sif</code>: Apptainer image with complete software stack. <code>apptainer run --writable overfocus.sif</code> to execute. It starts a Jupyterlab instance with two notebooks, one to genreate test data and the other to perform the interactive adjustment. This documents the software version that was used for the figures in the paper.</div> <div> </div> <div><code>requirements.txt</code>: Python package versions of dependencies in <code>overfocus.sif</code>. </div> <div> </div> <div><code>COM - Jupyter Notebook - Google Chrome 2023-01-25 12-40-07_processed.mp4</code>: Screen capture video with explanation of the first live calibration with an early prototype.</div> <div> </div> <div><code>video description.docx</code>: Explanation of the plots and adjustment process in the screen capture video.</div> <div> </div> <div><code>Microscope-Calibration.tar.gz</code>: Repository archive of the software and examples for calibration in the version used in the paper.</div> <div> </div> <div><code>TemGym.tar.gz</code>: Repository archive of TemGym Basic in the version used in the paper.</div> </div>
Revealing the microscopic mechanism of vortex pinning in superconductors
<p>Vortex pinning is a crucial factor that determines the critical current of practical superconductors, but its microscopic mechanism has long been elusive. Here using high-resolution scanning tunneling microscopy, we studied the pinning of single vortex by point defect in high-Tc FeSe-based superconductors. We found the defect-vortex interaction drives low-energy vortex bound states away from EF, which effectively lowered the energy of vortex and caused the pinning. It indicates the local pairing near the pinned vortex core is actually enhanced, which is in sharp contrast to the traditional understanding that non-superconducting regions pin the vortex, but is well captured by our microscopic quantum model. Furthermore, we directly obtained the elementary pinning energy from tunneling spectrum and estimated the pinning force via the spatial gradient of pinning energy. The obtained value aligns with the bulk critical current measurement. Our study thus established a general microscopic mechanism of vortex pinning in superconductors.</p>
Figure 4. Longitudinal section through I4 and transverse section through smaller I3. e in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 4. Longitudinal section through I4 and transverse section through smaller I3. e, disrupted enamel.
Plate 1. Crocidura nicobarica Microscopic structure a in Observation on the re-occurrence of Nicobar spiny shrew (Crocidura nicobarica Miller, 1902): A critically endangered mammal of Great Nicobar Island, India
Plate 1. Crocidura nicobarica Microscopic structure a) Fore limb, b) Hind limb, c) Tip of tail, d) Dorsal fur, e) Long black hairs in snout, f) Long white hairs in tail and g) White tooth.
Data for "Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions"
<p>Data for "Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions", Phys. Rev. A 104, 033301 (2021).</p>
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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.