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MPIData: MPS transfer function
<p>This data repository contains magnetic particle imaging data. The example file is stored in the <a href="https://arxiv.org/pdf/1602.06072.pdf">MDF file format</a> and the transfer function files are stored in the .s1p file format. The data is used in this code example: <a href="https://github.com/IBIResearch/MPSTransferfunction">https://github.com/IBIResearch/MPSTransferFunction</a></p>
Part 3: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/.</p> <p>The other subdirectories in the directory subtelomere contain instructions and scripts for reproducing many of the results in the manuscript. The subdirectory subtelomere/TwoCopies/ contains two subdirectories of instructions and scripts for reproducing the results in the table on the average coverage of Focb TR4 isolates. The subdirectory subtelomere/TEs/ contains four subdirectories, each of which provides instructions and scripts for estimating the copy numbers of one or two transposons in the table on the copy numbers of five transposons in Focb TR4 isolates. The subdirectory subtelomere/SVs/ explains how the results on SNPs and presence/absence polymorphisms could be reproduced. The subdirectory subtelomere/Fol/ contains three subdirectories, each of which includes information for reproducing one of the three columns in the table on mean SNP rates between Fol D11 and each of Fol4287, Fol069 and Fol072. The subdirectory subtelomere/Forc/ demonstrates how some of the programs and scripts developed by the author are used to analyze a genome assembly of Forc isolate Forc016. The subdirectory subtelomere/pub/ contains the source and executable code of those programs. See the README and z.cmd files in each leaf subdirectory for more information</p>
Data used in Knowledge Transfer Research for Drone Navigation
<p>Data used in Knowledge Transfer Research for Drone Navigation.</p>
Pervasive hydrous carbonatitic liquids mediate transfer of carbon from the slab to the subarc mantle
<p>Table S1:Compositions of starting materials and global subducting sediments; Table S2: Experimental run conditions and phase assemblage; Table S3-12:Electron microprobe analyses of experimental products</p>
Pervasive hydrous carbonatitic liquids mediate transfer of carbon from the slab to the subarc mantle
<p>File Name: Supplementary table 1</p> <p>Description: Compositions of starting materials and global subducting sediments</p> <p>File Name: Supplementary table 2</p> <p>Description: Experimental run conditions and phase assemblage</p> <p>File Name: Supplementary Data 1<br> Description: Electron microprobe analyses of silicate melt and carbonated silicate melt</p> <p>File Name: Supplementary Data 2<br> Description: Electron microprobe analyses of quenched carbonate</p> <p>File Name: Supplementary Data 3<br> Description: Electron microprobe analyses of equilibrium carbonates</p> <p>File Name: Supplementary Data 4<br> Description: Electron microprobe analyses of glass spheres</p> <p>File Name: Supplementary Data 5<br> Description: Electron microprobe analyses of bulk compositions of quenched liquids</p> <p>File Name: Supplementary Data 6<br> Description: Electron microprobe analyses of garnet</p> <p>File Name: Supplementary Data 7<br> Description: Electron microprobe analyses of clinopyroxene</p> <p>File Name: Supplementary Data 8<br> Description: Electron microprobe analyses of phengite</p> <p>File Name: Supplementary Data 9<br> Description: Electron microprobe analyses of kyanite</p> <p><br> File Name: Supplementary Data 10<br> Description: Electron microprobe analyses of magnetite</p>
Pervasive hydrous carbonatitic liquids mediate transfer of carbon from the slab to the subarc mantle
<p>File Name: Supplementary Data 1<br> Description: Electron microprobe analyses of silicate melt and carbonated silicate melt</p> <p>File Name: Supplementary Data 2<br> Description: Electron microprobe analyses of quenched carbonate</p> <p>File Name: Supplementary Data 3<br> Description: Electron microprobe analyses of equilibrium carbonates</p> <p>File Name: Supplementary Data 4<br> Description: Electron microprobe analyses of glass spheres</p> <p>File Name: Supplementary Data 5<br> Description: Electron microprobe analyses of bulk compositions of quenched liquids</p> <p>File Name: Supplementary Data 6<br> Description: Electron microprobe analyses of garnet</p> <p>File Name: Supplementary Data 7<br> Description: Electron microprobe analyses of clinopyroxene</p> <p>File Name: Supplementary Data 8<br> Description: Electron microprobe analyses of phengite</p> <p>File Name: Supplementary Data 9<br> Description: Electron microprobe analyses of kyanite</p> <p><br> File Name: Supplementary Data 10<br> Description: Electron microprobe analyses of magnetite</p>
FIGURE 9 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 9. Third-instar male nymph of Neogreenia osmanthus (Yang & Hu): A. Antenna; B. Dorsum of antennal segments I and II; C. Foreleg; D. Capitate seta; E. Claw; F. Thoracic spiracle; G. Sieve-like multilocular disc pore; H. Small tube-like spiracle; I. Posterior 3 pairs abdominal spiracles; J. Anal ring; K. Oblong structure; L. Large simple pore; M. Small simple pores; N. Multilocular disc pores; O. Hair-like seta; P. Short spine.
FIGURE 4 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 4. Adult male Neogreenia osmanthus (Yang & Hu): A. Venter; B. Dorsum; C. Fore wing. Each scale bar = 1 mm.
FIGURE 8 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 8. Third-instar female nymph Neogreenia osmanthus (Yang & Hu): A. Antenna; B. Clypeolabral shield and labium; C. Labium; D. Long hair-like seta; E. Thoracic spiracle; F. Sieve-like multilocular disc pore; G. Anterior 6 pairs abdominal spiracles; H. Small tube-like abdominal spiracle; I. Anal ring; J. Cuticular pouch; K. Simple pore; L. Multilocular disc pores; M. Hair-like seta; N. Short spine.
FIGURE 3 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 3. Adult female Neogreenia osmanthus (Yang & Hu): A. Antenna; B. Dorsum of antennal segments I and II; C. Hair-like seta; D. Sensory seta; E. Clypeolabral shield and labium; F. Foreleg; G. Capitate seta; H. Claw; I. Thoracic spiracle; J. Abdominal spiracle; K. Tube-like abdominal spiracle; L. Anal ring; M. Vulva; N. Cicatrix; O. Dermal micro-sculptures; P. Cuticular pouch; Q. Large simple pore; R. Small simple pore; S. Small multilocular disc pores; T. Large multilocular disc pores; U. Sieve-like multilocular disc pore; V. Spine.
FIGURE 1 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 1. Neogreenia osmanthus (Yang & Hu): A. Adult female; B. First-instar nymph, scale bar = 0.5 mm; C. Live thirdinstar male nymph; D. Pupa; E. Second- and third-instar nymphs under the bark, red arrows indicate second-instar nymphs and blue arrows indicate third-instar nymphs.
FIGURE 2 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 2. Adult female Neogreenia osmanthus (Yang & Hu): A. Dorsum; B. Venter. Each scale bar = 1 mm.
FIGURE 6 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 6. First-instar nymph Neogreenia osmanthus (Yang & Hu): A. Antenna; B. Dorsum of antennal segments I and II; C. Clypeolabral shield and labium; D. Labium; E. Foreleg; F. Claw; G. Thoracic spiracle; H. Abdominal spiracle; I. Cicatrices; J. Trilocular pores; K. Small multilocular disc pores; L. Bilocular pores; M. Large multilocular disc pores; N. Spine.
FIGURE 5 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 5. Adult male Neogreenia osmanthus (Yang & Hu): A. Setae; B. Loculate pores; C. Hind leg; D. Bifurcated setae; E. Tubular duct; F. Simple pore; G. Penial sheath and aedeagus; H. Dorsum of head; I. Venter of head; J. Satellite seta; K.Contiguous or interrupted post-tergite; L. Prosternum; M. Dorsal view of mesothorax; N. Ventral view of mesothorax; O. Hind wing.
FIGURE 10 in Morphology of all the developmental stages of Neogreenia osmanthus (Yang & Hu) (Hemiptera: Coccomorpha), and transfer of the genera Neogreenia MacGillivray and Jansenus Foldi to the family Qinococcidae
FIGURE 10. Male pupa of Neogreenia osmanthus (Yang & Hu): A. Thoracic spiracle; B. Abdominal spiracle; C. Rudiments of the genital segment; D. Multilocular disc pores.
Data for: Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome
<p><strong>Background:</strong> Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes.</p> <p><strong>Results:</strong> Here we studied the tempo and pattern of mitochondrial gene loss/transfer in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, <em>Ginkgo</em> and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants.</p> <p><strong>Conclusions: </strong>This study reveals a complete evolutionary scenario for mitochondrial genes of gymnosperms and the factors responsible for mitochondrial gene content variation in land plants.</p>
Chemically Transferable Generative Backmapping of Coarse-Grained Proteins
<p>Training, test datasets of the paper "Chemically Transferable Generative Backmapping of Coarse-Grained Proteins".</p> <p>The PDB files are downloaded from PED [1] and processed according to the instruction described in our paper [link]. </p> <p> </p> <p>[1] <strong>PED in 2021: a major update of the Protein Ensemble Database for intrinsically disordered proteins</strong></p> <p>Lazar, T., Martı́nez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L.B., Iserte, J.A., Méndez, N.A., Garrone, N.A., Saldaño, T.E., Marchetti, J., Velez Rueda, A.J., Bernadó, P., Blackledge, M., Cordeiro, T.N., Fagerberg, E., Forman-Kay, J.D., Fornasari, M.S., Gibson, T.J., Gomes, G-N.W., Gradinaru, C.C., Head-Gordon, T., Ringkjøbing Jensen, M., Lemke, E.A., Longhi, S., Marino-Buslje, C., Minervini, G., Mittag, T., Monzon, A.M., Pappu, R.V., Parisi, G., Ricard-Blum, S., Ruff, K.M., Salladini, E., Skepö, M., Svergun, D., Vallet, S.D., Varadi, M., Tompa, P., Tosatto, S.C.E., Piovesan D.</p> <p>(2021) <em>Nucleic Acids Research</em>, Database Issue, <a href="https://www.ncbi.nlm.nih.gov/pubmed/33305318"><strong>PubMed </strong><em>link</em></a>, <a href="https://academic.oup.com/nar/article/49/D1/D404/6030232"><strong>NAR </strong><em>link</em></a></p> <p> </p> <p> </p>
FIGURE 5. Dawydoffia kalonota Attems, 1953 in Integrative redescription of the sucking millipede genus Dawydoffia Attems, 1953 with a description of a new species and a transfer to the family Hirudisomatidae (Diplopoda, Polyzoniida)
FIGURE 5. Dawydoffia kalonota Attems, 1953, paralectotypes from Chapa, micro-preparations: A & B: (NHMW MY10336) types illustrated by Attems: A. First pair of legs. B. Posterior rings and anal valves of syntype. C, D and G: Anterior and posterior gonopods (recent micro-preparation, NHMW MY10334): C. Posterior view. D. Anterior view. G. Right posterior gonopod details. E–F: Gonopods of the type illustrated by Attems (NHMW MY2259): E. Anterior gonopod, showing 6 podomeres. F. Posterior gonopod. Abbreviations: aG = anterior gonopod; pG = posterior gonopod.
FIGURE 9. Dawydoffia siphonocryptida n in Integrative redescription of the sucking millipede genus Dawydoffia Attems, 1953 with a description of a new species and a transfer to the family Hirudisomatidae (Diplopoda, Polyzoniida)
FIGURE 9. Dawydoffia siphonocryptida n. sp., male holotype (SMF), scanning electron micrographs. A. Sternite 1 and 2, coxa of leg pair 2 with gonapophysis or pseudopenis, ventral view. Arrows point to sternal protuberances. B. Left gonapophysis or pseudopenis, ventral view. C. Anterior and posterior gonopod, lateral view. D. Gonopods, anterior view. E. Anterior and posterior gonopod, posterior view. F. Detail of podomere 5, posterior gonopod. Abbreviations: aG = anterior gonopod; aG-P = process on anterior gonopod; cp = coxal pouch; Cx = coxa; H = head; LP –= lateral process of podomere 6 of anterior gonopod; MP = mesal process of podomere 6 of anterior gonopod; pG = posterior gonopod; PP = pseudopenis; St = sternite; St-p = sternite process.
FIGURE 1 in Integrative redescription of the sucking millipede genus Dawydoffia Attems, 1953 with a description of a new species and a transfer to the family Hirudisomatidae (Diplopoda, Polyzoniida)
FIGURE 1. Locality and habitat of Dawydoffia kalonota Attems, 1953 and Dawydoffia siphonocryptida n. sp. in South East Asia. A. Locality of D. kalonota (yellow square) and localities of D. siphonocryptida n. sp. (red circle). B. Detail of map as indicated in A. C & D. Habitat of D. siphonocryptida n. sp., a forest with a creek in Luang Prabang Province (Laos), along Nam Khan River (photographs by P. Jäger). For D. kalonota approximate localities have been indicated based on Attems (1953) and Enghoff et al. (2004).
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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.