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112 results for “MIP”
WCRP Baseline Variables - MIP Prioritisation raw data
<p>Supplementary material for the publication: Juckes et al. (2024) Baseline Climate Variables for Earth System Modelling, accepted in GMD. Preprint: https://doi.org/10.5194/egusphere-2024-2363. </p> <p>This data summarises the WCRP Baseline Variables list, and includes the raw data from throughout the prioritisation process.</p>
ISS Mouse brain embryo - MIPPED images , all rounds all channels
<p>Repository containing the stitched, mipped and aligned images of all the cycles and channels used in the Mouse embryo ISS characterization from La Manno et al 2020 The repository contains:</p> <ul> <li>Stitched aligned and mipped images of all round and cycles for different samples (2A,2D, 6B,10B)</li> <li>A codebook with the code of every expected gene detecoded is included</li> <li>A preliminary decoding of the 4 samples included in the folder "decoded_spots"</li> <li>Information about channel order in a .txt</li> </ul>
Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics
<p>The original data used in the article: Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics</p> <p>Delineating the spatial multiomics landscape will pave the way to understanding the molecular basis of physiology and pathology. However, current spatial omics technology development is still in its infancy. Here, we developed a high-throughput targeted in situ sequencing strategy, multiomics in situ pairwise sequencing (MiP-Seq), to efficiently decipher multiplexed DNAs, RNAs, proteins, and small biomolecules at subcellular resolution. MiP-Seq simultaneously sequenced the dual barcode base of padlock probes, dramatically increasing the detection capacity to 10N by N rounds of sequencing. We delineated spatial gene profiles in the hypothalamus using MiP-Seq. Moreover, MiP-Seq was unitized to detect tumor gene mutations and allele-specific expression of parental genes and to differentiate sites with and without the m6A RNA modification at specific sites. MiP-Seq was combined with in vivo Ca2+ imaging and Raman imaging to obtain a spatial multiomics atlas correlated to neuronal activity and cellular biochemical fingerprints. Importantly, we proposed a “signal dilution strategy” to resolve the crowded signals that challenge the applicability of in situ sequencing. Together, our method improves spatial multiomics and precision diagnostics, and facilitates analyzing cell function in connection with gene profiles.</p>
EOL Microbes Patch (MIP) - active: EOL Microbes Patch 2023
<p>Bacteria, viruses & microbial Eukaryotes to complement NCBI & WoRMS coverage. Hierarchy follows NCBI & Adl et al. 2019.</p> <h3>References </h3> <p>Adam, Rodney D. 2017. Diplomonadida. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–28. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_1-1">https://doi.org/10.1007/978-3-319-32669-6_1-1</a></p> <p>Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. <a href="https://doi.org/10.1111/jeu.12691">https://doi.org/10.1111/jeu.12691 </a></p> <p>Azevedo, Carlos, and P. M. Hine. 2017. Haplosporidia. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–29. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_16-1">https://doi.org/10.1007/978-3-319-32669-6_16-1</a></p> <p>Baldauf, Sandra L., and Joan E. Strassmann. 2017. Dictyostelia. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–45. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_14-1">https://doi.org/10.1007/978-3-319-32669-6_14-1</a></p> <p>Beakes, Gordon W., and Marco Thines. Hyphochytriomycota and Oomycota. 2016. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–71. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_26-1">https://doi.org/10.1007/978-3-319-32669-6_26-1</a></p> <p>Bennett, R. M., D. Honda, G. W. Beakes, and M. Thines. 2017. Labyrinthulomycota. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–36. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_25-1">https://doi.org/10.1007/978-3-319-32669-6_25-1</a></p> <p>Boltovskoy, D., ed., 1999. South Atlantic zooplankton. Backhuys Publishers, Leiden. Boltovskoy, Demetrio, O. Roger Anderson, and Nancy M. Correa. 2017. Radiolaria and Phaeodaria. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–33. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_19-2">https://doi.org/10.1007/978-3-319-32669-6_19-2</a></p> <p>Brown, Matthew W., Jeffrey D. Silberman, and Frederick W. Spiegel. 2010. A Contemporary Evaluation of the Acrasids (Acrasidae, Heterolobosea, Excavata). European Journal of Protistology 48(2):103–23. <a href="https://doi.org/10.1016/j.ejop.2011.10.001">https://doi.org/10.1016/j.ejop.2011.10.001 </a></p> <p>Bulman, Simon, and Sigrid Neuhauser. 2017. Phytomyxea. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–21. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_24-1">https://doi.org/10.1007/978-3-319-32669-6_24-1</a></p> <p>Burki, F., 2014. The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harb Perspect Biol 6, a016147. <a href="https://doi.org/10.1101/cshperspect.a016147">https://doi.org/10.1101/cshperspect.a016147 </a></p> <p>Burki Fabien, Kaplan Maia, Tikhonenkov Denis V., Zlatogursky Vasily, Minh Bui Quang, Radaykina Liudmila V., Smirnov Alexey, Mylnikov Alexander P., Keeling Patrick J., 2016. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proceedings of the Royal Society B: Biological Sciences 283, 20152802. <a href="https://doi.org/10.1098/rspb.2015.2802">https://doi.org/10.1098/rspb.2015.2802 </a></p> <p>Burreson, Eugene M., and Susan E. Ford. 2004. A Review of Recent Information on the Haplosporidia, with Special Reference to Haplosporidium Nelsoni (MSX Disease). Aquatic Living Resources 17(4):499–517. <a href="https://doi.org/10.1051/alr:2004056">https://doi.org/10.1051/alr:2004056</a></p> <p>Cali, Ann, James J. Becnel, and Peter M. Takvorian. 2017. Microsporidia. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–60. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_27-1">https://doi.org/10.1007/978-3-319-32669-6_27-1</a></p> <p>Caragnano, A., Foetisch, A., Maneveldt, G.W., Millet, L., Liu, L.-C., Lin, S.-M., Rodondi, G., Payri, C.E., 2018. Revision of Corallinaceae (Corallinales, Rhodophyta): recognizing Dawsoniolithon gen. nov., Parvicellularium gen. nov. and Chamberlainoideae subfam. nov. containing Chamberlainium gen. nov. and Pneophyllum. Journal of Phycology 54, 391–409. <a href="https://doi.org/10.1111/jpy.12644">https://doi.org/10.1111/jpy.12644 </a></p> <p>Cavalier-Smith, T., 2016. Higher classification and phylogeny of Euglenozoa. European Journal of Protistology 56, 250–276. <a href="https://doi.org/10.1016/j.ejop.2016.09.003">https://doi.org/10.1016/j.ejop.2016.09.003 </a></p> <p>Cavalier-Smith, T., Chao, E.E., 2010. Phylogeny and Evolution of Apusomonadida (Protozoa: Apusozoa): New Genera and Species. Protist 161, 549–576. <a href="https://doi.org/10.1016/j.protis.2010.04.002">https://doi.org/10.1016/j.protis.2010.04.002 </a></p> <p>Cavalier-Smith, T., Chao, E.E., Lewis, R., 2018. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. Protoplasma 255, 1517–1574. <a href="https://doi.org/10.1007/s00709-018-1241-1">https://doi.org/10.1007/s00709-018-1241-1 </a></p> <p>Cavalier-Smith, T., Chao, E.E.-Y., 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J. Mol. Evol. 62, 388–420. <a href="https://doi.org/10.1007/s00239-004-0353-8">https://doi.org/10.1007/s00239-004-0353-8 </a></p> <p>Čepička, Ivan, Michael F. Dolan, and Gillian H. Gile. 2016. Parabasalia. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–44. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_9-1">https://doi.org/10.1007/978-3-319-32669-6_9-1</a></p> <p>Cook, Martha E., and Linda E. Graham. 2016. Chlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–20. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_36-1">https://doi.org/10.1007/978-3-319-32669-6_36-1</a></p> <p>Díaz-Tapia, P., Pasella, M.M., Verbruggen, H., Maggs, C.A., 2019. Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics. Molecular Phylogenetics and Evolution 137, 76–85. <a href="https://doi.org/10.1016/j.ympev.2019.04.022">https://doi.org/10.1016/j.ympev.2019.04.022 </a></p> <p>Eikrem, Wenche, Linda K Medlin, Jorijntje Henderiks, Sebastian Rokitta, Björn Rost, Ian Probert, Jahn Throndsen, and Bente Edvardsen. 2017. Haptophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–61. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_38-2">https://doi.org/10.1007/978-3-319-32669-6_38-2</a></p> <p>Eliáš, Marek, Raquel Amaral, Karen P. Fawley, Marvin W. Fawley, Yvonne Němcová, Jiří Neustupa, Pavel Přibyl, Lilia M. A. Santos, and Tereza Ševčíková. 2017. Eustigmatophyceae. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–39. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_39-1">https://doi.org/10.1007/978-3-319-32669-6_39-1</a></p> <p>Fang, Ling, Frederik Leliaert, Phil M. Novis, Zhenhua Zhang, Huan Zhu, Guoxiang Liu, David Penny, and Bojian Zhong. 2018. Improving Phylogenetic Inference of Core Chlorophyta Using Chloroplast Sequences with Strong Phylogenetic Signals and Heterogeneous Models. Molecular Phylogenetics and Evolution 127:248–55.<br> <a href="https://doi.org/10.1016/j.ympev.2018.06.006">https://doi.org/10.1016/j.ympev.2018.06.006</a></p> <p>Fang, Ling, Frederik Leliaert, Zhen-Hua Zhang, David Penny, and Bo-Jian Zhong. 2017. Evolution of the Chlorophyta: Insights from Chloroplast Phylogenomic Analyses. Journal of Systematics and Evolution 55(4):322–32. <a href="https://doi.org/10.1111/jse.12248">https://doi.org/10.1111/jse.12248</a></p> <p>Frank W. 1984. Non-Hemoparasitic Protozoans. In: Hoff G.L., Frye F.L., Jacobson E.R. (eds) Diseases of Amphibians and Reptiles. Springer, Boston, MA.<br> <a href="https://doi.org/10.1007/978-1-4615-9391-1_19">https://doi.org/10.1007/978-1-4615-9391-1_19 </a></p> <p>Fučíková, Karolina, Paul O Lewis, Suman Neupane, Kenneth G. Karol, and Louise A. Lewis. 2019. Order, Please! Uncertainty in the Ordinal-Level Classification of Chlorophyceae. PeerJ 7 e6899. <a href="https://doi.org/10.7717/peerj.6899">https://doi.org/10.7717/peerj.6899</a></p> <p>Gao, F., Warren, A., Zhang, Q., Gong, J., Miao, M., Sun, P., Xu, D., Huang, J., Yi, Z., Song, W., 2016. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata). Scientific Reports 6, 24874. <a href="https://doi.org/10.1038/srep24874">https://doi.org/10.1038/srep24874</a></p> <p>Gast, Rebecca J. 2017. Centrohelida and Other Heliozoan-Like Protists. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–17. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_28-1">https://doi.org/10.1007/978-3-319-32669-6_28-1</a></p> <p>Gibson, Wendy. 2016. Kinetoplastea. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–50. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_7-1">https://doi.org/10.1007/978-3-319-32669-6_7-1</a></p> <p>Gkelis, Spyros, Iordanis Ourailidis, Manthos Panou, and Nikos Pappas. 2016. Cyanobacteria of Greece: An Annotated Checklist. Biodiversity Data Journal 4: e10084. <a href="https://doi.org/10.3897/BDJ.4.e10084">https://doi.org/10.3897/BDJ.4.e10084</a></p> <p>Gomaa, F., Lahr, D.J.G., Todorov, M., Li, J., Lara, E., 2017. A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. Eur. J. Protistol. 59, 99–107. <a href="https://doi.org/10.1016/j.ejop.2017.03.005">https://doi.org/10.1016/j.ejop.2017.03.005 </a></p> <p>Gomez, F 2012. A checklist and classification of living dinoflagellates (Dinoflagellata, Alveolata). CICIMAR Oceanides 27:65–140. Gontcharov, A.A., 2008. Phylogeny and classification of Zygnematophyceae (Streptophyta): current state of affairs. Fottea 8, 87–104. <a href="https://doi.org/10.5507/fot.2008.004">https://doi.org/10.5507/fot.2008.004 </a></p> <p>Groves, John R., Demír Altiner, and Roberto Rettori. 2003. Origin and Early Evolutionary Radiation of the Order Lagenida (Foraminifera). Journal of Paleontology 77(5): 831–43.</p> <p>Guiry, M.D. & Guiry, G.M. 2020. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. <a href="https://www.algaebase.org">https://www.algaebase.org </a></p> <p>Hall, John D., and Richard McCourt. 2017. Zygnematophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–29. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_41-2">https://doi.org/10.1007/978-3-319-32669-6_41-2</a></p> <p>Hampl, Vladimir. 2016. Preaxostyla. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–36. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_8-1">https://doi.org/10.1007/978-3-319-32669-6_8-1</a></p> <p>Hauer, T. & Komárek, J. 2020: CyanoDB 2.0 - On-line database of cyanobacterial genera. - World-wide electronic publication, Univ. of South Bohemia & Inst. of Botany AS CR, <a href="http://www.cyanodb.cz">http://www.cyanodb.cz</a></p> <p>Heiss, Aaron A., Matthew W. Brown, and Alastair G. B. Simpson. 2016. Apusomonadida. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–27. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_15-1">https://doi.org/10.1007/978-3-319-32669-6_15-1</a></p> <p>Hoef-Emden, Kerstin, and John M. Archibald. 2016. Cryptophyta (Cryptomonads). In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–41. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_35-1">https://doi.org/10.1007/978-3-319-32669-6_35-1</a></p> <p>Horiguchi, Takeo. 2016. Raphidophyceae (Raphidophyta). In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–26. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_37-1">https://doi.org/10.1007/978-3-319-32669-6_37-1</a></p> <p>Jeon, Boo Seong, Seung Won Nam, Sunju Kim, Myung Gil Park, Boo Seong Jeon, Seung Won Nam, Sunju Kim, and Myung Gil Park. 2018. Revisiting the Parvilucifera Infectans / P. Sinerae (Alveolata, Perkinsozoa) Species Complex, Two Parasitoids of Dinoflagellates. Algae 33(1):1–19. <a href="https://doi.org/10.4490/algae.2018.33.3.6">https://doi.org/10.4490/algae.2018.33.3.6</a></p> <p>Karpov, S.A., López-García, P., Mamkaeva, M.A., Klimov, V.I., Vishnyakov, A.E., Tcvetkova, V.S., Moreira, D., 2018. The Chytrid-like Parasites of Algae Amoeboradix gromovi gen. et sp. nov. and Sanchytrium tribonematis Belong to a New Fungal Lineage. Protist 169, 122–140. <a href="https://doi.org/10.1016/j.protis.2017.11.002">https://doi.org/10.1016/j.protis.2017.11.002 </a></p> <p>Karpov, S.A., Vishnyakov, A.E., Moreira, D., López‐García, P., 2019. The Ultrastructure of Sanchytrium tribonematis (Sanchytriaceae, Fungi incertae sedis) Confirms its Close Relationship to Amoeboradix. Journal of Eukaryotic Microbiology 66, 892–898. <a href="https://doi.org/10.1111/jeu.12740">https://doi.org/10.1111/jeu.12740 </a></p> <p>Kawai, Hiroshi, and Eric C. Henry. 2016. Phaeophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–38. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_31-1">https://doi.org/10.1007/978-3-319-32669-6_31-1</a></p> <p>Keeling, Patrick J. 2016. Chlorarachniophytes. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–17. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_34-1">https://doi.org/10.1007/978-3-319-32669-6_34-1</a></p> <p>Komárek, J., Kaštovský, J., Mareš, J., & Johansen, J. R. 2014. Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) 2014, using a polyphasic approach. Preslia, 86(4):295-335.</p> <p>Kosakyan, A., Gomaa, F., Lara, E., Lahr, D.J.G., 2016. Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae. European Journal of Protistology, Special issue on Testate Amoebae – a tribute to Ralf Meisterfeld 55, 105–117. <a href="https://doi.org/10.1016/j.ejop.2016.02.001">https://doi.org/10.1016/j.ejop.2016.02.001 </a></p> <p>Kostka, Martin. 2016. Opalinata. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–23. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_4-1">https://doi.org/10.1007/978-3-319-32669-6_4-1</a></p> <p>Kristiansen, Jørgen, and Pavel Škaloud. 2016. Chrysophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–38. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_43-1">https://doi.org/10.1007/978-3-319-32669-6_43-1</a></p> <p>Kulda, Jaroslav, Eva Nohýnková, and Ivan Čepička. 2017. Retortamonadida (with Notes on Carpediemonas-Like Organisms and Caviomonadidae). In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–32. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_3-1">https://doi.org/10.1007/978-3-319-32669-6_3-1</a></p> <p>Lado, C., Eliasson, U., 2017. Chapter 7 - Taxonomy and Systematics: Current Knowledge and Approaches on the Taxonomic Treatment of Myxomycetes, in: Stephenson, S.L., Rojas, C. (Eds.), Myxomycetes. Academic Press, pp. 205–251. <a href="https://doi.org/10.1016/B978-0-12-805089-7.00007-X">https://doi.org/10.1016/B978-0-12-805089-7.00007-X </a></p> <p>Leander, Brian S., Gordon Lax, Anna Karnkowska, and Alastair G. B. Simpson. 2017. Euglenida. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–42. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_13-1">https://doi.org/10.1007/978-3-319-32669-6_13-1</a></p> <p>Lemieux, Claude, Antony T. Vincent, Aurélie Labarre, Christian Otis, and Monique Turmel. 2015. Chloroplast Phylogenomic Analysis of Chlorophyte Green Algae Identifies a Novel Lineage Sister to the Sphaeropleales (Chlorophyceae). BMC Evolutionary Biology 15(1): 264. <a href="https://doi.org/10.1186/s12862-015-0544-5">https://doi.org/10.1186/s12862-015-0544-5</a></p> <p>Lester, R. J. G., and P. M. Hine. 2017. Paramyxida. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–18. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_21-1">https://doi.org/10.1007/978-3-319-32669-6_21-1</a></p> <p>Letcher, Peter M., and Martha J. Powell. 2018. A Taxonomic Summary and Revision of Rozella (Cryptomycota). IMA Fungus 9:383–99. <a href="https://doi.org/10.5598/imafungus.2018.09.02.09">https://doi.org/10.5598/imafungus.2018.09.02.09</a></p> <p>Letcher, Peter M., and Martha J. Powell. 2019. A Taxonomic Summary of Aphelidiaceae. IMA Fungus 10(1):4. <a href="https://doi.org/10.1186/s43008-019-0005-7">https://doi.org/10.1186/s43008-019-0005-7</a></p> <p>Lynn, Denis. 2008. The Ciliated Protozoa: Characterization, Classification, and Guide to the Literature. 3rd ed. Springer Netherlands. <a href="https://doi.org/10.1007/978-1-4020-8239-9">https://doi.org/10.1007/978-1-4020-8239-9</a></p> <p>Lynn, Denis H. 2016. Ciliophora. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–52. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_23-1">https://doi.org/10.1007/978-3-319-32669-6_23-1</a></p> <p>Maistro, Silvia, Paul Broady, Carlo Andreoli, and Enrico Negrisolo. 2016. Xanthophyceae. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–28. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_30-1">https://doi.org/10.1007/978-3-319-32669-6_30-1</a></p> <p>Mandal, F. B., N. C. Nandi, and A. K. Mandal. 1993. Catalouge of the Protozoans occurring in Reptiles from India. Records of the Zoological Survey of India Occasional Paper 148:1-36.</p> <p>Mann, David G., Richard M. Crawford, and Frank E. Round. 2016. Bacillariophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–62. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_29-1">https://doi.org/10.1007/978-3-319-32669-6_29-1</a></p> <p>McCourt, Richard M., Kenneth G. Karol, John D. Hall, Michelle T. Casanova, and Michael C. Grant. 2017. Charophyceae (Charales). In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–19. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_40-2">https://doi.org/10.1007/978-3-319-32669-6_40-2</a></p> <p>Meriluoto, J., Spoof L., Codd, G. A., eds. 2017. Handbook of Cyanobacterial Monitoring and Cyanotoxin Analysis, First Edition. John Wiley & Sons, Ltd. Novozhilov, Y.K., van Hooff, H., Jagers, M., 2014. Trichioides iridescens, a new genus and new species (incertae sedis in Myxomycetes). Mycol Progress 14, 1018. <a href="https://doi.org/10.1007/s11557-014-1018-7">https://doi.org/10.1007/s11557-014-1018-7 </a></p> <p>Okamoto, Noriko, Ryan M. R. Gawryluk, Javier del Campo, Jürgen F. H. Strassert, Julius Lukeš, Thomas A. Richards, Alexandra Z. Worden, Alyson E. Santoro, and Patrick J. Keeling. 2019. A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. Fam. and a Type Species, Eupelagonema Oceanica n. Gen. & Sp. Journal of Eukaryotic Microbiology 66(3):519–24. <a href="https://doi.org/10.1111/jeu.12679">https://doi.org/10.1111/jeu.12679</a></p> <p>Pánek, Tomáš, Alastair G. B. Simpson, Matthew W. Brown, and Betsey Dexter Dyer. 2017. Heterolobosea. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–42. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_10-1">https://doi.org/10.1007/978-3-319-32669-6_10-1</a></p> <p>Parke, M. & Dixon, P. S. 1976. Check-list of British marine algae - third revision. Journal of the Marine Biological Association of the United Kingdom 56:527-594.</p> <p>Powell, Martha J. 2016. Blastocladiomycota. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–25. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_17-1">https://doi.org/10.1007/978-3-319-32669-6_17-1</a></p> <p>Powell, Martha J. 2016. Chytridiomycota. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–36. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_18-1">https://doi.org/10.1007/978-3-319-32669-6_18-1</a></p> <p>Price, Dana C., Jürgen M. Steiner, Hwan Su Yoon, Debashish Bhattacharya, and Wolfgang Löffelhardt. 2017. Glaucophyta. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–65. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_42-1">https://doi.org/10.1007/978-3-319-32669-6_42-1</a></p> <p>Richter, Daniel J., and Frank Nitsche. 2016. Choanoflagellatea. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–19. 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In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–32. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_6-1">https://doi.org/10.1007/978-3-319-32669-6_6-1</a></p> <p>Simpson, Alastair G. B., Claudio H. Slamovits, and John M. Archibald. 2017. Protist Diversity and Eukaryote Phylogeny. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–21. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_45-1">https://doi.org/10.1007/978-3-319-32669-6_45-1</a></p> <p>Spiegel, Frederick W., Lora L. Shadwick, George G. Ndiritu, Matthew W. Brown, Maria Aguilar, and John D. Shadwick. 2017. Protosteloid Amoebae (Protosteliida, Protosporangiida, Cavosteliida, Schizoplasmodiida, Fractoviteliida, and Sporocarpic Members of Vannellida, Centramoebida, and Pellitida). In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–38. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-32669-6_12-1">https://doi.org/10.1007/978-3-319-32669-6_12-1</a></p> <p>Stephenson, Steven L., and Martin Schnittler. 2017. Myxomycetes. In Handbook of the Protists, edited by John M. Archibald, Alastair G.B. Simpson, Claudio H. Slamovits, Lynn Margulis, Michael Melkonian, David J. Chapman, and John O. Corliss, 1–27. 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MiP-Seq 100 genes data
<p>Map out the spatial transcriptome of 100 genes in nucleus of the horizontal limb of the diagonal band (HDB) in hypothalamus by MiP-Seq.</p> <p> </p> <p>lefthyp.h5 - Raw image storage, can read and process using Innereye package(https://github.com/GangCaoLab/InnerEye).</p>
Fossil Fuel CO₂ Emissions for the OCO2 Model Intercomparison Project (MIP)
<p>These are fossil CO<sub>2</sub> fluxes updated through August 2024 for atmospheric CO<sub>2</sub> modeling. They were constructed primarily to be used for the OCO2 Model Intercomparison Project (MIP).</p> <ul> <li>For 2000-2022, they're based on <a href="https://db.cger.nies.go.jp/dataset/ODIAC/DL_odiac2023.html">ODIAC 2023</a>, which in turn uses BP's energy use statistics for 2021 and 2022.</li> <li>ODIAC monthly emissions have been disaggregated to hourly using the TIMES emission factors for day of week and time of day (<a href="https://urldefense.us/v3/__https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2012JD018196__;!!PvBDto6Hs4WbVuu7!YsQP_T-Vf3Fv83toql-90HY0NO5e92fR0D9kAi10tTzUd0Ugum9d3CTUMBp22qA0M-vYoU_fvd4$">https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2012JD018196</a>).</li> <li>For 2023 onwards, ODIAC's 2022 emissions have been scaled by the ratio of that month to 2022 emissions reported by <a href="https://www.nature.com/articles/s41597-020-00708-7">Carbon Monitor</a>, downloaded on October 15, 2024 from <a href="https://carbonmonitor.org">https://carbonmonitor.org/</a>. <ul> <li>ODIAC does not have sectoral decomposition to the degree provided by Carbon Monitor, so total ODIAC emissions for each region have been scaled by the total emission change between 2022 and each extended year reported by Carbon Monitor, i.e., power, ground transport, etc. have <strong>not</strong> been separately scaled.</li> <li>Carbon Monitor data are daily, but ODIAC emissions are monthly. So Carbon Monitor data have been aggregated to monthly totals before deriving scaling factors between 2022 and the extended years.</li> <li>Carbon Monitor reports international aviation emissions by country of origin, while ODIAC reports aviation emissions on a grid. Since there is no way to derive the points of emission for Carbon Monitor aviation emissions , all Carbon Monitor international aviation was aggregated to create a single number for each month, then that number was used to scale ODIAC's bunker fuel for each month in 2023-2024.</li> <li>CarbonMonitor data used for deriving 2023 and later emissions are now included in this dataset for convenience as netcdf files (converted from original CSV files).</li> </ul> </li> <li>Hourly global totals are given in the files as a check, in case you want to verify your units and file reading.</li> </ul> <p>These files can be downloaded from the browser, or from the command line following guides such as <a href="https://ict.ipbes.net/ipbes-ict-guide/data-and-knowledge-management/technical-guidelines/zenodo#b.-programmatically-using-r" target="_blank" rel="noopener">this</a>.</p>
Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear
<p>Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear (A-1) compared with control (A-2) mouse ear. (B) PET/CT images demonstrate preferential tumor (MCF-7) accumulation of 39, compared with longer blood circulation and higher non-specific binding of 41 at 1 hour post-injection. (C) Structures of the tracers used in the preceding panels are shown.</p>
SNDlib-MIPs: A new set of homogeneous MILP instances
<p>We constructed 289 MILP instances based on the Survivable Network Design Library (SNDLib) <a href="http://sndlib.zib.de/home.action">http://sndlib.zib.de/home.action</a> and the models presented within. Our models differ from the formulations provided in that SOS constraints are used in place of big-M constraints, a set of edge disjoint paths are used in place of all possible paths, pre-installed capacity is only available if links are included, and in the bidirectional case capacities are the sum of both capacities instead of the maximum. The models were constructed using SCIP 8.0.3, with the code available at <a href="https://github.com/Opt-Mucca/branching-via-cut-selection">https://github.com/Opt-Mucca/branching-via-cut-selection</a>. Please see the attached PDF for a complete model description.</p>
A Phase 2 Study With MIP-1404 in Men With High-Risk PC Scheduled for RP and EPLND Compared to Histopathology
ClinicalTrials.gov study NCT01667536. IPD Sharing: Not stated. Countries: 8. Publications: 18.
Application of regional meteorology and air quality models based on MIPS and LoongArch CPU Platform
<p>bcfile.zip: the clean boundary condition files.</p> <p>emisfile.zip: the emission files.</p> <p>icfile.zip: the clean initial condition files.</p> <p>tuvfile.zip and o3mapfile.zip: the photolysis files.</p> <p>outputfile.zip: the computation results outputted by CAMx model for MIPS and X86 platforms.</p> <p>wrfcamx.zip: meteorological files.</p> <p>outputfile_LoongArch_platform.tar.gz: the computation results outputted by CAMx model for LoongArch platforms.</p> <p>bin_executable_on_LoongArch_platform.tar.gz: The executable files of CAMx model which can run stably on LoongArch platform, including noMPI, MPICH and OpenMP version.</p> <p>bin_executable_on_MIPS_platform.tar.gz: The executable files of CAMx model which can run stably on MIPS platform, including noMPI, MPICH and OpenMP version</p>
ETIN-MIP (Extra-Tropical Interaction Model Intercomparison Project) data
<p>This is long term mean atmospheric data of ETIN-MIP (Extra-Tropical Interaction Model Intercomparison Project)</p> <p>Detail descriptions about the experiments and preliminary results would be published in Kang et al., 2019 (BAMS, in preparation)</p> <p> </p> <p>Data description</p> <p>CTL : 31-150 year mean<br> NEXT : 101-150 year mean<br> SEXT : 101-150 year mean<br> STRO : 101-150 year mean<br> For MIROC model, STRO experiment does not exist<br> For NORESM model, NEXT experiment is not available</p> <p> </p> <p>Full data is accessible through FTP sever with personal contact<br> Please send e-mail if you want further data or have any question about the data<br> E-mail adress : hanjunkim0617@gmail.com</p>
Online accompaniment to MIP Relaxations in Factorable Programming
<p>This dataset contains polynomial optimization instances and sample formulations used in a paper entitled <em>MIP Relaxations in Factorable Programming</em> by Taotao He and Mohit Tawarmalani.</p> <p>Nonlinear models are implemented using <a href="http://jump.dev/JuMP.jl/stable/">JuMP</a>. JuMP models can be created from <a href="https://en.wikipedia.org/wiki/Nl_(format)">AMPL's NL</a> files using <a href="https://jump.dev/JuMP.jl/stable/api/JuMP/#JuMP.read_from_file"><code>read_from_file</code></a>. </p> <p>Sample formulations of MIP and CRMIP used in the paper are included in .rtf files. </p> <p> </p> <p> </p>
Microbiome in Immunotherapy naïve NSCLC Patients Receiving PD-1/L1 Blockade (MIP_NSCLC)
ClinicalTrials.gov study NCT04636775. IPD Sharing: NO. Countries: 1. Publications: 2.
A Phase 1 Pilot Study of 99mTc-MIP-1404 SPECT/CT Imaging to Histology in Men With Prostate Cancer
ClinicalTrials.gov study NCT01615406. IPD Sharing: Not stated. Countries: 1. Publications: 16.
MIP Versus PCNL for Kidney Stone Disease
ClinicalTrials.gov study NCT04767919. IPD Sharing: NO. Countries: 2. Publications: 25.
Study to Evaluate 99mTc-MIP-1404 SPECT/CT Imaging in Men With Biopsy Proven Low-Grade Prostate Cancer
ClinicalTrials.gov study NCT02615067. IPD Sharing: UNDECIDED. Countries: 2. Publications: 3.
99mTc-MIP-1404 for Imaging Prostate Cancer: Phase I Clinical Study to Assess the Image Quality of a Simplified Kit Formulation Compared to a Multi-step Preparation of 99mTc-MIP-1404
ClinicalTrials.gov study NCT01654874. IPD Sharing: Not stated. Countries: 1. Publications: 14.
Use of an Experimental Radiopharmaceutical (131I-MIP-1095) in Men With Metastatic Castration-Resistant Prostate Cancer (mCRPC)
ClinicalTrials.gov study NCT03030885. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pilot Study of 99mTc-MIP-1404 SPECT/CT Imaging in Men With Prostate Cancer Undergoing Prostatectomy and/or Pelvic Lymph Node Dissection
ClinicalTrials.gov study NCT01572701. IPD Sharing: Not stated. Countries: 1. Publications: 13.
Red ceramic brick from Vale de Gândara – Mercury Intrusion Porosimetry (MIP)
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ScienceDex guides
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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.