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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sreekar, Rachakonda; Koh, Lian Pin; Lamba, Aakash; Mammides, Christos; +3 Authors

    The 'Table_PA_info' contains information on all 80 Protected Areas analyzed in this study. The 'Synth_plots' includes synthetic control model fits for all 80 Protected Areas analyzed in this study. The number displayed on the top-left of each plot corresponds to the WDPA-ID of the respective protected area. For further details on each protected area, please refer to the 'Table_PA_info' document. The 'placebos' document consists of placebo test plots. The number on the top-left of each plot indicates the WDPA-ID of the protected area. Refer to the 'Table_PA_info' document for more information on each protected area.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fishman, Lior; Modak, Avani; Nechooshtan, Gal; Razin, Tayla; +4 Authors

    During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response. This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Harnik, Yotam; Yakubovsky, Oran; Hoefflin, Rouven; Itzkovitz, Shalev;

    QuPath project containing all highly-multiplex images generated with the PhenoCycler Fusion platform from the publication “A spatial expression atlas of the adult human proximal small intestine” including nuclear segmentation masks and cell annotations. Whole slide scans of staining with Hyaluronic-Acid binding protein and H&E staining of the same sections are provided. Moreover, the following matrices needed to reproduce the main results are provided: "cells.csv": cells table including centroid coordinates and annotations "raw_mat.csv": protein expression matrix without pre-processing "norm_mat.csv": protein expression matrix after log2-transformation and per sample z-scoring

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 122, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 3. Circoniscus mendesi López-Orozco, Campos-Filho & Bichuette sp. nov., ♀, paratype (LES 0028768). A. Left mandible. B. Right mandible. C. Maxillula. D. Maxilla. E. Maxilliped, arrow illustrating the endite in caudal view. F. Uropod. Figure not to scale.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 128, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 7. Circoniscus xikrin López-Orozco, Campos-Filho & Carpio-Díaz sp. nov., ♂, holotype (LES 0028772). A. Pereopod 1, arrow illustrating the dactylus in rostral view. B. Pereopod 7. C. Genital papilla and pleopod 1. D. Pleopod 2. E. Pleopod 3 exopod. F. Pleopod 4 exopod. G. Pleopod 5 exopod. Figure not to scale.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 130, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 8. A. Circoniscus mendesi López-Orozco, Campos-Filho & Bichuette sp. nov., specimen from CAV-N1-0174. B. Parauapebas, Pará, in moist soil. C. Ctenorillo ferrarai Campos-Filho, Araujo & Taiti, 2014, specimen from CAV-SB-0049 (also known as Samuel II by local people). D. Canaã dos Carajás, Pará, in moist soil.

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 127, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 6. Circoniscus xikrin López-Orozco, Campos-Filho & Carpio-Díaz sp. nov., ♂, holotype (LES 0028772). A. Left mandible. B. Right mandible. C. Maxillula. D. Maxilla. E. Maxilliped, arrow illustrating the endite in caudal view. F. Uropod. Figure not to scale.

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 126, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 5. Circoniscus xikrin López-Orozco, Campos-Filho & Carpio-Díaz sp. nov., ♂, holotype (LES 0028772). A. Habitus, lateral view. B. Dorsal scale-seta. C. Cephalon, dorsal view. D. Cephalon, back view. E. Cephalon and pereonites 1 and 2, frontal view. F. Pereonite 1 and 2 epimera, ventral view. G. Pleonites 3–5, telson and uropods. H. Antennula. I. Antenna, with flagellum detail.

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 118, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 1. Study area. A. Distribution of the species. B. Vegetation of FLONA de Carajás. C. Mineral exploitation mine.

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 121, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 2. Circoniscus mendesi López-Orozco, Campos-Filho & Bichuette sp. nov., ♀, paratype (LES 0028768). A. Habitus, lateral view. B. Dorsal scale-seta. C. Cephalon, dorsal view. D. Cephalon, back view. E. Cephalon and pereonites 1 and 2, frontal view. F. Pereonite 1 and 2 epimera, ventral view. G. Pleonites 3–5, telson and uropods. H. Antennula. I. Antenna, with flagellum detail.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sreekar, Rachakonda; Koh, Lian Pin; Lamba, Aakash; Mammides, Christos; +3 Authors

    The 'Table_PA_info' contains information on all 80 Protected Areas analyzed in this study. The 'Synth_plots' includes synthetic control model fits for all 80 Protected Areas analyzed in this study. The number displayed on the top-left of each plot corresponds to the WDPA-ID of the respective protected area. For further details on each protected area, please refer to the 'Table_PA_info' document. The 'placebos' document consists of placebo test plots. The number on the top-left of each plot indicates the WDPA-ID of the protected area. Refer to the 'Table_PA_info' document for more information on each protected area.

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    Authors: Fishman, Lior; Modak, Avani; Nechooshtan, Gal; Razin, Tayla; +4 Authors

    During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response. This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

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    Authors: Harnik, Yotam; Yakubovsky, Oran; Hoefflin, Rouven; Itzkovitz, Shalev;

    QuPath project containing all highly-multiplex images generated with the PhenoCycler Fusion platform from the publication “A spatial expression atlas of the adult human proximal small intestine” including nuclear segmentation masks and cell annotations. Whole slide scans of staining with Hyaluronic-Acid binding protein and H&E staining of the same sections are provided. Moreover, the following matrices needed to reproduce the main results are provided: "cells.csv": cells table including centroid coordinates and annotations "raw_mat.csv": protein expression matrix without pre-processing "norm_mat.csv": protein expression matrix after log2-transformation and per sample z-scoring

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 122, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 3. Circoniscus mendesi López-Orozco, Campos-Filho & Bichuette sp. nov., ♀, paratype (LES 0028768). A. Left mandible. B. Right mandible. C. Maxillula. D. Maxilla. E. Maxilliped, arrow illustrating the endite in caudal view. F. Uropod. Figure not to scale.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 128, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 7. Circoniscus xikrin López-Orozco, Campos-Filho & Carpio-Díaz sp. nov., ♂, holotype (LES 0028772). A. Pereopod 1, arrow illustrating the dactylus in rostral view. B. Pereopod 7. C. Genital papilla and pleopod 1. D. Pleopod 2. E. Pleopod 3 exopod. F. Pleopod 4 exopod. G. Pleopod 5 exopod. Figure not to scale.

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    Authors: López-Orozco, Carlos Mario; Campos-Filho, Ivanklin Soares; Gallo, Jéssica S.; Gallão, Jonas E.; +3 Authors

    Published as part of López-Orozco, Carlos Mario, Campos-Filho, Ivanklin Soares, Gallo, Jéssica S., Gallão, Jonas E., Carpio-Díaz, Yesenia M., Borja-Arrieta, Ricardo & Bichuette, Maria Elina, 2024, Iron-isopods: new records and new species of terrestrial isopods (Isopoda, Oniscidea) from Brazilian Amazon iron ore caves, pp. 116-135 in European Journal of Taxonomy 921 (1) on page 130, DOI: 10.5852/ejt.2024.921.2421, http://zenodo.org/record/10623397 Fig. 8. A. Circoniscus mendesi López-Orozco, Campos-Filho & Bichuette sp. nov., specimen from CAV-N1-0174. B. Parauapebas, Pará, in moist soil. C. Ctenorillo ferrarai Campos-Filho, Araujo & Taiti, 2014, specimen from CAV-SB-0049 (also known as Samuel II by local people). D. Canaã dos Carajás, Pará, in moist soil.

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