DOI: 10.1016/j.xcrm.2024.101554

Resource: (PhosphoSolutions Cat# 1832-RBPMS, RRID:AB_2492226)

Curator: @scibot

SciCrunch record: RRID:AB_2492226

---

What is this?

DOI: 10.1016/j.xcrm.2024.101554

Resource: (Abcam Cat# ab194213, RRID:AB_2920590)

Curator: @scibot

SciCrunch record: RRID:AB_2920590

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (RRID:CVCL_GR23)

Curator: @scibot

SciCrunch record: RRID:CVCL_GR23

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (RGD Cat# 734476,RRID:RGD_734476)

Curator: @scibot

SciCrunch record: RRID:RGD_734476

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (ATCC Cat# CRL-2755, RRID:CVCL_1923)

Curator: @scibot

SciCrunch record: RRID:CVCL_1923

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (RRID:CVCL_5423)

Curator: @scibot

SciCrunch record: RRID:CVCL_5423

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (DSMZ Cat# ACC-738, RRID:CVCL_0419)

Curator: @scibot

SciCrunch record: RRID:CVCL_0419

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (ATCC Cat# CRM-HTB-26, RRID:CVCL_0062)

Curator: @scibot

SciCrunch record: RRID:CVCL_0062

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 7074, RRID:AB_2099233)

Curator: @scibot

SciCrunch record: RRID:AB_2099233

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 7076, RRID:AB_330924)

Curator: @scibot

SciCrunch record: RRID:AB_330924

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 11815, RRID:AB_2616025)

Curator: @scibot

SciCrunch record: RRID:AB_2616025

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 5324, RRID:AB_10692650)

Curator: @scibot

SciCrunch record: RRID:AB_10692650

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 3398, RRID:AB_2096481)

Curator: @scibot

SciCrunch record: RRID:AB_2096481

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 3192, RRID:AB_2095847)

Curator: @scibot

SciCrunch record: RRID:AB_2095847

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2876, RRID:AB_2064177)

Curator: @scibot

SciCrunch record: RRID:AB_2064177

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 5023, RRID:AB_10557411)

Curator: @scibot

SciCrunch record: RRID:AB_10557411

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 3686, RRID:AB_2077850)

Curator: @scibot

SciCrunch record: RRID:AB_2077850

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2947, RRID:AB_823586)

Curator: @scibot

SciCrunch record: RRID:AB_823586

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# PA5-27281, RRID:AB_2544757)

Curator: @scibot

SciCrunch record: RRID:AB_2544757

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# PA5-62977, RRID:AB_2646776)

Curator: @scibot

SciCrunch record: RRID:AB_2646776

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Novus Cat# NBP1-80025, RRID:AB_11002635)

Curator: @scibot

SciCrunch record: RRID:AB_11002635

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Novus Cat# NBP1-80804, RRID:AB_11017106)

Curator: @scibot

SciCrunch record: RRID:AB_11017106

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# 37-3000, RRID:AB_2533310)

Curator: @scibot

SciCrunch record: RRID:AB_2533310

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# PA5-52245, RRID:AB_2646744)

Curator: @scibot

SciCrunch record: RRID:AB_2646744

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# PA5-88906, RRID:AB_2805210)

Curator: @scibot

SciCrunch record: RRID:AB_2805210

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: AB_2646745

Curator: @scibot

SciCrunch record: RRID:AB_2646745

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 12496, RRID:AB_2721252)

Curator: @scibot

SciCrunch record: RRID:AB_2721252

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Novus Cat# NBP1-56654, RRID:AB_11030684)

Curator: @scibot

SciCrunch record: RRID:AB_11030684

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2013, RRID:AB_2097363)

Curator: @scibot

SciCrunch record: RRID:AB_2097363

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2490, RRID:AB_823487)

Curator: @scibot

SciCrunch record: RRID:AB_823487

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2441, RRID:AB_2277632)

Curator: @scibot

SciCrunch record: RRID:AB_2277632

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Thermo Fisher Scientific Cat# PA5-51472, RRID:AB_2640977)

Curator: @scibot

SciCrunch record: RRID:AB_2640977

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 3263, RRID:AB_2293295)

Curator: @scibot

SciCrunch record: RRID:AB_2293295

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Novus Cat# NB600-302SS, RRID:AB_2037063)

Curator: @scibot

SciCrunch record: RRID:AB_2037063

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2211, RRID:AB_331679)

Curator: @scibot

SciCrunch record: RRID:AB_331679

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 9208, RRID:AB_330990)

Curator: @scibot

SciCrunch record: RRID:AB_330990

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 9234, RRID:AB_2269803)

Curator: @scibot

SciCrunch record: RRID:AB_2269803

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 2983, RRID:AB_2105622)

Curator: @scibot

SciCrunch record: RRID:AB_2105622

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 5536, RRID:AB_10691552)

Curator: @scibot

SciCrunch record: RRID:AB_10691552

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 4202, RRID:AB_1950384)

Curator: @scibot

SciCrunch record: RRID:AB_1950384

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 4970, RRID:AB_2223172)

Curator: @scibot

SciCrunch record: RRID:AB_2223172

---

What is this?

DOI: 10.1016/j.xcrm.2024.101552

Resource: (Cell Signaling Technology Cat# 3377, RRID:AB_1549592)

Curator: @scibot

SciCrunch record: RRID:AB_1549592

---

What is this?

DOI: 10.1016/j.bioactmat.2024.05.006

Resource: RRID:Addgene_62629

Curator: @scibot

SciCrunch record: RRID:Addgene_62629

---

What is this?

DOI: 10.1016/j.bioactmat.2024.05.006

Resource: University of California at San Diego Electron Microscopy Core Facility (RRID:SCR_022039)

Curator: @scibot

SciCrunch record: RRID:SCR_022039

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: Elephant (RRID:SCR_003833)

Curator: @scibot

SciCrunch record: RRID:SCR_003833

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: DeepLabCut Project (RRID:SCR_021398)

Curator: @scibot

SciCrunch record: RRID:SCR_021398

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: Python Programming Language (RRID:SCR_008394)

Curator: @scibot

SciCrunch record: RRID:SCR_008394

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: IGOR Pro (RRID:SCR_000325)

Curator: @scibot

SciCrunch record: RRID:SCR_000325

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: Chemdraw (RRID:SCR_016768)

Curator: @scibot

SciCrunch record: RRID:SCR_016768

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: GraphPad Prism (RRID:SCR_002798)

Curator: @scibot

SciCrunch record: RRID:SCR_002798

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: pClamp (RRID:SCR_011323)

Curator: @scibot

SciCrunch record: RRID:SCR_011323

---

What is this?

DOI: 10.1016/j.chembiol.2024.04.003

Resource: MATLAB (RRID:SCR_001622)

Curator: @abever99

SciCrunch record: RRID:SCR_001622

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: RRID:Addgene_51406

Curator: @scibot

SciCrunch record: RRID:Addgene_51406

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: RRID:Addgene_158384

Curator: @scibot

SciCrunch record: RRID:Addgene_158384

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: RRID:Addgene_52963

Curator: @scibot

SciCrunch record: RRID:Addgene_52963

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217)

Curator: @scibot

SciCrunch record: RRID:AB_2576217

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (Thermo Fisher Scientific Cat# A-11029, RRID:AB_2534088)

Curator: @scibot

SciCrunch record: RRID:AB_2534088

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (Thermo Fisher Scientific Cat# A-11006, RRID:AB_2534074)

Curator: @scibot

SciCrunch record: RRID:AB_2534074

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 400202, RRID:AB_2927399)

Curator: @scibot

SciCrunch record: RRID:AB_2927399

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 354506, RRID:AB_11219600)

Curator: @scibot

SciCrunch record: RRID:AB_11219600

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 400508, RRID:AB_326530)

Curator: @scibot

SciCrunch record: RRID:AB_326530

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 145204, RRID:AB_2561928)

Curator: @scibot

SciCrunch record: RRID:AB_2561928

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 354502, RRID:AB_2564475)

Curator: @scibot

SciCrunch record: RRID:AB_2564475

---

What is this?

DOI: 10.1016/j.chom.2024.04.014

Resource: (BioLegend Cat# 145202, RRID:AB_2561841)

Curator: @scibot

SciCrunch record: RRID:AB_2561841

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: PyTorch (RRID:SCR_018536)

Curator: @scibot

SciCrunch record: RRID:SCR_018536

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: lifelines (RRID:SCR_024899)

Curator: @scibot

SciCrunch record: RRID:SCR_024899

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: scikit-learn (RRID:SCR_002577)

Curator: @scibot

SciCrunch record: RRID:SCR_002577

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: SciPy (RRID:SCR_008058)

Curator: @scibot

SciCrunch record: RRID:SCR_008058

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: Pandas (RRID:SCR_018214)

Curator: @scibot

SciCrunch record: RRID:SCR_018214

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: MatPlotLib (RRID:SCR_008624)

Curator: @scibot

SciCrunch record: RRID:SCR_008624

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: NumPy (RRID:SCR_008633)

Curator: @scibot

SciCrunch record: RRID:SCR_008633

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: Napari (RRID:SCR_022765)

Curator: @scibot

SciCrunch record: RRID:SCR_022765

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: pillow (RRID:SCR_023337)

Curator: @scibot

SciCrunch record: RRID:SCR_023337

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: OpenCV (RRID:SCR_015526)

Curator: @scibot

SciCrunch record: RRID:SCR_015526

---

What is this?

DOI: 10.1016/j.cell.2024.03.035

Resource: Python Programming Language (RRID:SCR_008394)

Curator: @scibot

SciCrunch record: RRID:SCR_008394

---

What is this?

DOI: 10.1016/j.intimp.2024.112212

Resource: GraphPad Prism (RRID:SCR_002798)

Curator: @scibot

SciCrunch record: RRID:SCR_002798

---

What is this?

DOI: 10.1016/j.intimp.2024.112212

Resource: SPSS (RRID:SCR_002865)

Curator: @scibot

SciCrunch record: RRID:SCR_002865

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (Cell Signaling Technology Cat# 7074, RRID:AB_2099233)

Curator: @scibot

SciCrunch record: RRID:AB_2099233

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (Abcam Cat# ab1187, RRID:AB_298652)

Curator: @scibot

SciCrunch record: RRID:AB_298652

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (AgriSera Cat# AS13 2640, RRID:AB_2722610)

Curator: @scibot

SciCrunch record: RRID:AB_2722610

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (Santa Cruz Biotechnology Cat# sc-9996, RRID:AB_627695)

Curator: @scibot

SciCrunch record: RRID:AB_627695

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (Abcam Cat# ab9344, RRID:AB_307195)

Curator: @scibot

SciCrunch record: RRID:AB_307195

---

What is this?

DOI: 10.1016/j.cell.2024.04.007

Resource: (Cell Signaling Technology Cat# 4370, RRID:AB_2315112)

Curator: @scibot

SciCrunch record: RRID:AB_2315112

---

What is this?

DOI: 10.1016/j.cell.2024.03.016

Resource: Python Programming Language (RRID:SCR_008394)

Curator: @scibot

SciCrunch record: RRID:SCR_008394

---

What is this?

DOI: 10.1016/j.cell.2024.03.016

Resource: tidyverse (RRID:SCR_019186)

Curator: @scibot

SciCrunch record: RRID:SCR_019186

---

What is this?

DOI: 10.1016/j.cell.2024.03.016

Resource: ggplot2 (RRID:SCR_014601)

Curator: @scibot

SciCrunch record: RRID:SCR_014601

---

What is this?

DOI: 10.1016/j.cell.2024.03.016

Resource: R Project for Statistical Computing (RRID:SCR_001905)

Curator: @scibot

SciCrunch record: RRID:SCR_001905

---

What is this?

DOI: 10.1016/j.jns.2024.123041

Resource: RRID:Addgene_126463

Curator: @scibot

SciCrunch record: RRID:Addgene_126463

---

What is this?

DOI: 10.1016/j.jns.2024.123041

Resource: RRID:Addgene_126463

Curator: @abever99

SciCrunch record: RRID:Addgene_126463

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Boster Biological Technology Cat# BA1054, RRID:AB_2734136)

Curator: @scibot

SciCrunch record: RRID:AB_2734136

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Abcam Cat# ab8226, RRID:AB_306371)

Curator: @scibot

SciCrunch record: RRID:AB_306371

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Cell Signaling Technology Cat# 12640, RRID:AB_2629499)

Curator: @scibot

SciCrunch record: RRID:AB_2629499

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Cell Signaling Technology Cat# 9145, RRID:AB_2491009)

Curator: @scibot

SciCrunch record: RRID:AB_2491009

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Thermo Fisher Scientific Cat# 701283, RRID:AB_2532457)

Curator: @scibot

SciCrunch record: RRID:AB_2532457

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 103204, RRID:AB_312989)

Curator: @scibot

SciCrunch record: RRID:AB_312989

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 100704, RRID:AB_312743)

Curator: @scibot

SciCrunch record: RRID:AB_312743

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 102004, RRID:AB_312853)

Curator: @scibot

SciCrunch record: RRID:AB_312853

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 103522, RRID:AB_2566366)

Curator: @scibot

SciCrunch record: RRID:AB_2566366

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 101204, RRID:AB_312787)

Curator: @scibot

SciCrunch record: RRID:AB_312787

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 117304, RRID:AB_313773)

Curator: @scibot

SciCrunch record: RRID:AB_313773

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 100516, RRID:AB_312719)

Curator: @scibot

SciCrunch record: RRID:AB_312719

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 104512, RRID:AB_493564)

Curator: @scibot

SciCrunch record: RRID:AB_493564

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 124608, RRID:AB_1134096)

Curator: @scibot

SciCrunch record: RRID:AB_1134096

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 107626, RRID:AB_2191071)

Curator: @scibot

SciCrunch record: RRID:AB_2191071

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 105014, RRID:AB_439783)

Curator: @scibot

SciCrunch record: RRID:AB_439783

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 104706, RRID:AB_313127)

Curator: @scibot

SciCrunch record: RRID:AB_313127

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 126406, RRID:AB_1089113)

Curator: @scibot

SciCrunch record: RRID:AB_1089113

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 505810, RRID:AB_315404)

Curator: @scibot

SciCrunch record: RRID:AB_315404

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 506940, RRID:AB_2565781)

Curator: @scibot

SciCrunch record: RRID:AB_2565781

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 504303, RRID:AB_315327)

Curator: @scibot

SciCrunch record: RRID:AB_315327

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 123116, RRID:AB_893481)

Curator: @scibot

SciCrunch record: RRID:AB_893481

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What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 504118, RRID:AB_10898116)

Curator: @scibot

SciCrunch record: RRID:AB_10898116

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 127624, RRID:AB_10640819)

Curator: @scibot

SciCrunch record: RRID:AB_10640819

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What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 155508, RRID:AB_2750237)

Curator: @scibot

SciCrunch record: RRID:AB_2750237

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 101216, RRID:AB_312799)

Curator: @scibot

SciCrunch record: RRID:AB_312799

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 117308, RRID:AB_313777)

Curator: @scibot

SciCrunch record: RRID:AB_313777

---

What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (BioLegend Cat# 103132, RRID:AB_893340)

Curator: @scibot

SciCrunch record: RRID:AB_893340

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What is this?

DOI: 10.1016/j.isci.2024.109818

Resource: (Thermo Fisher Scientific Cat# 25-5773-82, RRID:AB_891552)

Curator: @scibot

SciCrunch record: RRID:AB_891552

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What is this?

DOI: 10.1126/scitranslmed.adl4317

Resource: (ATCC Cat# CRL-7924, RRID:CVCL_0058)

Curator: @scibot

SciCrunch record: RRID:CVCL_0058

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What is this?

DOI: 10.1126/scitranslmed.adl4317

Resource: (BCRC Cat# 60005, RRID:CVCL_0030)

Curator: @scibot

SciCrunch record: RRID:CVCL_0030

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What is this?

DOI: 10.1021/jacs.3c12048

Resource: University of Pittsburgh Center for Research Computing Core Facility (RRID:SCR_022735)

Curator: @scibot

SciCrunch record: RRID:SCR_022735

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What is this?

DOI: 10.1021/jacs.3c11511

Resource: University of California at Santa Cruz Biomolecular Cryo Electron Microscopy Core Facility (RRID:SCR_021755)

Curator: @scibot

SciCrunch record: RRID:SCR_021755

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What is this?

DOI: 10.1126/sciadv.adj6380

Resource: Massachusetts Institute of Technology Swanson Biotechnology Center Nanotechnology Materials Core Facility (RRID:SCR_018674)

Curator: @scibot

SciCrunch record: RRID:SCR_018674

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What is this?

DOI: 10.1088/1741-2552/ab603f

Resource: RRID:Addgene_100837

Curator: @scibot

SciCrunch record: RRID:Addgene_100837

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What is this?

DOI: 10.1101/2024.02.15.580426

Resource: (Rockland Cat# 600-401-379, RRID:AB_2209751)

Curator: @anisehay

SciCrunch record: RRID:AB_2209751

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What is this?

DOI: 10.21203/rs.3.rs-4166090/v1

Resource: ImageJ (RRID:SCR_003070)

Curator: @evieth

SciCrunch record: RRID:SCR_003070

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What is this?

DOI: 10.1101/2024.01.31.578330

Resource: Fiji (RRID:SCR_002285)

Curator: @anisehay

SciCrunch record: RRID:SCR_002285

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What is this?

DOI: 10.1101/2024.01.31.578330

Resource: (WB Cat# WBStrain00041971,RRID:WB-STRAIN:WBStrain00041971)

Curator: @anisehay

SciCrunch record: RRID:WB-STRAIN:WBStrain00041971

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What is this?

DOI: 10.1101/2024.01.31.578239

Resource: (IMSR Cat# JAX_000664,RRID:IMSR_JAX:000664)

Curator: @anisehay

SciCrunch record: RRID:IMSR_JAX:000664

---

What is this?

DOI: 10.1016/j.isci.2024.109789

Resource: (WB Cat# WBStrain00000001,RRID:WB-STRAIN:WBStrain00000001)

Curator: @AniH

SciCrunch record: RRID:WB-STRAIN:WBStrain00000001

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What is this?

DOI: 10.1016/j.isci.2024.109798

Resource: GraphPad Prism (RRID:SCR_002798)

Curator: @AniH

SciCrunch record: RRID:SCR_002798

---

What is this?

El tipo de mensaje es keyword porque son aquellos mensajes que consisten en uno o más nombres de argumentos precedidos por dos puntos (:). Su composición parte de:

Un receptor (objeto), el mensaje (método a utilizar) y el argumento que son los valores que se pasan al método para que pueda realizar la tarea. En los mensajes keyword, los argumentos están precedidos por dos puntos (:) y separados por comas (,).

Para este caso: * El objeto es: sessions. * El mensaje es: to * y el argumento pasado por el método to es el 11, Esto indica que la secuencia de números enteros debe ir desde 1 hasta 11 inclusive.

Para este ejercicio el tipo de mensaje es binario porque se compone de tres partes: receptor (objeto), selector (mensaje) y argumento.

1. Objeto: es el receptor del mensaje. En este caso, el objeto es el número 27.
2. Mensaje: es la acción que se le está enviando al objeto. Para este ejemplo, el mensaje es la operación de multiplicación representada por el selector ( * ), que indica que se debe multiplicar el objeto con el argumento.
3. Argumento: es el valor que se pasa al mensaje o con el que se realizar la operación. Para este caso, el argumento es el número 23.

En concusión, devuelve como resultado.

Es un mensaje tipo keyword

• El objeto es: memories
• El mensaje es: do
• El argumento del mensaje es: do es el bloque proporcionado entre corchetes [:doc | .... ] aquí el iterador es el do, el cual se utiliza para recorrer cada elemento de la colección o objeto memories y ejecutar el bloque proporcionado para cada uno de ellos.

Resultado devuelto al ejecutar todo el bloque:

Este mensaje es tipo Keyword y dentro de este el

• Objeto (receptor): es memories el cual invoca el método.
• Mensaje (selector): es doWithIndex: Este es un mensaje de Pharo que se utiliza para iterar sobre una colección y proporciona tanto el elemento actual como su índice en cada iteración.
• Argumento: es el mensaje doWithIndex el cual es un bloque de código que define la acción que se realizará en cada elemento de la colección. En este caso, el bloque es [:item :index | ........ ], es decir, todo lo que encierran los corchetes y recibe dos parámetros: item, que representa cada elemento de la colección, y index, que representa el índice del elemento en la colección.

Dentro del bloque: * El objeto: item es el elemento actual de la colección memories. * El mensaje enviado: es metadata, que es un mensaje enviado al objeto item. Este mensaje obtiene los metadatos asociados con el elemento actual. * El argumento del mensaje at:put: es una clave, en este caso 'title', y el nuevo valor 'Unidades semanticas, sesión ', que se asigna a la clave 'title' en los metadatos del elemento actual.

Al ejecutar todo el código se devuelve el siguiente resultado:

Este ejemplo en Pharo se refiere a la manipulación de colecciones y al uso de bloques en combinación con mensajes Keyword.

Ahora bien, a continuación se explica las dos partes del ejercicio: En mensaje en keyword es: 1. Objeto: sessions 2. Mensaje: collect<br /> 3. Argumento: [:session |

Dentro del bloque el código funciona así: 1. Objeto: para este se crea un nuevo objeto de tipo HedgeDoc utilizando el mensaje new. Este objeto se asigna a la variable doc. 2. Ahora el mensajes new envían varios mensajes al objeto doc: tales como: * url: Configura la URL del objeto doc. Toma como argumento la concatenación de commonAddress (una dirección común) y la representación de cadena de session. * Ahora utiliza retrieveContents: el cual es un mensaje que permite recuperar el contenido de la URL configurada en el objeto doc.

En general, el código utiliza el iterador collect: el cual controla la iteración sobre la colección sessions y aplica el bloque definido [:session | a cada elemento de la colección.

Al ejecutar todo este código se obtiene el siguiente resultado:

A picture of a census document from 1850, showing that the ratio of men to women in the United States 2 years following the artifact. By stating that these are the sentiments shared by HALF of the population of the country, Stanton makes a bold statement about the numbers behind her fight, as well as the injustice of the way things had been going for women for decades prior.

Wesleyan College, Middletown, Connecticut The first college to open it's doors to female students in 1836

Consider the implications being made beyond the actual statements being made within the artifact * Stanton crosses a line of distinction here to go so far as stating that men haven't only limited women politically and economically, but they have dehumanized them as well. By limiting women in the world of employment and refusing to allow them the freedom to explore, men effectively hindered women's' ability to grow, develop, think critically, etc. Stanton asserts that halting the progress of women's success and achievements within society is an agenda that has been longstanding and will continue to go on, if it is not dismantled by the efforts of the very women that it affects.

Consider the author/speaker of the artifact and their role/position on the subject matter. Does the person satisfy any aspect of ethos? * Elizabeth Cady Stanton was chosen to be the speaker for the Declaration of Sentiments primarily because of the leadership role she took on throughout the movement. She was one of the principal organizers of the convention along with Lucretia Mott and Susan B. Anthony. Stanton was solidified as one of the prominent figures of the Women's Right's Movement early on. * Stanton employs ethos by being the speaker for the artifact, as at this point, she is well known for her activism and support for Women's rights. She later does justice upon her ethos by presenting well though out, concise, and harrowing statements about the U.S. government's lack of consideration towards the female population.

Consider the pathos employed by the rhetor throughout the artifact and the contributions it makes to the overall impact * Stanton has just consecutively listed the grievances of the American women against the American government, evoking strong emotions with her choices of oppressive keywords including "denied" and "withheld." In doing so, she appeals to her female audience and unites their struggles together in one powerful voice demanding change.

Consider the economic climate of the time period your artifact takes place in * Until 1900, women in all states of America did not have protection over their wages, which meant their father or husband had ownership over their earned wages. Therefore, property is sold, bought and exchanged, and women are entirely excluded from any economic aspect of society. With that, women have been excluded economically by denying them the right to their money, politically by denying them the right to their voting opinions, and socially by denying them the respect of fellow human beings and degrading them on the sole basis of their gender.

Consider the social climate of the time period that the artifact takes place in. * In 18th and 19th century America, marriages were simple and private, usually involving the parties being married, their immediate family, and a Priest. Before marriage, a young woman was considered to be the property of her father. Following marriage, she became the property of her husband. * While the concept of a father transferring ownership of his daughter to her husband sounds traditional and "old cultured," think about wedding traditions that are still widely practiced today. The father, walking his daughter down the aisle, the removal of the garter - and consider what these practices reassert about how our society views and treats women.

A political cartoon that portrays the trivial nature of voting in early America - Captioned: "The Early Days of Voting in America: A Lot of White Men Drinking in Taverns."

With Feminist Critique Theory, identify the gendered language and the contributions made to the artifact overall * Stanton states "sufferance of women" as she appeals to a crowd of primarily white women, along with men. Jefferson wrote "sufferance of these colonies" as he appealed only to white, land owning men.

Identify the rhetorical choices made by the author and identify how they contribute to the artifact. * By echoing Thomas Jefferson's voice in "The Declaration of Independence," Stanton strategically aligns the struggles of the Women's Rights Movement with the foundational democratic principles of the United States Government. Not only does this help emphasize contradictions between the ideals of the nation and the lack of Women's rights, it underscores the legitimacy of the movement as an extension of American values. * With Feminist Critique Theory, identify the choices of gendered language. Stanton chooses to state "all men and women" rather than "all men" as Thomas Jefferson did. In doing so, Stanton deconstructs the idea of male superiority and asserts equality for men and women.

Consider the structure of the artifact and how it contributes to it's rhetorical success * Stanton follows in suit of "The Declaration of Independence," which aids her in aligning women's fights for rights with the United States' fight for independence from Great Britain. * With Feminist Critique Theory, examine the choice of words that follow: compelled, withheld, deprived etc., through which Stanton demands amendments to the grievances of women.

Consider the audience the artifact was presented to, and how it affects the purpose/goal of the artifact, how it may have been received. * The artifact was presented at the Seneca Falls Convention which had a primarily female audience and was made up of individuals who were either fighting for or had an interest in fighting for Women's rights. Frederick Douglass, a frontrunner of the abolitionist movement was in attendance as well as activists such as Lucretia Mott and Susan B. Anthony. We can assume that the sentiments and feelings evoked in the artifact were relatable to the audience and received with passion and power towards coming together to fight for the civil liberties of women. * With Feminist Critique Theory, analyzing the intersectionality's of the audience such as race and gender emphasizes the interconnected nature of gender with other social identities.

Es un mensaje tipo keyword

• El objeto es: memories
• El mensaje es: do
• El argumento del mensaje do es el bloque proporcionado entre corchetes [:doc | .... ] aquí el iterador es el do, el cual se utiliza para recorrer cada elemento de la colección o objeto memories y ejecutar el bloque proporcionado para cada uno de ellos.

Resultado devuelto al ejecutar todo el bloque:

Este es un tipo de mensaje binario en donde

Objeto:

• El objeto principal en este ejemplo es FileLocator, que es una clase en Pharo utilizada para ubicar archivos en el sistema de archivos.

Mensaje:

• El mensaje principal enviado es /, que es un mensaje binario. Este mensaje se utiliza para combinar dos rutas de archivos o directorios.

Argumento:

• El argumento del mensaje / es la cadena 'USemanticas\leidy-palma\Wiki\es\sesiones', que representa la ruta relativa de un directorio en el sistema de archivos.

Este ejercicio devuelve como resultado:

Este mensaje es tipo Keyword y dentro de este el

• Objeto (receptor): es memories el cual invoca el método.
• Mensaje (selector) es doWithIndex: Este es un mensaje de Pharo que se utiliza para iterar sobre una colección y proporciona tanto el elemento actual como su índice en cada iteración.
• Argumento: Es el mensaje doWithIndex el cual es un bloque de código que define la acción que se realizará en cada elemento de la colección. En este caso, el bloque es [:item :index | ........ ], es decir, todo lo que encierran los corchetes y recibe dos parámetros: item, que representa cada elemento de la colección, y index, que representa el índice del elemento en la colección.

Dentro del bloque: * El objeto item es el elemento actual de la colección memories. * El mensaje enviado es metadata, que es un mensaje enviado al objeto item. Este mensaje obtiene los metadatos asociados con el elemento actual. * El argumento del mensaje at:put: es una clave, en este caso 'title', y el nuevo valor 'Unidades semanticas, sesión ', que se asigna a la clave 'title' en los metadatos del elemento actual.

Al ejecutar todo el código se devuelve el siguiente resultado:

Este ejemplo en Pharo se refiere a la manipulación de colecciones y al uso de bloques en combinación con mensajes Keyword.

Ahora bien, a continuación se explica las dos partes del ejercicio: En mensaje en keyword es: 1. Objeto es: sessions 2. Mensaje es: collect<br /> 3. Argumento: [:session |

Dentro del bloque el código funciona así: 1. Objeto: para este se crea un nuevo objeto de tipo HedgeDoc utilizando el mensaje new. Este objeto se asigna a la variable doc. 2. Ahora el mensajes new envían varios mensajes al objeto doc: tales como: * url: Configura la URL del objeto doc. Toma como argumento la concatenación de commonAddress (una dirección común) y la representación de cadena de session. * Ahora utiliza retrieveContents: el cual es un mensaje que permite recuperar el contenido de la URL configurada en el objeto doc.

En general, el código utiliza el iterador collect: el cual controla la iteración sobre la colección sessions y aplica el bloque definido [:session | a cada elemento de la colección.

Al ejecutar todo este código se obtiene el siguiente resultado:

El tipo de mensaje es keyword porque son aquellos mensajes que consisten en uno o más nombres de argumentos precedidos por dos puntos (:). Su composición parte de:

Un receptor (objeto), el mensaje (método a utilizar) y el argumento que son los valores que se pasan al método para que pueda realizar la tarea. En los mensajes keyword, los argumentos están precedidos por dos puntos (:) y separados por comas (,).

Para este caso: * El objeto es sessions. * El mensaje es to * y el argumento pasado por el método to es el 11, Esto indica que la secuencia de números enteros debe ir desde 1 hasta 11 inclusive.

Para este caso es un tipo de mensaje unario en donde

• El objeto es 'https://docutopia.sustrato.red/semanticas:24A', siendo esta un literal de cadena (string).

• Seguidamente, el mensaje es la variable commonAddress que al ejecutar esta acción devuelve como resultado

看来我得去看看内核啊

入門の範囲を超えているかもしれませんが、このキャッシュをGitHubActionsなどのCIで保存できるかを知りたいです。

スクロール表示自体の長さは固定でしょうか？

MyST Notebookを単体で実行する方法があれば知りたいです。

JupytextにはMyST形式からNotebookにする方法だけではなくPythonスクリプトからNotebookにする方法もあり個人的にはそちらがおすすめです。

「コンテンツ」と「コンテンツファイル」で表記ゆれがあります。

入門であればreStructuredTextの説明は混乱するので省いても良いかと思います。

ディレクティブとロールについてここで詳しく説明してほしいです。

コンテンツの種類の説明が目次の前にあるとわかりやすいと思います。

設定しなくてもビルドはできるのか知りたいです。ビルド速度に影響があるか否かの情報もあると嬉しいです。

「に設定しない」という表現のほうがわかりやすいです。

ディレクティブの説明が必要だと思います。Sphinxのディレクティブについても言及があると背景がわかりやすくなると思います。

Listing 21から変更した部分を強調表示していただきたいです。

どのファイルの話なのかが読んでいて分からなくなりました。説明をお願いいたします。

The historical examples of crowdsourcing showcase humanity's knack for collaborative problem-solving long before the internet era. Take the Tang Dynasty's joint-stock company, a primitive form of crowdfunding born out of necessity during cold periods that disrupted agriculture. Similarly, in 1567, King Philip II of Spain dangled a cash prize to spur innovation in calculating longitude at sea, demonstrating early recognition of the power of incentives to mobilize collective effort.

The British government's longitude rewards in 1714 further underscored this concept, offering a bounty for a solution to a navigational conundrum. Even King Louis XVI of France got in on the action in 1783, offering a prize for a cost-effective method of producing alkali from sea salt. These instances illustrate how authorities leveraged financial incentives to tap into the wisdom of the masses.

Beyond monetary rewards, initiatives like Matthew Fontaine Maury's distribution of Wind and Current Charts in the 19th century and Joseph Henry's Meteorological Project in 1849 exemplify crowdsourcing's altruistic side. Maury's provision of charts in exchange for sailors' voyage logs and Henry's network of weather observers, enabled by telegraph communication, demonstrate early forms of collaborative data gathering for societal benefit.

These historical vignettes reveal that crowdsourcing isn't just a modern phenomenon; it's a timeless strategy rooted in human ingenuity and collaboration.

I read the article "Nearly All of Wikipedia is Written By Just 1 Percent of Its Editors" from Vice. This article from 2017 speaks on the work that Wikipedia editors do. It is stated that "only about 1 percent of Wikipedia's editors have generated 77 percent of the site's content." It also talks about how the number of Wikipedia editors has been on the decline. It makes me wonder how this number will change over the next 10 years. Will people want to take on the challenge? How will Wikipedia change over the next 10 years? Will AI ever be involved?

one detailed information about this website states that "Biographical information on various politicians was edited by their own staff to remove undesirable information (including pejorative statements quoted, or broken campaign promises)". Since a lot of people can edit the information at will, is there still credibility on Wikipedia? Similar Websites such as Baidu Baike also arise this problem, and ended up with little credibility.

Crowdsourcing is like a giant potluck where everyone brings a dish to share. It's this cool concept where instead of one person doing all the work, a bunch of folks chip in with their own small contributions. Think of Wikipedia – anyone with internet access can edit it. People from all walks of life come together, some are asked to join, others just jump in because they're interested.

It's fascinating because it taps into the power of the crowd. You've got this huge pool of potential talent, and by opening up the task to everyone, you're more likely to get diverse perspectives and skills. Plus, it's a win-win – the crowd gets to be part of something bigger, and the task gets done quicker and often better because of all the different inputs.

It's kind of like a modern-day barn raising, where the whole community comes together to build something awesome. Except instead of a barn, it might be designing a logo, solving a problem, or creating content. It's pretty cool how technology has made it possible for us to collaborate on such a massive scale, even if we're miles apart.

Lo que me llamó más la atención con respecto a la lectura es que recomiendan a los docentes recuperar conocimientos ancestrales de los pueblos indígenas y oprimidos lo que permitirá tener una educación más libre y justa dejando de lado la educación eurocentrica que solo limita a los estudiantes a un determinado conocimiento y dejando de lado valores, y cinstumnres que vienen durante años en su cultura.

コードブロックとファイルの内容の表記がどちらもListingなので両者を区別できるようにしてほしいです。

「結果ファイル」のほうがわかりやすい表現だと思います。ファイル名もあるとよりわかりやすいです。

ここまで作成したサンプルプロジェクトを使用しない理由がわからず読んでいてもやもやしました。前節までのサンプルを使用するか、理由を説明してほしいです。

文章内に組み込むのではなくシェルのコードブロックで記述したほうが読んでいてわかりやすいです。

「さまざまな」を削除しても情報量は変わらないので削除したほうがわかりやすいです。

On remarque ici la phrase de transition marquant la fin de l'introduction, et qui délimite donc le sujet. D'une part la population concernée correspond aux enfants autistes, pas aux adultes ce qui peut poser problème car nombre de patient autistes ne sont diagnostiqués que très tardivement. D'autre part la definition de lautisme ainsi que des problèmes qui lui sont associes n'est ici faite que sous le prisme de la sociabilité, or les personnes autistes peuvent rencontrer d'autres types de difficultées ( comme les Troubles du Sommeil, les troubles psychiatriques ( anxiété dépression) ).

Définition de l' autisme qui permet de mieux cerner la problématique rencontrée par les personnes autistes au quotidien : les nouvelles technologies pourraient elles donc faire partie des solutions possibles pour aider ces personnes ?

I chose this section because racial identity never was on my radar beforehand, but brought to my attention I have noticed and agree there is a lack of minority inclusion in healthcare. This directly relates to designing for equity and inclusion into the healthcare workspace due to the fact that different racial backgrounds may offer better advising and knowledge to a specific racial group than others. This relates to me because as a female, I would prefer to be advised by another female who has the same autonomy as my own.

The 710 freeway displaced a large number of people between 1965 and 1974 in West Pasadena.

A visceral example without direct connection to visualization. According to your earlier linkage of maps as the primary visualization of the slave trade, it seems that the poor passengers on the Zong would have benefited from MORE visualization.

It would be more elegant, and more respectful, if you figured out a different way to highlight aspects of the original than redrawing it. Redrawing seems to imply that the original is not enough for modern viewers. That SVG is somehow better. (It's not.)

I get a broken image.

Clear link to data, perhaps. But not clearly to data visualization. It feels that your argument would be better made against the data table, not the data visualization.

This seems more linked to relational and pictorial diagrams, not data visualization save for perhaps some later thematic maps.

This statistic makes me wonder how representative the people who choose to do this work are. Is it mainly the same demographic of people taking on these positions? How does this change the way we intake our information? Is the information biased? Questions like this come to mind for me when hearing this information.

Would be using a Incognito window provide us with the same amount of privacy protection as DuckDuckGo or StartPage? As I believe that incognito doesn't save our information, or collect personal data.

standing out. not playing on their field

Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

Learn more at Review Commons

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Reply to the reviewers

Reply to the Reviewers

We sincerely thank the Referees for providing important and constructive comments. We have addressed their concerns point-by-point as described below.

Associated to Reviewer#1's comments

*- Diploid embryos are used as controls. Gynogenetic diploids seem to be better controls to ensure that the observed phenotypes are not related to loss of heterozygosity. To limit the amount of work, the use of gynogenetic diploids could be restricted to spindle polarity and centrosome number experiments. *

Response 1-1

__[Experimental plan] __Following the reviewer's suggestion, we will conduct immunostaining of a-tubulin and centrin (for visualizing the spindles and centrioles, respectively) in gynogenetic diploids that will be generated by applying heat shock to gynogenetic haploid embryos during the 1st - 2nd cleavage stage. We will observe the head area of gynogenetic diploid larvae at 3-dpf when the haploid counterparts suffer particularly drastic centrosome loss and spindle monopolarization.

• *

• *

*- As the authors discuss, it would be necessary to rescue centrosome loss to establish a causal relationship between centrosome loss and haploid viability. I certainly acknowledge that this is difficult (if not impossible), but it currently limits the significance of the results. *

Response 1-2

We agree that rescuing centrosome loss would provide an important advancement in understanding the cause of haploid syndrome in the context of our study. However, as the reviewer also pointed out in the above comment, this poses a significant technical challenge. As described in Discussion in the original manuscript, we have attempted to restore normal centrosome number through cell cycle modulations. However, we have not found a condition that rescues centrosome loss without damaging larval viability. As an alternative approach, we have also tried to induce centriole amplification by injecting mRNA encoding plk4, an essential centriole duplication inducer. However, this caused earlier embryonic death, precluding us from observing its effects on larval morphology after 1 dpf. The main challenge is that any treatment to increase centrosome number can cause centrosome overduplication, which is as deleterious to development as centrosome loss. Efforts to identify a key factor enabling the rescue of centrosome loss in haploid larvae are underway in our laboratory, which requires new explorations over several years and is beyond the scope of the present study. Reflecting on the reviewer's comment, we added a new sentence explaining the situation on this issue (line 395, page 19). To further discuss possible contributions of centrosome loss and mitotic defects to haploidy-linked embryonic defects, we also added a citation of a previous study reporting that depletion of centrosomal proteins caused mitotic defects leading to embryonic defects similar to those observed in haploid embryos in zebrafish (Novorol et al., 2013 Open Biology; line 380, page 19).

__[Experimental plan] __Meanwhile, as a new trial to induce centriole amplification in a scalable and temporally controllable manner, we plan the following experiment, which can be conducted within the time range of the revision schedule: We will investigate the effects of low dose treatment of a plk4 inhibitor centrinone B on tissue growth and viability of haploid larvae. A recent study reported that centrinone B had complicated effects on the centriole duplication process, which is highly dose-sensitive (Tkach et al., 2022 Elife, PMID: 35758262). While it blocks centriole duplication at sufficiently high concentrations for blocking plk4 activities, it paradoxically causes centriole amplification at suboptimal conditions, presumably though over-stabilizing plk4 by blocking its autophosphorylation-dependent degradation (while its centriole duplicating function remains active). Since a previous study showed that centrinone B is also effective in zebrafish embryos (Rathbun et al., 2020 Current Biology, PMID: 32916112), we try to find optimal centrinone B treatment condition that potentially restores tissue growth or viability of haploid embryos. If we find such a rescuing condition, we will address the principle of the rescuing effects by investigating the possession of centrioles in mitotic cells in these haploid larvae.

*- Some experiments are not, or arguably, quantified/statistically analyzed. *

o Figure 2, Active caspase level. Larvae are sorted into three categories, and no statistical test is performed on the obtained contingency table. A Fisher'*s exact test here, or much better, the active caspase-3 levels should be quantified, instead of sorting larvae into categories. *

Response 1-3

We apologize that we showed only "zoomed-out" images of the immunostained embryos in the original figures (Fig. 2A), which precluded a clear presentation of the haploidy-associated aggravation of apoptosis and mitotic arrest. We could clearly distinguish cleaved caspase-3- and pH3-positive cells from non-specific background staining with an enlarged view of the same immunostaining data. Therefore, to quantitatively evaluate the extent of the haploidy-linked apoptosis and mitotic arrest, we compared the density of these cells within the right midbrain. This new quantification demonstrated a statistically significant increase in cleaved caspase-3- or pH3-positive cells in haploids compared to diploids.

In the revised manuscript, we added the enlarged views of cleaved-caspase and pH3 immunostaining (Fig. 2B) and new quantifications with statistical analyses (Fig. 2C). Accompanying these revisions, we omitted the categorization of the severeness of the apoptosis, which was pointed out to be subjective in the reviewer#2's comment (see Response 2-3). We rewrote the corresponding section of the manuscript to explain the new quantitative analyses (line 143, page 7).

o Same comment for 3E-F. Larvae are scored as Scarce, Mild or Severe. Looking at Fig S3A, I see one mild p53MO embryo, but the two others are not that different from 'severe' cases, which would completely change the contingency table. Again, a proper quantification would be better.

Response 1-4

We also quantified the frequency of cleaved caspase-3-positive cells in control and p53MO larvae (original Fig. 3E and F) as described in Response 1-3. While conducting the cell counting with enlarged images, we realized that staining quality within the inner larval layers of morphants was relatively poor in these experiments. This problem precluded us from counting cleaved caspase-3-positive cells within the inner larval layers. Therefore, we tentatively quantified only the surface larval layers of these morphants and found that cleaved caspase-3-positive cells were significantly reduced in haploids upon depletion of p53. We currently show this quantification in Fig. 3G of the revised manuscript. While this quantification confirmed the trend of p53MO-dependent decrease in apoptosis, we think it more appropriate to newly conduct the same experiment with better quality of the staining to apply the same standard of quantification for Fig. 3 as Fig. 2.

---

__[Experimental plan] __For the reason described above, we propose to re-conduct immunostaining of cleaved caspase-3 in control and p53MO-injected haploid larvae to improve the visibility of the inner layer of the larvae for better quality of the quantitation.

Meanwhile, we revised Fig. 3 by adding an enlarged view of immunostaining in Fig. 3F and omitting the subjective categorization shown in the original Fig. 3F and S3A. We plan to replace these data with new images and quantification to be obtained during the next revision. We also rewrote the main text to update these changes (line 166, page 8).

*o Figure 4D-E, no stats. *

Response 1-5

We conducted the ANOVA followed by the post-hoc Tukey test for new Fig. 4D and the Fisher exact test with Benjamini-Hochberg multiple testing correction for new Fig. 4E. Please note that statistical analyses were conducted after adding the data from original Fig. 6B-C following the reviewer's suggestion (see also Response 1-6).

*o Figure 6, Reversine treated haploid should be compared to haploid embryos (on the graphs and statistically). If no specific controls have been quantified for this experiment, data could be reused from previous figures, provided this is stated. *

Response 1-6

The live imaging data shown in original Fig. 4C-E and Fig. 6A-C were obtained within the same experimental series conducted in parallel at the same period under the same experimental condition. In the original manuscript, we separated them into two different figures according to the logical flow. However, following the reviewers' comments (see also Response 2-1), we realized it more appropriate to show them as a single figure panel as in the original experimental design. Therefore, we moved the reversine-treated haploid data from the original Fig. 6A-C to Fig. 4C-E to facilitate direct comparison among conditions with statistical analyses (see also Response 1-5).

*o Rescue by p53MO and Reversine, it would be nice to also include diploid measurements on the graphs, so that the reader can appreciate the extent of the rescue. *

Response 1-7

Following the reviewer's comment, we added control MO-injected or DMSO-treated diploid larval data in the corresponding graphs in Fig. 3I and 6G, respectively. Please refer to Response 2-6 for further discussion on the extent of the rescue.

Minor comments:

*- Lines 221-223, authors claim that centriole loss and spindle monopolarization commence earlier in the eyes and brain than in skin. I am note sure I see this in Fig. S5. It could as well be that the defect is less pronounced in skin. *

Response 1-8

We rewrote the manuscript to include the possible interpretation suggested by the reviewer on the result (line 225, page 11).

• *

- Lines 227-229, authors claim that 'The developmental stage when haploid larvae suffered the gradual aggravation of centrosome loss corresponded to the stage when larval cell size gradually decreased through successive cell divisions'. I did not get that. Doesn'*t cell size decrease since the first division? Fig 5D shows that cell size decreases all along development. *

Response 1-9

We agree that the original sentence implies, against our intention, that cell size does not decrease before the developmental stage mentioned here. To correct this problem, we rewrote the corresponding part of Discussion as below (line 230, page 11):

"Since the first division, embryonic cell size continuously reduces through successive cell divisions during early development (Menon et al., 2020). Cell size reduction continued at the developmental stage when we observed the gradual aggravation of the centrosome loss in haploid larvae."

*- Some correlations are used to draw conclusions: *

o Line 301-303. "The correlation between centrosome loss and spindle monopolarization indicates that haploid larval cells fail to form bipolar spindle because of the haploidy-linked centrosome loss."*. As stated by the authors, this is a correlation only. I agree it points in this direction. *

Response 1-10

We added a note to the corresponding sentence to draw readers' attention to the discussion on the limitation of the study with respect to the lack of centrosome rescue experiment (line 332, page 16).

O Line 305-308. "*Interestingly, centrosome loss occurred almost exclusively in haploid cells whose size became smaller than a certain border (Fig. 5), indicating that cell size is a key determinant of centrosome number homeostasis in the haploid state." This one is more problematic. There is no causal link established between cell size and centrosome number homeostasis. It could very well be that some unidentified problem induces both a reduction in cell size and the loss of centrioles. *

Response 1-11

To avoid an over-speculative description, we deleted the subsentence "indicating that cell size is a key determinant of centrosome number homeostasis in the haploid state." (line 336, page 17). We also added a new sentence, "Alternatively, it is also possible that other primary causes, such as the lack of second active allele producing sufficient protein pools induced cell size reduction and centrosome loss in parallel without causality between them." to discuss the possibility raised by the reviewer (line 348, page 17), in association with another comment from the reviewer #3 (see also Response 3-3).

• *

*I have concerns regarding the significance of the reported findings. Haploid zebrafish embryos show numerous developmental defects (some as early as gastrulation, as previously shown by the authors, Menon 2020), and they die by 4 dpf. That they experience massive apoptosis at day 3 does not seem very surprising, and that inhibiting p53 transiently improves the phenotype is not a big surprise. *

Response 1-12

Many reports have revealed tissue-level developmental abnormalities in haploid embryos since the discovery of haploid lethality in vertebrates more than 100 years ago. This has stimulated speculation of underlying causes of haploid intolerance for decades. However, there have been surprisingly few descriptions of cellular abnormalities underlying these tissue defects, precluding an evidence-based understanding of the principle that limits developmental ability in haploid embryos. Our findings of the haploidy-linked p53 upregulation and mitotic defects illustrate what happens in the dying haploid embryos at a cellular level. These findings would provide an evidence-based frame of reference for understanding why vertebrates cannot develop in the haploid state and also provide clues to controlling haploidy-linked embryonic defects in future studies. We added a new section in Discussion to discuss the importance of addressing the haploidy-linked defects at a cellular level (line 276, page 14).

*This reminds me of the non-specific effects of morpholino injection, which can be partially rescued by knocking down p53. *

Response 1-13

We believe the reviewer refers to the previous findings that different morpholinos generally have off-target effects activating p53-mediated apoptosis (e.g., Robu et al., 2007 PLoS Genet, PMID:17530925). However, p53 upregulation and apoptosis aggravation were also observed in uninjected haploid embryos free from morpholinos' artificial effects (Fig. 2, Fig. 3A, and B). To further address this issue, we plan to compare the frequency of cleavage caspase-3-positive cells between uninjected and control MO-injected haploids after revising the immunostaining of morphants in the original Fig. 3E-F (see Response 1-4 for details).

*The observation of mitotic arrest and mitotic defects and the observation that haploid cells often lack a centrosome is interesting. However, I felt that the manuscript suggested that these observations were novel and could explain the haploid syndrome specifically in non-mammalian embryos, when the authors reported the same observations in human haploid cells as well as in mouse haploid embryos (Yaguchi 2018). To me, this manuscript mainly confirms that their previous observation is not mammalian specific, but at least conserved in vertebrates. *

Response 1-14

As we originally wrote (line 341, page 17 in the original manuscript), we think these haploidy-linked cellular defects are conserved among mammalian and non-mammalian vertebrates. To improve the clarity of our interpretation, we rewrote a corresponding part of the manuscript (line 50, page 2).

*While I am no expert at centrosome duplication, I find the observation that haploidy leads to centrosome loss very intriguing, but have the impression that this manuscript falls short of improving our understanding of this phenomenon. *

Response 1-15

We express our gratitude to the reviewer for being interested in our findings. We hope the revisions made in the manuscript and the new results provided by the planned experiments will strengthen the contribution of this study to our understanding of haploidy-linked cellular defects.

• *

• *

Associated to Reviewer#2's comments

- Lack of proper controls in many experiments. For example, in the experiments where the authors treated haploids with reversine to suppress the SAC, there was no no-treatment control (Fig. 6A-C).

Response 2-1

We addressed the same point in__ Response 1-6__. In the original manuscript, we separately presented control and experimental conditions in the same experiment series in Fig. 4 and Fig. 6. We rejoined them in Fig. 4 as in the original experimental design. Please refer to __Response 1-6 __for further details.

• In Fig. 6D, when a DMSO control was included, the control fish were from 3 dpf while the reversine-treated fish were from 0.5-3 dpf. This is a big flaw in experimental design, especially considering the authors were looking at mitotic index, which is hugely impacted by developmental time. *

Response 2-2

In this experiment, we treated haploid larvae with either DMSO or reversine from 0.5 to 3 dpf, isolated cells from the larvae at 3 dpf, and subjected them to flow cytometry. Both DMSO- and reversine-treated larval cells were from 3-dpf larvae. Therefore, this experiment does not have the problem noted by the reviewer. To improve the clarity of the description of the experimental design, we rewrote the corresponding part of the figure legend (line 646, page 34).

- Subjective and inadequate data quantification. In the immunostaining experiments to detect caspase-3 and pH3, the authors either did not quantify at all and only showed single micrographs that might or might not be representative (for pH3), or only did very subjective and unconvincing quantification (for caspase-3). Objective measurements of fluorescence intensity could have been done, but the authors instead chose to categorize the staining into arbitrary categories with unclear standards. In example images they showed in the supplementary data, it is not obvious at all why some of the samples were classified as "mild" and others as "*severe" when their staining did not appear to be very different. *

Response 2-3

We apologize that we showed only "zoomed-out" images of the immunostained embryos in the original figures (Fig. 2A, 3E, and 6F), in which the distribution of individual cleaved caspase-3- or pH3-positive cells could not be clearly recognized. We added the enlarged view of identical immunostaining where these cells were clearly visualized in a countable manner (Fig. 2B, 3F, and 6D). Following the reviewer's suggestion, we newly conducted quantification by comparing the density of these cells within the right midbrain in haploids and diploids.

This new quantification demonstrated the haploidy-linked increase in cleaved caspase-3- or pH3-positive cells and a reversine-dependent decrease in pH3-positive cells. We added these new quantifications with statistical analyses to the revised manuscript (Fig. 2C and 6E). Accompanying these revisions, we omitted the categorization of the severeness of apoptosis, which was pointed out to be subjective. We rewrote the corresponding section of the manuscript to explain the new quantitative analyses (line 143, page 7; line 260, page 12).

While we also quantified cleaved caspase-3-positive cells in control and p53MO larvae in the original Fig. 3E, we realized that the staining quality of the inner larval layers of these morphants was relatively poor and could not apply the same standard of quantification as Fig. 2. Though we confirmed a statistically significant reduction in cleaved caspase-3-positive cells upon p53 depletion by quantified limited number of confocal sections (shown in Fig. 3G, please see also Response 1-4 for details), we decided to re-conduct this experiment for improving the staining quality to apply the same criteria of quantification for Fig 3 as Fig. 2 (Experimental plan is provided in Response 1-4).

Please note that we also tried to evaluate the extent of apoptosis and mitotic arrest based on the fluorescence intensity of organ areas. However, background staining outside the dead cell area precluded the precise quantification.

Additionally, the authors claimed that "*clusters of apoptotic cells" were only present in haploids but not diploids or p53 MO haploids, but they did not show any quantification. From the few example images (Fig.S3A), apoptotic clusters can be seen in p53 MO treated fish. Also, in some cases, the clusters were visible only because those fish were mounted in an incorrect orientation. For example, in Fig. S3A, control #2, that fish was visualized from its side, thus exposing areas around its eye that contained such clusters. These areas are not visible in other images where the fish were visualized from the top. *

__Response 2-4 __

We agree that the definition of "apoptotic clusters" was ambiguous in the original manuscript. We also agree that the visuals of the clusters could be affected by sample conditions, making them less reliable criteria for judging the severity of apoptotic upregulation in larvae. Following the reviewer's suggestion, we newly conducted apoptotic cell counting (Response 2-3), which recapitulated more reliably ploidy- or condition-dependent changes in the extent of apoptosis. Therefore, we decided to omit the description of the clusters in the new version of the manuscript.

*- Subpar data quality. Aside from issues with qualification, the IF data was not convincing as staining appeared to be inconsistent and uneven, with potential artefacts. *

Response 2-5

We apologize that the zoomed-out images in the original figures did not appropriately demonstrate the specific visualization of individual apoptotic or mitotic cells. As described in Response 2-3, we added enlarged views of the immunostaining to the revised manuscript, in which these individual cells are clearly distinguished from non-specific background staining (Fig. 2B, 3F, and 6D). Because of the poorer staining of inner layers of control and p53 morphants, we plan to re-conduct immunostaining for Fig. 3 and Fig. S3 (please refer to Response 1-4 for further detail). The current version of immunostaining and quantification in these figures will be replaced in the next revision.

- Unsupported and overstated claims. There were many overstatements. For one, in line 268, the authors claimed that "*the haploidy-linked mitotic stress with SAC activation is a primary constraint for organ growth in haploid larvae", while what they were actually showed was that reversine treatment, which suppresses the SAC, was partially rescued 2 out of the 3 growth defects they assessed, to such a small extent that the difference between haploid and haploid rescue was only Response 2-6

Following the reviewer's comment, we added control MO-injected or DMSO-treated diploid larval data in the corresponding graphs in Fig. 3I and 6G, respectively. We newly estimated the relative extent of the recovery in Results (line 174, page 8; line 268, page 13).

Reflecting the estimation, we rewrote the manuscript to discuss that haploidy-linked cell death or mitotic defects are a partial cause of organ growth retardation but that there could be other unaddressed cellular defects that also contribute to the growth retardation (line 305, page 15). We also discussed the possibility that incomplete resolution of cell death by p53MO or mitotic defects by reversine treatment may have limited their rescue effects on organ growth retardation (line 303, page 15). We also toned down several descriptions in our manuscript (lines 48 and 50, page 2; line 111, page 5; line 271, page 13; line 298, page 15; line 403, page 20) to achieve a more balanced interpretation on the potential contributions of cell death and mitotic defects to the formation of haploid syndrome.

In association with this issue, we also discussed the difficulty of assuming a priori "fully-rescued" haploid larval size in this context. This is because even normally developing haploid larvae in haplodiplontic species tend to be much smaller than their diploid counterparts. We newly cited a few cases of haplodiplontic species where haploids are smaller than or the same in size as diploids (line 307, page 15).

*With so many fundamental flaws, the data seem unreliable and the paper does not meet publishable standards. *

Response 2-7

We express our gratitude to the reviewer for providing important suggestions to improve the quality of analyses, data presentations, and interpretations in this study. We sincerely hope that one-by-one verifications of the points raised by the reviewer have improved the credibility of the paper and made it suitable for publication.

*The low quality of the analysis makes the significance low. *

*Reviewers have expertise in vertebrate embryogenesis and ploidy manipulation. *

Response 2-8

We hope that by addressing and solving the concerns pointed out by the reviewer, we could have clarified the significance of the study.

Associated to Reviewer#3's comments

*There seem to be a discrepancy between the microscopic images from Figure 2A and the quantification of pH3 positive cells using flow cytometry in Figure 4. According to the flow cytometric results the proportion of pH3 positive cells is about 3 times higher in haploid larvae compared to the control. The increase in mitotic cells in the imaging results however seems much more drastic. It would be helpful if the authors explain here. *

Response 3-1

Following comments provided by other reviewers (see also Response 1-2, 1-4, and__ 2-3__), we newly compared the frequency of pH3 positive cells between the immunostained haploid and diploid larvae. In this new analysis, pH3-positive cells were 6.4 times more frequent in haploids than in diploids, which is a more substantial difference than the one estimated based on the flow cytometric analysis.

The apparent discrepancy between the immunostaining and flow cytometric quantification would arise because pH3-positive mitotic cells tended to be more localized on the surface than in the inner region of larvae. This inevitably results in higher pH3-positive cell density in immunostaining, in which only larval surface is analyzed. To discuss this point, we newly conducted pH3 immunostaining in haploid larvae made transparent using RapiClear reagent and showed a vertical section of 3-d reconstituted larval image of pH3 immunostaining in Fig. S4E. We rewrote the manuscript to add our interpretation of this issue (line 652, page 34).

*Mitotic slippage that the authors observe to be increased in the haploid larvae to up to 5% of cells should result in an increase in the number of aneuploid cells. I am wondering why this is not recapitulated in the analyses of the DNA content in Figure S1. *

Response 3-2

A possible interpretation would be that the limited viability of newly formed aneuploid progenies precluded the detection of these populations in flow cytometric analyses. We discussed the possible generation of aneuploid progenies with our interpretation of their absence in the flow cytometric analyses in Discussion (line 293, page 14).

*Discussion: *

*I find the explanation of centrosomal loss due to depletion of centrosomal protein pools in the cytoplasm during drastic cell reduction interesting. I wonder if the reduction in size is not necessarily caused by the reduction in cells, but rather the result of the absence of a second active allele that produces centrosomal proteins? *

Response 3-3

We added the possible interpretation provided by the reviewer to the corresponding part of Discussion, in association with another comment from reviewer #1 (line 348, page 17; see also Response 1-11).

Reviewer #3 (Significance (Required)):

• *

*Overall, I find the study interesting even to a broader audience since diploid development is a fundamental feature of most animals. The authors also manage to discuss their findings on the consequences of haploidy in this bigger context of the restricted diploid development in animals. The study is very well-written even to non-experts. *

Response 3-4

We express our gratitude to the reviewer for providing positive comments on the significance of our findings. We sincerely hope that one-by-one verifications of the points raised by the reviewer further improve the quality of the paper.

I am not an expert of the literature describing previous characterizations of the consequences associated with haploid cell development in animals, which is why I cannot comment on the novelty of their study. Based on my expertise on centromeres and genome organisation I can however assess the results regarding the mitotic defects observed in haploid larvae (see comments).

Response 3-5

We sincerely thank the reviewer for providing constructive suggestions and critiques based on the expertise.

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Referee #3

Evidence, reproducibility and clarity

In this study the authors aim to shed light onto the molecular reasons why most animals are restricted to diploid cell generations. In mammals, haploid intolerance has been previously attributed to defects linked to genomic imprinting, but the molecular defects associated with haploidy in non-mammalian species are unknown. To fill these gaps, the authors in this study investigate defects associated with haploidy in zebrafish larvae. They found that haploid larvae show elevated numbers of apoptotic cells that could be partially rescued by inhibition of p53. The also detected many cells with prolonged mitosis reflected by an increase of cells positive for the mitotic histone modification phospho- histone H3 (pH3) as well as cell division defects specific to the haploid larvae. These defects are likely caused by the loss of centrosomes in haploid larval cells resulting in an increase of monopolar spindle formation. Loss of centrosomes was particularly pronounced in smaller cells and occurred concomitant with a reduction in cell size through continous cell divisions. The authors could rescue the increase of cells with prolonged mitosis by inhibiting the SAC. Both restoration of mitotic length and decreased apoptosis (by p53 inhibition) also improved some organ growth defects observed in haploid larvae.

I only have some minor comments particularly regarding the mitotic defects.

There seem to be a discrepancy between the microscopic images from Figure 2A and the quantification of pH3 positive cells using flow cytometry in Figure 4. According to the flow cytometric results the proportion of pH3 positive cells is about 3 times higher in haploid larvae compared to the control. The increase in mitotic cells in the imaging results however seems much more drastic. It would be helpful if the authors explain here. Mitotic slippage that the authors observe to be increased in the haploid larvae to up to 5% of cells should result in an increase in the number of aneuploid cells. I am wondering why this is not recapitulated in the analyses of the DNA content in Figure S1.

Discussion:

I find the explanation of centrosomal loss due to depletion of centrosomal protein pools in the cytoplasm during drastic cell reduction interesting. I wonder if the reduction in size is not necessarily caused by the reduction in cells, but rather the result of the absence of a second active allele that produces centrosomal proteins?

Significance

Overall, I find the study interesting even to a broader audience since diploid development is a fundamental feature of most animals. The authors also manage to discuss their findings on the consequences of haploidy in this bigger context of the restricted diploid development in animals. The study is very well-written even to non-experts.

I am not an expert of the literature describing previous characterizations of the consequences associated with haploid cell development in animals, which is why I cannot comment on the novelty of their study. Based on my expertise on centromeres and genome organisation I can however assess the results regarding the mitotic defects observed in haploid larvae (see comments).

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Referee #2

Evidence, reproducibility and clarity

This study examined cell proliferation and death in haploid and diploid zebrafish and attempted to provide insights into cellular mechanisms underlying haploidy-linked defects in non-mammalian vertebrates. While some of the ideas were potentially interesting, the experiments were not rigorous and inadequate data analyses were performed. Major issues include: - Lack of proper controls in many experiments. For example, in the experiments where the authors treated haploids with reversine to suppress the SAC, there was no no-treatment control (Fig. 6A-C). In Fig. 6D, when a DMSO control was included, the control fish were from 3 dpf while the reversine-treated fish were from 0.5-3 dpf. This is a big flaw in experimental design, especially considering the authors were looking at mitotic index, which is hugely impacted by developmental time. - Subjective and inadequate data quantification. In the immunostaining experiments to detect caspase-3 and pH3, the authors either did not quantify at all and only showed single micrographs that might or might not be representative (for pH3), or only did very subjective and unconvincing quantification (for caspase-3). Objective measurements of fluorescence intensity could have been done, but the authors instead chose to categorize the staining into arbitrary categories with unclear standards. In example images they showed in the supplementary data, it is not obvious at all why some of the samples were classified as "mild" and others as "severe" when their staining did not appear to be very different. Additionally, the authors claimed that "clusters of apoptotic cells" were only present in haploids but not diploids or p53 MO haploids, but they did not show any quantification. From the few example images (Fig.S3A), apoptotic clusters can be seen in p53 MO treated fish. Also, in some cases, the clusters were visible only because those fish were mounted in an incorrect orientation. For example, in Fig. S3A, control #2, that fish was visualized from its side, thus exposing areas around its eye that contained such clusters. These areas are not visible in other images where the fish were visualized from the top. - Subpar data quality. Aside from issues with qualification, the IF data was not convincing as staining appeared to be inconsistent and uneven, with potential artefacts. - Unsupported and overstated claims. There were many overstatements. For one, in line 268, the authors claimed that "the haploidy-linked mitotic stress with SAC activation is a primary constraint for organ growth in haploid larvae", while what they were actually showed was that reversine treatment, which suppresses the SAC, was partially rescued 2 out of the 3 growth defects they assessed, to such a small extent that the difference between haploid and haploid rescue was only <20% of that between haploid and diploid. Again, they did not include proper controls so haploid, haploid rescue, and diploid were never in one experiment together - they were in different figures, plotted in drastically different scales - and 20% is only an estimate. With so many fundamental flaws, the data seem unreliable and the paper does not meet publishable standards.

Significance

The low quality of the analysis makes the significance low.

Reviewers have expertise in vertebrate embryogenesis and ploidy manipulation.

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Referee #1

Evidence, reproducibility and clarity

Summary:

Yaguchi et al. investigate the causes of the "haploid syndrome" in the zebrafish embryo, the old observation that haploid embryos suffer from severe developmental defects and growth retardation of organs such as the brain and eyes (these defects are not simply a consequence of loss of heterozygosity, as they are rescued by forced diploidization of haploid larvae). Looking at apoptosis and proliferation, the authors show an increase in the number of apoptotic and mitotic cells in haploid larvae. Regarding apoptosis, they show an increase in p53 levels and demonstrate that knockdown of p53 limits apoptosis and leads to some phenotypic improvement. Regarding mitosis, they show an increase in mitotic delays and failures in haploid larvae. Inhibition of the spindle assembly checkpoint can reduce these defects and leads to some improvement in body axis length and eye size. Looking at the cause of the mitotic defects, the authors show that haploid cells often have monopolar spindles and loss of one centrosome, defects that appear to correlate with cell size.

Major comments:

While some experiments could be better quantified and/or statistically analyzed (see below), overall the results are convincing and clearly presented.

• Diploid embryos are used as controls. Gynogenetic diploids seem to be better controls to ensure that the observed phenotypes are not related to loss of heterozygosity. To limit the amount of work, the use of gynogenetic diploids could be restricted to spindle polarity and centrosome number experiments.
• As the authors discuss, it would be necessary to rescue centrosome loss to establish a causal relationship between centrosome loss and haploid viability. I certainly acknowledge that this is difficult (if not impossible), but it currently limits the significance of the results.
• Some experiments are not, or arguably, quantified/statistically analyzed.
  • Figure 2, Active caspase level. Larvae are sorted into three categories, and no statistical test is performed on the obtained contingency table. A Fisher's exact test here, or much better, the active caspase-3 levels should be quantified, instead of sorting larvae into categories.
  • Same comment for 3E-F. Larvae are scored as Scarce, Mild or Severe. Looking at Fig S3A, I see one mild p53MO embryo, but the two others are not that different from 'severe' cases, which would completely change the contingency table. Again, a proper quantification would be better.
  • Figure 4D-E, no stats.
  • Figure 6, Reversine treated haploid should be compared to haploid embryos (on the graphs and statistically). If no specific controls have been quantified for this experiment, data could be reused from previous figures, provided this is stated.
  • Rescue by p53MO and Reversine, it would be nice to also include diploid measurements on the graphs, so that the reader can appreciate the extent of the rescue.

Minor comments:

• Lines 221-223, authors claim that centriole loss and spindle monopolarization commence earlier in the eyes and brain than in skin. I am note sure I see this in Fig. S5. It could as well be that the defect is less pronounced in skin.
• Lines 227-229, authors claim that 'The developmental stage when haploid larvae suffered the gradual aggravation of centrosome loss corresponded to the stage when larval cell size gradually decreased through successive cell divisions'. I did not get that. Doesn't cell size decrease since the first division? Fig 5D shows that cell size decreases all along development.

• Some correlations are used to draw conclusions:

• Line 301-303. "The correlation between centrosome loss and spindle monopolarization indicates that haploid larval cells fail to form bipolar spindle because of the haploidy-linked centrosome loss.". As stated by the authors, this is a correlation only. I agree it points in this direction.

• Line 305-308. "Interestingly, centrosome loss occurred almost exclusively in haploid cells whose size became smaller than a certain border (Fig. 5), indicating that cell size is a key determinant of centrosome number homeostasis in the haploid state." This one is more problematic. There is no causal link established between cell size and centrosome number homeostasis. It could very well be that some unidentified problem induces both a reduction in cell size and the loss of centrioles.

Significance

I have concerns regarding the significance of the reported findings. Haploid zebrafish embryos show numerous developmental defects (some as early as gastrulation, as previously shown by the authors, Menon 2020), and they die by 4 dpf. That they experience massive apoptosis at day 3 does not seem very surprising, and that inhibiting p53 transiently improves the phenotype is not a big surprise. This reminds me of the non-specific effects of morpholino injection, which can be partially rescued by knocking down p53. The observation of mitotic arrest and mitotic defects and the observation that haploid cells often lack a centrosome is interesting. However, I felt that the manuscript suggested that these observations were novel and could explain the haploid syndrome specifically in non-mammalian embryos, when the authors reported the same observations in human haploid cells as well as in mouse haploid embryos (Yaguchi 2018). To me, this manuscript mainly confirms that their previous observation is not mammalian specific, but at least conserved in vertebrates.

While I am no expert at centrosome duplication, I find the observation that haploidy leads to centrosome loss very intriguing, but have the impression that this manuscript falls short of improving our understanding of this phenomenon.

Proyecto "Anotación PFR",

https://github.com/lmichan/PFR,

Tema/mesh/D012016/ReferenceValues,

TipoDePrueba/mesh/D002000/ForcedSpirometry,

TipoDePrueba/mesh/D010993/PlethysmographyWholeBody,

TipoDePrueba/mesh/D011653/PulmonaryDiffusingCapacity,

EtapaPrueba/Interpretacion,

PatronFuncional/Obstruccion,

PatronFuncional/PosibleRestriccion,

PatronFuncional/PosibleMixto,

PatronFuncional/Normal,

PatronFuncional/Broncodilatacion,

PatronFuncional/NoBroncodilatacion,

PatronFuncional/RestriccionSimple,

PatronFuncional/RestriccionCompleja,

PatronFuncional/TrastornoMixto,

PatronFuncional/VolumenesNormales,

PatronFuncional/Hiperinflacion,

PatronFuncional/PulmonesGrandes,

PatronFuncional/AumentoFlujoSanguineo,

PatronFuncional/AnormalidadVascularPulmonar,

PatronFuncional/PerdidaVolumenLocalizada,

PatronFuncional/PerdidaAlveoloCapilar,

PatronFuncional/DifusionNormal,

Enfermedad/mesh/D001249/Asthma,

Enfermedad/mesh/D029424/ChronicObstructivePulmonaryDisease,

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