Welcome to our monthly saunter through preprints on developmental and stem cell biology (and related fields).

The preprints this month are hosted on bioRxiv, arXiv and preprints.org – use these links to get to the section you want.

Developmental biology

• Patterning & signalling
• Morphogenesis & mechanics
• Genes & genomes
• Stem cells, regeneration & disease modelling
• Plant development
• Evo-devo

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Positive Feedback Regulation of fzd7 Expression Robustly Shapes Wnt Signaling Range in Early Heart Development
Takayoshi Yamamoto, Yuta Kambayashi, Boni Afouda, Yuta Otsuka, Claudiu Giuraniuc, Tatsuo Michiue, Stefan Hoppler

Hedgehog signaling can enhance glycolytic ATP production in the Drosophila wing disc
Ioannis Nellas, K. Venkatesan Iyer, Juan M. Iglesias-Artola, André Nadler, Natalie A. Dye, Suzanne Eaton

Visceral mesoderm signaling regulates assembly position and function of the Drosophila testis niche
Lauren Anllo, Stephen DiNardo

Essential functions of mosquito ecdysone importers in development and reproduction
Lewis V Hun, Naoki Okamoto, Eisuke Imura, Roilea Maxson, Riyan Bittar, Naoki Yamanaka

SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning
Julie Gamart, Iros Barozzi, Frédéric Laurent, Robert Reinhardt, Laurène Ramos Martins, Thomas Oberholzer, Axel Visel, Rolf Zeller, Aimée Zuniga

Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo
Natalia Benetti, Quentin Gouil, Andres Tapia del Fierro, Tamara Beck, Kelsey Breslin, Andrew Keniry, Edwina McGlinn, Marnie E. Blewitt

Sex-specific association between urinary kisspeptin and pubertal development
Rafaella Sales de Freitas, Thiago F. A. França, Sabine Pompeia

SUMOylation of Dorsal attenuates Toll/NF-κB signalling
Sushmitha Hegde, Ashley Sreejan, Chetan J Gadgil, Girish S Ratnaparkhi

Synthetic deconstruction of hunchback regulation by Bicoid
Goncalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez-Romero, Cécile Fradin, Mathieu Coppey, Aleksandra M. Walczak, Nathalie Dostatni

The NDNF-like factor Nord is a Hedgehog-induced extracellular BMP modulator that regulates Drosophila wing patterning and growth
Shu Yang, Xuefeng Wu, Euphrosyne I. Daoutidou, Ya Zhang, MaryJane Shimell, Kun-Han Chuang, Aidan J. Peterson, Michael B. O’Connor, Xiaoyan Zheng

Entry to and exit from diapause arrest in Caenorhabditis elegans are both regulated by a steroid hormone pathway
Mark G Zhang, Paul W Sternberg

Hippo pathway and Bonus control developmental cell fate decisions in the Drosophila eye
Heya Zhao, Kenneth H. Moberg, Alexey Veraksa

FOXO1 represses Sprouty2 and Sprouty4 expression in endothelial cells to promote arterial specification and vascular remodeling in the mouse yolk sac
Nanbing Li-Villarreal, Rebecca Lee Yean Wong, Monica D. Garcia, Ryan S. Udan, Ross A. Poché, Tara L. Rasmussen, Alexander M. Rhyner, Joshua D. Wythe, Mary E. Dickinson

Endothelial cell signature in muscle stem cells validated by VEGFA-FLT1-AKT1 axis promoting survival of muscle stem cell
Mayank Verma, Yoko Asakura, Xuerui Wang, Kasey Zhou, Mahmut Ünverdi, Allison P. Kann, Robert S. Krauss, Atsushi Asakura

Osteoblasts pattern endothelium and somatosensory axons during zebrafish caudal fin organogenesis
Rosalind G Bump, Camille EA Goo, Emma C Horton, Jeff Rasmussen

Unique functions for Notch4 in murine embryonic lymphangiogenesis
Ajit Muley, Minji Kim Uh, Glicella Salazar-De Simone, Bhairavi Swaminathan, Jennifer M James, Aino Murtomaki, Joseph D McCarron, Chris Kitajewski, Maria Gnarra, Gloria Riitano, Yoh-suke Mukouyama, Jan Kitajewski, Carrie J Shawber

Omics profiling identifies MAPK/ERK pathway as a gatekeeper of nephron progenitor metabolism
Hyuk Nam Kwon, Kristen Kurtzeborn, Xing Jin, Bruno Reversade, Sunghyouk Park, Satu Kuure

CHEK2 SIGNALING IS THE KEY REGULATOR OF OOCYTE SURVIVAL AFTER CHEMOTHERAPY
Chihiro Emori, Zachary Boucher, Ewelina Bolcun-Filas

Early anteroposterior regionalisation of human neural crest is shaped by a pro-mesodermal factor
Antigoni Gogolou, Celine Souilhol, Ilaria Granata, Filip J Wymeersch, Ichcha Manipur, Matthew Wind, Thomas JR Frith, Maria Guarini, Alessandro Bertero, Christoph Bock, Florian Halbritter, Minoru Takasato, Mario R Guarracino, Anestis Tsakiridis

Progenitor-intrinsic Metabolic Sensing Promotes Hematopoietic Homeostasis
Hannah A. Pizzato, Yahui Wang, Michael J. Wolfgang, Brian N. Finck, Gary J. Patti, Deepta Bhattacharya

An early signaling GARP transcription factor regulates the entry point for differentiation in Giardia
Han-Wei Shih, Germain C.M. Alas, Daria S. Rydell, Bailin Zhang, Greyson A. Hamilton, Benjamin Kerr, Alexander R. Paredez

N-myc Downstream Regulated Gene 1 (NDRG1) functions as a molecular switch for cellular adaptation to hypoxia
Jong S. Park, Austin M. Gabel, Lois Kang, Bryanna Canales, Polina Kassir, Afia Osei-Ntansah, Neil D. Tran, Soujanya Viswanathan, Young-Sam Lee, Rachel Brewster

Origin, specification and differentiation of a rare supporting-like lineage in the developing mouse gonad
Chloé Mayère, Violaine Regard, Aitana Perea-Gomez, Corey Bunce, Yasmine Neirijnck, Cyril Djari, Pauline Sararols, Richard Reeves, Simon Greenaway, Michelle Simon, Pam Siggers, Diana Condrea, Françoise Kühne, Ivana Gantar, Furong Tang, Isabelle Stévant, Laura Batti, Norbert B. Ghyselinck, Dagmar Wilhelm, Andy Greenfield, Blanche Capel, Marie-Christine Chaboissier, Serge Nef

Sonic hedgehog is essential for proximal-distal outgrowth of the limb bud in salamanders
Sruthi Purushothaman, Brianda B. Lopez Aviña, Ashley W. Seifert

Effect of Endoplasmic Reticulum Stress on Human Trophoblast Cells: Survival Triggering or Catastrophe Resulting in Death
Gurur Garip, Berrin Ozdil, Duygu Calik-Kocaturk, Fatih Oltulu, Fatma Zuhal Eroglu, Huseyin Aktug, Aysegul Uysal

Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Brianna L. Oliver, Caryl A. Young, Vidhya Munnamalai

How Dickkopf molecules and Wnt/β-catenin interplay to self-organise the Hydra body axis
Moritz Mercker, Alexey Kazarnikov, Anja Tursch, Suat Özbek, Thomas Holstein, Anna Marciniak-Czochra

Gsx2 but not Gsx1 is necessary for early forebrain patterning and long-term survival in zebrafish
RA Coltogirone, EI Sherfinski, ZA Dobler, SN Peterson, AR Andlinger, LC Fadel, RL Patrick, SA Bergeron

Optogenetic control of NOTCH1 signalling
Joanna Kałafut, Jakub Czapiński, Alicja Przybyszewska-Podstawka, Arkadiusz Czerwonka, Cecilia Sahlgren, Adolfo Rivero-Müller

Non-canonical Wnt signaling promotes directed migration of intestinal stem cells to sites of injury
Daniel Jun-Kit Hu, Jina Yun, Justin Elstrott, Heinrich Jasper

Wnt signaling rescues amyloid beta induced stem cell loss
Prameet Kaur, Ellora Hui Zhen Chua, Wen Kin Lim, Nathan Harmston, Nicholas S. Tolwinski

| Morphogenesis & mechanics

Mechanical Causation of Biological Structure: Productive Pulls Produce Persistent Filaments in a Human Fibroblast Model of Matrix Development
Alexandra A. Silverman, Seyed Mohammad Siadat, Jason D. Olszewski, Jeffrey W. Ruberti

Myosin-1b interacts with UNC45A and controls intestinal epithelial morphogenesis
Céline Revenu des Courtils, Marianna Parlato, Marion Rosello, Karine Duroure, Rémi Duclaux-Loras, Ophélie Nicolle, Marie-Thérèse Prospéri, Julie Stoufflet, Juliette Vougny, Corinne Lebreton, Priscilla Lépine, Grégoire Michaux, Nadine Cerf-Benssusan, Evelyne Coudrier, Filippo Del Bene

A unique form of collective epithelial migration is crucial for tissue fusion in the secondary palate and can overcome loss of epithelial apoptosis
Teng Teng, Camilla Teng, Vesa Kaartinen, Jeffrey O. Bush

Self-organized morphogenesis of a human neural tube in vitro by geometric constraints
Eyal Karzbrun, Aimal H. Khankhel, Heitor C. Megale, Stella M. K. Glasauer, Yofiel Wyle, George Britton, Aryeh Warmflash, Kenneth S. Kosik, Eric D. Siggia, Boris I. Shraiman, Sebastian J. Streichan

Tissue scale properties of the extracellular matrix regulates nuclear shape, organisation and fate in the embryonic midline sutures
Diana Alves-Afonso, Allyson Quinn Ryan, Adrian Lahola-Chomiak, Mangal Prakash, Florian Jug, Carl D. Modes, Jacqueline M. Tabler

Amino acid transporter SLC38A5 regulates developmental and pathological retinal angiogenesis
Zhongxiao Wang, Felix Yemanyi, Shuo Huang, Chi-Hsiu Liu, William R. Britton, Steve S. Cho, Alexandra K. Blomfield, Yohei Tomita, Zhongjie Fu, Jian-Xing Ma, Wen-Hong Li, Jing Chen

H+/K+ ion pump enhances cytoskeletal polarity to drive gastrulation in sea urchin embryo
Kaichi Watanabe, Yuhei Yasui, Yuta Kurose, Masashi Fujii, Takashi Yamamoto, Naoaki Sakamoto, Akinori Awazu

Synaptotagmin 13 orchestrates pancreatic endocrine cell egression and islet morphogenesis
Mostafa Bakhti, Aimée Bastidas-Ponce, Sophie Tritschler, Marta Tarquis-Medina, Eva Nedvedova, Katharina Scheibner, Jessica Jaki, Perla Cota, Ciro Salinno, Karsten Boldt, Stefanie J. Willmann, Nicola Horn, Marius Ueffing, Ingo Burtscher, Fabian J. Theis, Ünal Coskun, Heiko Lickert

Admp regulates tail bending by controlling the intercalation of the ventral epidermis through myosin phosphorylation
Yuki S. Kogure, Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit Godard, C. P. Heisenberg, Kotaro Oka, Kohji Hotta

Progenitor cell integration into a barrier epithelium during adult organ turnover
Paola Moreno-Roman, Yu-Han Su, Anthony Galenza, Lehi Acosta, Alain Debec, Antoine Guichet, Jon-Michael Knapp, Caroline Kizilyaprak, Bruno M. Humbel, Irina Kolotuev, Lucy Erin O’Brien

Programmed cell death recruits macrophages into the developing mouse cochlea
Vikrant Borse, Tejbeer Kaur, Ashley Hinton, Kevin Ohlemiller, Mark E. Warchol

Androglobin, a chimeric mammalian globin, is required for male fertility
Anna Keppner, Miguel Correia, Sara Santambrogio, Teng Wei Koay, Darko Maric, Carina Osterhof, Denise V Winter, Angèle Clerc, Michael Stumpe, Frédéric Chalmel, Sylvia Dewilde, Alex Odermatt, Dieter Kressler, Thomas Hankeln, Roland H. Wenger, David Hoogewijs

Levels of Notch-regulated transcription are modulated by tissue movements at gastrulation
Julia Falo-Sanjuan, Sarah J. Bray

Dinophiliformia early neurogenesis suggests the evolution of conservative neural structures across the Annelida phylogenetic tree
Elizaveta Fofanova, Tatiana D. Mayorova, Elena E. Voronezhskaya

Lmo7 recruits myosin II heavy chain to induce apical constriction in Xenopus ectoderm
Miho Matsuda, Chih-Wen Chu, Sergei Y Sokol

Competition Between Cell-Cell and Cell-Substrate Adhesion Determines Epithelial Monolayer Architecture in Culture
Christian M. Cammarota, Nicole S. Dawney, Qingyuan Jia, Maren M. Jüng, Joseph A. Glichowski, Philip M. Bellomio, Alexander G. Fletcher, Dan T. Bergstralh

The function of α-Catenin mechanosensing in tissue morphogenesis
Luka Sheppard, Ulrich Tepass

Collagen polarization promotes epithelial elongation by stimulating locoregional cell proliferation
Hiroko Katsuno-Kambe, Jessica L. Teo, Robert J. Ju, James E. Hudson, Samantha J. Stehbens, Alpha S. Yap

ELTD1 Activation Induces an Endothelial-EMT Transition to a Myofibroblast Phenotype
Helen Sheldon , John Alexander , Esther M. Bridges , Lucia Moreira , Svetlana Reilly , Koon Hwee Ang , Dian Wang , Salwa Lin , Syed Haider ORCID logo , Alison H. Banham , Adrian L. Harris ORCID logo

| Genes & genomes

The histone deacetylase activity of HDAC1/2 is required to safeguard zygotic genome activation in mice and cattle
Yanna Dang, Shuang Li, Panpan Zhao, Lieying Xiao, Lefeng Wang, Yan Shi, Lei Luo, Shaohua Wang, Huanan Wang, Kun Zhang

Genetic-epigenetic interactions in paternal transgenerational inheritance of metabolic disorders
Anne-Sophie Pepin, Christine Lafleur, Romain Lambrot, Vanessa Dumeaux, Sarah Kimmins

Distal regulation, silencers and a shared combinatorial syntax are hallmarks of animal embryogenesis
Paola Cornejo-Páramo, Kathrein Roper, Sandie M Degnan, Bernard M Degnan, Emily S Wong

Polycomb group protein CBX7 represses cardiomyocyte proliferation via modulation of the TARDBP/Rbm38 axis
Kyu-Won Cho, Mark Andrade, Seongho Bae, Sangsung Kim, Jin Eyun Kim, Er Yearn Jang, Ahsan Husain, Roy L. Sutliff, John W. Calvert, Changwon Park, Young-sup Yoon

Characterization of Histone Lysine β-hydroxybutyrylation in bovine tissues, cells, and cumulus-oocyte complexes
Juliano Rodrigues Sangalli, Ricardo Perecin Nociti, Maite del Collado, Rafael Vilar Sampaio, Juliano Coelho da Silveira, Felipe Perecin, Lawrence Charles Smith, Pablo Juan Ross, Flávio Vieira Meirelles

Retrospective analysis of enhancer activity and transcriptome history
Ruben Boers, Joachim Boers, Beatrice Tan, Evelyne Wassenaar, Erlantz Gonzalez Sanchez, Esther Sleddens, Yasha Tenhagen, Marieke E. van Leeuwen, Eskeatnaf Mulugeta, Joop Laven, Menno Creyghton, Willy Baarends, Wilfred F. J. van IJcken, Joost Gribnau

The second lineage differentiation of bovine embryos fails in the absence of OCT4/POU5F1
Kilian Simmet, Mayuko Kurome, Valeri Zakhartchenko, Horst-Dieter Reichenbach, Claudia Springer, Andrea Bähr, Helmut Blum, Julia Philippou-Massier, Eckhard Wolf

The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo
Jayson J. Smith, Yutong Xiao, Nithin Parsan, Taylor N. Medwig-Kinney, Michael A. Q. Martinez, Frances E. Q. Moore, Nicholas J. Palmisano, Abraham Q. Kohrman, Mana Chandhok Delos Reyes, Rebecca C. Adikes, Simeiyun Liu, Sydney A. Bracht, Wan Zhang, Kailong Wen, Paschalis Kratsios, David Q. Matus

Forkhead transcription factor FKH-8 is a master regulator of primary cilia in C. elegans
Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martinez, Peter Swoboda, Juan Tena, Nuria Flames

Noise Distorts the Epigenetic Landscape and Shapes Cell Fate Decisions
Megan A. Coomer, Lucy Ham, Michael P. H. Stumpf

Developmental dynamics of sex reprogramming by high incubation temperatures in a dragon lizard
Sarah L. Whiteley, Clare E. Holleley, Arthur Georges

Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots
Ying Li, Deqiang Zhang, Yongfeng Lou, An Xinmin, Zhimin Gao

TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation
Jianfang Li, Xinwei Wu, Minjung Lee, Jie Ke, Qingping Lan, Jia Li, Yun Huang, De-Qiang Sun, Ruiyu Xie

Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions
Viktor Demko, Tatiana Belova, Maxim Messerer, Torgeir R. Hvidsten, Pierre-François Perroud, Ako Eugene Ako, Wenche Johansen, Klaus F.X. Mayer, Odd-Arne Olsen, Daniel Lang

A constraints-based theory of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk
Felipe A. Veloso

Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells
Gurmannat Kalra, Danielle Lenz, Dunia Abdul-Aziz, Craig Hanna, Brian R. Herb, Carlo Colantuoni, Beatrice Milon, Madhurima Saxena, Amol C. Shetty, Ronna P. Hertzano, Ramesh A. Shivdasani, Seth A. Ament, Albert S. B. Edge

Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis
Dennis A Sun, Nipam H Patel

Epicardial HDAC3 promotes myocardial growth through a novel microRNA pathway
Jihyun Jang, Guang Song, Qinshan Li, Xiaosu Song, Chenleng Cai, Sunjay Kaushal, Deqiang Li

Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival
Oana Kubinyecz, Fatima Santos, Deborah Drage, Wolf Reik, Melanie A Eckersley-Maslin

Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development
Jonathan M. Werner, Sara Ballouz, John Hover, Jesse Gillis

Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish
Yu-Huan Shih, Daneal Portman, Feston Idrizi, Ann Grosse, Nathan D. Lawson

| Stem cells, regeneration & disease modelling

p57Kip2 regulates embryonic haematopoietic stem cell numbers by controlling the size of the sympathoadrenal progenitor pool
Chrysa Kapeni, Leslie Nitsche, Alastair Kilpatrick, Nicola Wilson, Kankan Xia, Bahar Mirshekar-Syahkal, Camille Malouf, Berthold Gottgens, Kristina Kirschner, Simon Tomlinson, Katrin Ottersbach

Fluctuation of cellular differentiation in limb regeneration is regulated by Pde4b in urodele amphibians
Akira Satoh, Rena Kashimoto, Ayaka Ohashi, Saya Furukawa, Sakiya Yamamoto, Takeshi Inoue, Toshinori Hayashi, Kiyokazu Agata

A transcriptome atlas of the mouse iris at single cell resolution defines cell types and the genomic response to pupil dilation
Jeremy Nathans

Human-specific enrichment of schizophrenia risk-genes in callosal neurons of the developing neocortex
Emanuela Zuccaro, Vanessa Murek, Kwanho Kim, Hsu-Hsin Chen, Sara Mancinelli, Paul Oyler-Castrillo, Laura T. Jimenez Barron, Chiara Gerhardinger, Juliana R. Brown, Andrea Byrnes, Benjamin Neale, Joshua Zvi Levin, Michael J. Ziller, Simona Lodato, Paola Arlotta

N-myc Downstream Regulated Gene 1 (NDRG1) functions as a molecular switch for cellular adaptation to hypoxia
Jong S Park, Austin M Gabel, Lois Kang, Bryanna Canales, Polina Kassir, Afia Osei-Ntansah, Neil D Tran, Soujanya Viswanathan, Young-Sam Lee, Rachel Brewster

PAEP and cilia gene splicing changes in endometrial glands during the implantation window in women with recurrent pregnancy loss
J.E. Pearson-Farr, G Wheway, M.S.A Jongen, P. Goggin, R.M. Lewis, Y. Cheong, J.K. Cleal

Abnormal Differentiation and Proliferation of Coronary Arterial Endothelium in Hypoplastic Left Heart Syndrome
Zhiyun Yu, Xin Zhou, Victor Pastrana-Gomez, Lei Tian, Timothy J. Nelson, Michael P. Snyder, Nian Wang, Seema Mital, David Chitayat, Joseph C. Wu, Marlene Rabinovitch, Sean M. Wu, Yifei Miao, Mingxia Gu

The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling
Yanyan Ding, Yuzhe Li, Qiangfeng Cliff Zhang, Feng Liu

Generation of CD34+CD43+ hematopoietic progenitors to induce thymocytes from human pluripotent stem cells
Léa Flippe, Anne Gaignerie, Céline Sérazin, Olivier Baron, Xavier Saulquin, Ignacio Anegon, Laurent David, Carole Guillonneau

Regulation of stem cell identity by miR-200a during spinal cord regeneration
Sarah E. Walker, Keith Z. Sabin, Micah D. Gearhart, Kenta Yamamoto, Karen Echeverri

Inflammatory response in hematopoietic stem and progenitor cells triggered by activating SHP2 mutations potentiates leukemogenesis
Maja Solman, Sasja Blokzijl-Franke, Florian Piques, Chuan Yan, Qiqi Yang, Marion Strullu, Sarah M. Kamel, Pakize Ak, Jeroen Bakkers, David M. Langenau, Hélène Cavé, Jeroen den Hertog

Birth and delineation of the intestinal stem cell niche
Neil McCarthy, Guodong Tie, Shariq Madha, Adrianna Maglieri, Judith Kraiczy, Ramesh Shivdasani

Pollutants corrupt resilience pathways of aging in the nematode C. elegans
Andrea Scharf, Annette Limke, Karl-Heinz Guehrs, Anna von Mikecz

Sex differences and risk factors for bleeding in Alagille syndrome
Simona Hankeova, Noemi Van Hul, Jakub Laznovsky, Katrin Mangold, Naomi Hensens, Elvira Verhoef, Tomas Zikmund, Feven Dawit, Michaela Kavkova, Jakub Salplachta, Marika Sjöqvist, Bengt R. Johansson, Mohamed Hassan, Linda Fredriksson, Vitezslav Bryja, Urban Lendahl, Andrew Jheon, Florian Alten, Kristina Teär Fahnehjelm, Björn Fischler, Jozef Kaiser, Emma R. Andersson

Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development
Karla T. Falcon, Kristin E.N. Watt, Soma Dash, Annita Achilleos, Ruonan Zhao, Daisuke Sakai, Emma L. Moore, Sharien Fitriasari, Melissa Childers, Mihaela E. Sardiu, Selene Swanson, Dai Tsuchiya, Jay Unruh, George Bugarinovic, Lin Li, Rita Shiang, Jill Dixon, Michael J. Dixon, Paul A. Trainor

Tig1 regulates proximo-distal identity during salamander limb regeneration
Catarina R. Oliveira, Dunja Knapp, Ahmed Elewa, Tobias Gerber, Sandra G. Gonzalez Malagon, Phillip B. Gates, Hannah E. Walters, Andreas Petzold, Hernan Arce, Rodrigo C. Cordoba, Elaiyaraja Subramanian, Osvaldo Chara, Elly M. Tanaka, András Simon, Maximina H. Yun

Placental gene expression-based cell type deconvolution: Cell proportions drive preeclampsia gene expression differences
Kyle A Campbell, Justin A Colacino, Muraly Puttabyatappa, John F Dou, Elana R Elkin, Saher S Hammoud, Steven E Domino, Dana C Dolinoy, Jaclyn M Goodrich, Rita Loch-Caruso, Vasantha Padmanabhan, Kelly M Bakulski

Delayed implantation induced by letrozole in mice
Fang Wang, Shijie Li, Lingshuai Meng, Ye Kuang, Zhonghua Liu, Xinghong Ma

Endothelial-specific Gata3 expression is required for haematopoietic stem cell generation
Nada Zaidan, Evangelia Diamanti, Leslie Nitsche, Antonella Fidanza, Nicola K. Wilson, Lesley M. Forrester, Berthold Göttgens, Katrin Ottersbach

Nucleolin loss-of-function leads to aberrant FGF signaling and craniofacial anomalies
Soma Dash, Paul A. Trainor

Human iPSC-Based Model Reveals NOX4 as Therapeutic Target in Duchenne Cardiomyopathy
Robin Duelen, Domiziana Costamagna, Guillaume Gilbert, Liesbeth De Waele, Nathalie Goemans, Kaat Desloovere, Catherine M. Verfaillie, Karin R. Sipido, Gunnar M. Buyse, Maurilio Sampaolesi

Fluctuation of cellular differentiation in limb regeneration is regulated by Pde4b in urodele amphibians
Akira Satoh, Rena Kashimoto, Ayaka Ohashi, Furukawa Saya, Sakiya Yamamoto, Takeshi Inoue, Toshinori Hayashi, Kiyokazu Agata

Rod-genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor compositions and progressive retinal degeneration
Fei Liu, Yayun Qin, Yuwen Huang, Pan Gao, Jingzhen Li, Shanshan Yu, Danna Jia, Xiang Chen, Yuexia Lv, Jiayi Tu, Kui Sun, Yunqiao Han, James Reilly, Xinhua Shu, Qunwei Lu, Zhaohui Tang, Chengqi Xu, Daji Luo, Mugen Liu

Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning in FSHD
Katherine Williams, Xiangduo Kong, Nam Viet Nguyen, Cassandra McGill, Rabi Tawil, Kyoko Yokomori, Ali Mortazavi

Generation of iPSC lines with high cytogenetic stability from peripheral blood mononuclear cells (PBMCs)
Lindsay Panther, Loren Ornelas, Michelle R Jones, Andrew R. Gross, Emilda Gomez, Chunyan Liu, Benjamin Berman, Clive N. Svendsen, Dhruv Sareen

A Drosophila Su(H) Model of Adams-Oliver Syndrome Reveals Notch Cofactor Titration as a Mechanism Underlying Developmental Defects
Ellen K. Gagliani, Lisa M. Gutzwiller, Yi Kuang, Yoshinobu Odaka, Phillipp Hoffmeister, Stefanie Hauff, Aleksandra Turkiewicz, Emily Harding-Theobald, Patrick J. Dolph, Tilman Borggrefe, Franz Oswald, Brian Gebelein, Rhett A. Kovall

Genetic studies of human-chimpanzee divergence using stem cell fusions
Janet H.T. Song, Rachel L. Grant, Veronica C. Behrens, Marek Kucka, Garrett A. Roberts Kingman, Volker Soltys, Yingguang Frank Chan, David M. Kingsley

AMPK regulates germline stem cell integrity and quiescence through a mir-1/tbc-7/rab-7 pathway in C. elegans
Christopher Wong, Pratik Kadekar, Elena Jurczak, Richard Roy

Pathological LSD1 mutations repress enhancer-mediated gene regulatory networks in early differentiation
Daria Bunina, Pierre-Luc Germain, Alejandro Lopez Tobon, Nadine Fernandez-Novel Marx, Christian Arnold, Andrew Ahern, Annique Claringbould, Mang Ching Lai, Sampath Rangasamy, Vinodh Narayanan, Peter Lorentzen, Karen M. Park, Antonio Adamo, Giuseppe Testa, Judith Zaugg, Kyung-Min Noh

Knockout of E-cadherin in adult mouse epithelium results in emphysema and airway disease
Baishakhi Ghosh, Jeffrey Loube, Shreeti Thapa, Erin Capodanno, Saborny Mahmud, Mirit Girgis, Si Chen, Kristine Nishida, Linyan Ying, Carter Swaby, Ara Wally, Debarshi Bhowmik, Michael Zaykaner, Wayne Mitzner, Venkataramana K. Sidhaye

Yap/Taz-Activated Tert-Expressing Acinar Cells Are Required for Pancreatic Regeneration
Han Na Suh, Moon Jong Kim, Sung Ho Lee, Sohee Jun, Jie Zhang, Randy L. Johnson, Jae-Il Park

Folic Acid Exerts Dose-Dependent Biphasic Effects on Cardiac Development of Zebrafish Embryos
Xuhui Han , Bingqi Wang , Hongjie Wang , Yao Zu

Long-term Transplant Effects of iPSC-RPE Monolayer in Immunodeficient RCS Rats
Deepthi S. Rajendran Nair , Danhong Zhu , Ruchi Sharma , Juan Carlos Martinez Camarillo , Kapil Bharti , David R. Hinton , Mark S. Humayun , Biju B. Thomas

| Plant development

PIN-FORMED1 polarity in the shoot is insensitive to the polarity of neighbouring cells
Abdul Kareem, Neha Bhatia, Carolyn Ohno, Marcus G. Heisler

Temporal Changes in Transcripts of MITE Transposable Elements during Rice Endosperm Development
Hiroki Nagata, Akemi Ono, Kaoru Tonosaki, Taiji Kawakatsu, Kentaro Yano, Yuji Kishima, Tetsu Kinoshita

miPEP858/miR858-MYB3-PSK4 module regulates growth and development in Arabidopsis
Poorwa Kamal Badola, Ashish Sharma, Himanshi Gautam, Prabodh Kumar Trivedi

Differed cell division angle, position of cell proliferative area, and localization of ANGUSTIFOLIA3 in lateral organs
Ayaka Kinoshita, Makiko Naito, Hirokazu Tsukaya

DcPAR1 is Required for Development and Carotenoid Synthesis in the Dark-Grown Carrot Taproot
Daniela Arias, Angélica Ortega, Christian González, Luis Felipe Quiroz, Jordi Moreno-Romero, Jaime F. Martínez-García, Claudia Stange

Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex
Francisco Ortigosa, César Lobato-Fernández, Hitomi Shikano, Concepción Ávila, Shu Taira, Francisco M. Cánovas, Rafael A. Cañas

small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems
Mark A. A. Minow, Viktoriya Coneva, Victoria Lesy, Max Misyura, Joseph Colasanti

AtRBOHC/RHD2 vesicular delivery to the apical plasma membrane domain during root hair development
Lenka Kuběnová, Michaela Tichá, Jozef Šamaj, Miroslav Ovečka

A vacuolar hexose transport is required for xylem development in the inflorescence stem of Arabidopsis
Emilie Aubry, Beate Hoffmann, Françoise Vilaine, Françoise Gilard, Patrick A.W. Klemens, Florence Guérard, Bertrand Gakière, H. Ekkehard Neuhaus, Catherine Bellini, Sylvie Dinant, Rozenn Le Hir

Developmental integration cannot explain major features of stomatal anatomical evolution in seed plants
Christopher D. Muir, Miquel Àngel Conesa, Jeroni Galmés, Varsha S. Pathare, Patricia Rivera, Rosana López Rodríguez, Teresa Terrazas, Dongliang Xiong

| Evo-devo

The pseudobranch of jawed vertebrates is a mandibular arch-derived gill
Christine Hirschberger, J. Andrew Gillis

Single-cell transcriptomic analysis unveils spinal motor neuron subtype diversity underpinning the water-to-land transition in vertebrates
Ee Shan Liau, Suoqin Jin, Yen-Chung Chen, Wei-Szu Liu, Luok Wen Yong, Chang-Tai Tsai, Maëliss Calon, Jr-Kai Yu, Yi-Hsien Su, Stéphane Nedelec, Qing Nie, Jun-An Chen

Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy
Katie Mika, Camilla M. Whittington, Bronwyn M. McAllan, Vincent J. Lynch

Glue genes are subjected to diverse selective forces during Drosophila development
Flora Borne, Rob J. Kulathinal, Virginie Courtier-Orgogozo

The genetic basis of tail-loss evolution in humans and apes
Bo Xia, Weimin Zhang, Aleksandra Wudzinska, Emily Huang, Ran Brosh, Maayan Pour, Alexander Miller, Jeremy S. Dasen, Matthew T. Maurano, Sang Y. Kim, Jef D. Boeke, Itai Yanai

Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish
Lucia Irazábal-González, Daniel Shane Wright, Martine Maan

Cell Biology

Production of Offspring from Azoospermic Mice with Meiotic Failure: Precise Biparental Meiosis within Halved Oocytes
Narumi Ogonuki, Hirohisa Kyogoku, Toshiaki Hino, Yuki Osawa, Yasuhiro Fujiwara, Kimiko Inoue, Tetsuo Kunieda, Seiya Mizuno, Hiroyuki Tateno, Fumihiro Sugiyama, Tomoya S. Kitajima, Atsuo Ogura

Promyelocytic leukemia nuclear body (PML-NB) -free intranuclear milieu facilitates development of oocytes in mice
Osamu Udagawa, Ayaka Kato-Udagawa, Seishiro Hirano

A genetic bottleneck of mitochondrial DNA during human lymphocyte development
Zhongjie Tang, Zhaolian Lu, Baizhen Chen, Weixing Zhang, Howard Chang, Zheng Hu, Jin Xu

The retromer complex regulates C. elegans development and mammalian ciliogenesis
Shuwei Xie, Ellie Smith, Carter Dierlam, Danita Mathew, Angelina Davis, Allana Williams, Naava Naslavsky, Jyoti Iyer, Steve Caplan

Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection
Andrew K. Beppu, Juanjuan Zhao, Changfu Yao, Gianni Carraro, Edo Israely, Anna Lucia Coelho, Cory M Hogaboam, William C. Parks, Jay K. Kolls, Barry R. Stripp

A condensate dynamic instability orchestrates oocyte actomyosin cortex activation
Victoria Tianjing Yan, Arjun Narayanan, Frank Jülicher, Stephan W. Grill

Blm Helicase Facilitates Rapid Replication of Repetitive DNA Sequences in early Drosophila Development
Jolee M. Ruchert, Morgan M Brady, Susan McMahan, Karly J. Lacey, Leigh C. Latta, Jeff Sekelsky, Eric P. Stoffregen

Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis
Dorothee Stöckle, Blanca Jazmin Reyes-Hernández, Amaya Vilches Barro, Milica Nenadic, Zsófia Winter, Sophie Marc-Martin, Lotte Bald, Robertas Ursache, Satoshi Fujita, Alexis Maizel, Joop EM Vermeer

ERM-1 phosphorylation and NRFL-1 redundantly control lumen formation in the C. elegans intestine
Jorian J. Sepers, João J. Ramalho, Jason R. Kroll, Ruben Schmidt, Mike Boxem

Modelling

Time to stop; agent-based modelling of chemoaffinity with competition
Sebastian S. James, Stuart P. Wilson

Mathematical model reveals that heterogeneity in the number of ion transporters regulates the fraction of mouse sperm capacitation
Alejandro Aguado-García, Daniel A. Priego-Espinosa, Andrés Aldana, Alberto Darszon, Gustavo Martínez-Mekler

How Our Cells Become Our Selves: The Cellular Phylodynamic Biology of Growth and Development
Philip Chodrow, Jessica Su, Daniel Lee, Tahmid Ahmed, Neil He, De Man Ruben, Ankur Tiwari, William Mannherz, Luca Citi, Daniel DiCorpo, James Selib Michaelson

How the naked mole-rat resists senescence: a constraints-based theory
Felipe A. Veloso

Deconstructing Gastrulation at the Single Cell Level
Tomer Stern, Sebastian J. Streichan, Stanislav Y. Shvartsman, Eric F. Wieschaus

Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor
Weikang Wang, Dante Poe, Yaxuan Yang, Thomas Hyatt, Jianhua Xing

Modelling the collective mechanical regulation of the structure and morphology of epithelial cell layers
Hamid Khataee, Madeleine Fraser, Zoltan Neufeld

Swapping in lattice-based cell migration models
Shahzeb Raja Noureen, Jennifer P. Owen, Richard L. Mort, Christian A. Yates

Shear-driven solidification and nonlinear elasticity in epithelial tissues
Junxiang Huang, James O. Cochran, Suzanne M. Fielding, M. Cristina Marchetti, Dapeng Bi

Motility switching and front-back synchronisation in polarized cells
Gissell Estrada-Rodriguez, Benoit Perthame

Mechanisms for spontaneous symmetry breaking in developing visual cortex
Francesco Fumarola, Bettina Hein, Kenneth D. Miller

Dynamical-systems theory of cellular reprogramming
Yuuki Matsushita, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko

Is Cell segregation just like oil and water?
Florian Franke, Sebatian Aland, Hans-Joachim Böhme, Anja Voss-Böhme, Steffen Lange

Multi-StyleGAN: Towards Image-Based Simulation of Time-Lapse Live-Cell Microscopy
Christoph Reich, Tim Prangemeier, Christian Wildner, Heinz Koeppl

Morphogen-regulated contact-mediated signaling between cells can drive the transitions underlying body segmentation in vertebrates
Chandrashekar Kuyyamudi, Shakti N. Menon, Sitabhra Sinha

Reviews

Regenerating Damaged Myocardium: A Review of Stem-Cell Therapies for Heart Failure
Dihan Fan , Hanrong Wu , Huashan Peng , Kaichao Pan , Rongxue Wu

Epigenetic Clock, Circadian Rhythms and Cell Aging
Ekaterina Samoilova , Vladimir Belopasov , Evgenia Ekusheva , Chao Zhang ORCID logo , Alexander Troitskiy , Vladimir Baklaushev

Tools & Resources

The temporal dynamics of the sea urchin regulome
Roberto Feuda

A cellular and molecular atlas reveals the basis of chytrid development
Davis Laundon, Nathan Chrismas, Kimberley Bird, Seth Thomas, Thomas Mock, Michael Cunliffe

A cell atlas of the fly kidney
Jun Xu, Yifang Liu, Hongjie Li, Alexander J. Tarashansky, Colin H. Kalicki, Ruei-Jiun Hung, Yanhui Hu, Aram Comjean, Sai Saroja Kolluru, Bo Wang, Stephen R Quake, Liqun Luo, Andrew P. McMahon, Julian A.T. Dow, Norbert Perrimon

GraviKit: an easy-to-implement microscope add-on for observation of gravitation dependent processes
Christian Feldhaus, Martina Kolb, Michelle Küppers, Steffen Hardy, Ralph Palmisano

Direct cryopreservation of poultry/avian embryonic reproductive cells: A low-tech, cost-effective and efficient method for safeguarding genetic diversity
Tuanjun Hu, Lorna Taylor, Adrian Sherman, Christian Keambou Tiambo, Steven J Kemp, Rachel J Hawken, Bruce Whitelaw, Appolinaire Dijkeng, Michael J McGrew

Tracking cell lineages in 3D by incremental deep learning
Ko Sugawara, Cagri Cevrim, Michalis Averof

Extraembryonic endoderm cells induce neuroepithelial tissue in gastruloids
Noémie M. L. P. Bérenger-Currias, Maria Mircea, Esmée Adegeest, Patrick R. van den Berg, Marleen Feliksik, Mazène Hochane, Timon Idema, Sander Tans, Stefan Semrau

SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo
Mattias Malaguti, Rosa Portero Migueles, Jennifer Annoh, Daina Sadurska, Guillaume Blin, Sally Lowell

ZAF – The First Open Source Fully Automated Feeder for Aquatic Facilities
Merlin Lange, AhmetCan Solak, Shruthi Vijay Kumar, Hirofumi Kobayashi, Bin Yang, Loic A. Royer

Symmetry breaking of hPSCs in micropattern generates a polarized spinal cord-like organoid (pSCO) with dorsoventral organization
Kyubin Seo, Subin Cho, Ju-Hyun Lee, June Hoan Kim, Boram Lee, Hwanseok Jang, Youngju Kim, Hyo Min Cho, Sanghyuk Lee, Yongdoo Park, Hee Youn Kim, Taeseob Lee, Woong-Yang Park, Yong Jun Kim, Esther Yang, Dongho Geum, Hyun Kim, Jae Ryun Ryu, Woong Sun

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology
Anthony J Geneva, Sungdae Park, Dan Bock, Pietro de Mello, Fatih Sarigol, Marc Tollis, Colin Donihue, R Graham Reynolds, Nathalie Feiner, Ashley Rasys, James Lauderdale, Sergio G Minchey, Aaron J Alcala, Carlos Infante, Jason J Kolbe, Dolph Schluter, Douglas B Menke, Jonathan B Losos

Protein visualization and manipulation in Drosophila through the use of epitope tags recognized by nanobodies
Jun Xu, Ah-Ram Kim, Ross W Cheloha, Fabian A Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie Mohr, Jonathan Zirin, Hidde Ploegh, Norbert Perrimon

JaponicusDB: Rapid deployment of a model organism database for an emerging model species
Kim M. Rutherford, Midori A. Harris, Snezhana Oliferenko, Valerie Wood

LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data
Wenjing Ma, Sumeet Sharma, Peng Jin, Shannon L. Gourley, Zhaohui Qin

Zebrafish Information Network, the knowledgebase for Danio rerio research
Yvonne M. Bradford, Ceri E. Van Slyke, Amy Singer, Holly Paddock, Anne Eagle, David Fashena, Douglas G. Howe, Ken Frazer, Ryan Martin, Christian Pich, Sridhar Ramachandran, Leyla Ruzicka, Monte Westerfield

Context-aware deconvolution of cell-cell communication with Tensor-cell2cell
Erick Armingol, Hratch M. Baghdassarian, Cameron Martino, Araceli Perez-Lopez, Rob Knight, Nathan E. Lewis

deCS: A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues
Guangsheng Pei, Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao

The Incubascope : a simple, compact and large field of view microscope for long-term imaging inside an incubator
Amaury Badon, Laetitia Andrique, Amaël Mombereau, Louis Rivet, Adeline Boyreau, Pierre Nassoy, Gaëlle Recher

Self-organized emergence of hyaline cartilage in hiPSC-derived multi-tissue organoids
Manci Li, Juan E. Abrahante, Amanda Vegoe, Yi Wen Chai, Beth Lindborg, Ferenc Toth, Peter A. Larsen, Timothy D. O’Brien

Bringing TrackMate into the era of machine-learning and deep-learning
Dmitry Ershov, Minh-Son Phan, Joanna W. Pylvänäinen, Stéphane U. Rigaud, Laure Le Blanc, Arthur Charles-Orszag, James R. W. Conway, Romain F. Laine, Nathan H. Roy, Daria Bonazzi, Guillaume Duménil, Guillaume Jacquemet, Jean-Yves Tinevez

Evaluation of cell segmentation methods without reference segmentations
Haoran Chen, Robert F. Murphy

OmicsView: omics data analysis through interactive visual analytics
Fergal Casey, Soumya Negi, Jing Zhu, Maria Zavodszky, Derrick Cheng, Dongdong Lin, Sally John, Michelle A. Penny, David Sexton, Baohong Zhang

Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)
Hugo G.J. Damstra, Boaz Mohar, Mark Eddison, Anna Akhmanova, Lukas C. Kapitein, Paul W. Tillberg

A reference tissue atlas for the human kidney
Jens Hansen, Rachel Sealfon, Rajasree Menon, Michael T. Eadon, Blue B. Lake, Becky Steck, Dejan Dobi, Samir Parikh, Tara K. Sigdel, Guanshi Zhang, Dusan Velickovic, Daria Barwinska, Theodore Alexandrov, Priyanka Rashmi, Edgar A. Otto, Michael P. Rose, Christopher R. Anderton, John P. Shapiro, Annapurna Pamreddy, Seth Winfree, Yongqun He, Ian H. de Boer, Jeffrey B. Hodgin, Laura Barisoni, Abhijit S. Naik, Kumar Sharma, Minnie M. Sarwal, Kun Zhang, Jonathan Himmelfarb, Brad Rovin, Tarek M. El-Achkar, Zoltan Laszik, John Cijiang He, Pierre C. Dagher, M. Todd Valerius, Sanjay Jain, Lisa Satlin, Olga G. Troyanskaya, Matthias Kretzler, Ravi Iyengar, Evren U. Azeloglu, for the Kidney Precision Medicine Project

Versatile, do-it-yourself, low-cost spinning disk confocal microscope
Aaron R. Halpern, Min Yen Lee, Marco D. Howard, Marcus A. Woodworth, Philip R. Nicovich, Joshua C. Vaughan

ShareLoc – an open platform for sharing localization microscopy data
Jiachuan Bai, Wei Ouyang, Manish Kumar Singh, Christophe Leterrier, Paul Barthelemy, Samuel F.H. Barnett, Teresa Klein, Markus Sauer, Pakorn Kanchanawong, Nicolas Bourg, Mickael M. Cohen, Benoît Lelandais, Christophe Zimmer

Julia for Biologists
Elisabeth Roesch, Joe G. Greener, Adam L. MacLean, Huda Nassar, Christopher Rackauckas, Timothy E. Holy, Michael P.H. Stumpf

Plotgardener: Cultivating precise multi-panel figures in R
Nicole E Kramer, Eric S Davis, Craig D Wenger, Erika M Deoudes, Sarah M Parker, Michael I Love, Douglas H Phanstiel

How to address cellular heterogeneity by distribution biology
Niko Komin, Alexander Skupin

BioLCNet: Reward-modulated Locally Connected Spiking Neural Networks
Hafez Ghaemi, Erfan Mirzaei, Mahbod Nouri, Saeed Reza Kheradpisheh

Equivariant Filters for Efficient Tracking in 3D Imaging
Daniel Moyer, Esra Abaci Turk, P Ellen Grant, William M. Wells, Polina Golland

Research practice & education

The apportionment of citations: A scientometric analysis of Lewontin, 1972
Jedidiah Carlson, Kelley Harris

Free for all, or free-for-all? A content analysis of Australian university open access policies
Simon Wakeling, Danny Kingsley, Hamid R. Jamali, Mary Anne Kennan, Hamid Jamali, Maryam Sarrafzadeh

Finding a Balance: Characterizing Teaching and Research Anxieties in Biology Graduate Teaching Assistants (GTAs)
Miranda M. Chen Musgrove, Kate Petrie, Alyssa Cooley, Elisabeth E. Schussler

Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors
Nicholas Fraser, Philipp Mayr, Isabella Peters

The Case for Standardising Gene Nomenclature Across Vertebrates
Fiona M. McCarthy , Tamsin E.M. Jones , Anne E. Kwitek , Cynthia L. Smith , Peter D. Vize , Monte Westerfield , Elspeth A. Bruford

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