[{"oa_version":"Published Version","publication_status":"published","publisher":"Oxford University Press","type":"journal_article","article_type":"original","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awac145"}],"keyword":["Neurology (clinical)"],"date_updated":"2026-06-18T17:24:52Z","title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","department":[{"_id":"GaNo"}],"pmid":1,"ec_funded":1,"_id":"12174","publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"isi":1,"year":"2022","issue":"8","publication":"Brain","language":[{"iso":"eng"}],"page":"2687-2703","author":[{"first_name":"Renzo","full_name":"Guerrini, Renzo","last_name":"Guerrini"},{"last_name":"Mei","full_name":"Mei, Davide","first_name":"Davide"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","last_name":"Szigeti","orcid":"0000-0001-9500-8758","full_name":"Szigeti, Margit Katalin","first_name":"Margit Katalin"},{"full_name":"Pepe, Sara","last_name":"Pepe","first_name":"Sara"},{"full_name":"Koenig, Mary Kay","last_name":"Koenig","first_name":"Mary Kay"},{"last_name":"Von Allmen","full_name":"Von Allmen, Gretchen","first_name":"Gretchen"},{"first_name":"Megan T","last_name":"Cho","full_name":"Cho, Megan T"},{"last_name":"McDonald","full_name":"McDonald, Kimberly","first_name":"Kimberly"},{"last_name":"Baker","full_name":"Baker, Janice","first_name":"Janice"},{"first_name":"Vikas","full_name":"Bhambhani, Vikas","last_name":"Bhambhani"},{"last_name":"Powis","full_name":"Powis, Zöe","first_name":"Zöe"},{"first_name":"Lance","last_name":"Rodan","full_name":"Rodan, Lance"},{"last_name":"Nabbout","full_name":"Nabbout, Rima","first_name":"Rima"},{"first_name":"Giulia","full_name":"Barcia, Giulia","last_name":"Barcia"},{"first_name":"Jill A","last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A"},{"full_name":"Bacino, Carlos A","last_name":"Bacino","first_name":"Carlos A"},{"full_name":"Mignot, Cyril","last_name":"Mignot","first_name":"Cyril"},{"full_name":"Power, Lillian H","last_name":"Power","first_name":"Lillian H"},{"first_name":"Catharine J","full_name":"Harris, Catharine J","last_name":"Harris"},{"first_name":"Dragan","full_name":"Marjanovic, Dragan","last_name":"Marjanovic"},{"full_name":"Møller, Rikke S","last_name":"Møller","first_name":"Rikke S"},{"first_name":"Trine B","full_name":"Hammer, Trine B","last_name":"Hammer"},{"full_name":"Keski Filppula, Riikka","last_name":"Keski Filppula","first_name":"Riikka"},{"last_name":"Vieira","full_name":"Vieira, Päivi","first_name":"Päivi"},{"full_name":"Hildebrandt, Clara","last_name":"Hildebrandt","first_name":"Clara"},{"first_name":"Stephanie","last_name":"Sacharow","full_name":"Sacharow, Stephanie"},{"first_name":"Luca","last_name":"Maragliano","full_name":"Maragliano, Luca"},{"first_name":"Fabio","full_name":"Benfenati, Fabio","last_name":"Benfenati"},{"full_name":"Lachlan, Katherine","last_name":"Lachlan","first_name":"Katherine"},{"first_name":"Andreas","last_name":"Benneche","full_name":"Benneche, Andreas"},{"last_name":"Petit","full_name":"Petit, Florence","first_name":"Florence"},{"last_name":"de Sainte Agathe","full_name":"de Sainte Agathe, Jean Madeleine","first_name":"Jean Madeleine"},{"full_name":"Hallinan, Barbara","last_name":"Hallinan","first_name":"Barbara"},{"first_name":"Yue","last_name":"Si","full_name":"Si, Yue"},{"first_name":"Ingrid M","last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M"},{"first_name":"Fanggeng","full_name":"Zou, Fanggeng","last_name":"Zou"},{"first_name":"Vinodh","last_name":"Narayanan","full_name":"Narayanan, Vinodh"},{"first_name":"Naomichi","last_name":"Matsumoto","full_name":"Matsumoto, Naomichi"},{"first_name":"Alessandra","full_name":"Boncristiano, Alessandra","last_name":"Boncristiano"},{"first_name":"Giancarlo","last_name":"la Marca","full_name":"la Marca, Giancarlo"},{"first_name":"Mitsuhiro","last_name":"Kato","full_name":"Kato, Mitsuhiro"},{"first_name":"Kristin","full_name":"Anderson, Kristin","last_name":"Anderson"},{"first_name":"Carmen","full_name":"Barba, Carmen","last_name":"Barba"},{"last_name":"Sturiale","full_name":"Sturiale, Luisa","first_name":"Luisa"},{"first_name":"Domenico","full_name":"Garozzo, Domenico","last_name":"Garozzo"},{"first_name":"Roberto","full_name":"Bei, Roberto","last_name":"Bei"},{"full_name":"Masuelli, Laura","last_name":"Masuelli","first_name":"Laura"},{"first_name":"Valerio","last_name":"Conti","full_name":"Conti, Valerio"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"last_name":"Fassio","full_name":"Fassio, Anna","first_name":"Anna"}],"external_id":{"isi":["000807770000001"],"pmid":["35675510"]},"volume":145,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-01T00:00:00Z","status":"public","acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","article_processing_charge":"No","oa":1,"ddc":["570"],"abstract":[{"text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.\r\n Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.","lang":"eng"}],"doi":"10.1093/brain/awac145","intvolume":" 145","day":"01","scopus_import":"1","citation":{"short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703.","ieee":"R. Guerrini et al., “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” Brain, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022.","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 2022;145(8):2687-2703. doi:10.1093/brain/awac145","ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. Oxford University Press. https://doi.org/10.1093/brain/awac145","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:10.1093/brain/awac145.","chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain. Oxford University Press, 2022. https://doi.org/10.1093/brain/awac145."},"date_created":"2023-01-12T12:11:45Z","quality_controlled":"1"},{"pmid":1,"_id":"12238","publication_identifier":{"issn":["1534-5807"]},"OA_place":"publisher","isi":1,"date_updated":"2026-06-18T17:25:21Z","department":[{"_id":"CaHe"}],"title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","article_type":"original","month":"10","OA_type":"free access","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.09.003","open_access":"1"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"oa_version":"Published Version","publication_status":"published","publisher":"Elsevier","type":"journal_article","doi":"10.1016/j.devcel.2022.09.003","intvolume":" 57","day":"01","corr_author":"1","quality_controlled":"1","date_created":"2023-01-16T09:51:39Z","citation":{"ama":"Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 2022;57(19):2290-2304.e7. doi:10.1016/j.devcel.2022.09.003","short":"N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji, K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57 (2022) 2290–2304.e7.","ieee":"N. Hino et al., “A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration,” Developmental Cell, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.","ista":"Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K, Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 57(19), 2290–2304.e7.","mla":"Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” Developmental Cell, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:10.1016/j.devcel.2022.09.003.","apa":"Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda, M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.09.003","chicago":"Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.09.003."},"scopus_import":"1","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration."}],"ddc":["570"],"volume":57,"external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"author":[{"first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"last_name":"Matsuda","full_name":"Matsuda, Kimiya","first_name":"Kimiya"},{"last_name":"Jikko","full_name":"Jikko, Yuya","first_name":"Yuya"},{"last_name":"Maryu","full_name":"Maryu, Gembu","first_name":"Gembu"},{"first_name":"Katsuya","full_name":"Sakai, Katsuya","last_name":"Sakai"},{"first_name":"Ryu","full_name":"Imamura, Ryu","last_name":"Imamura"},{"last_name":"Tsukiji","full_name":"Tsukiji, Shinya","first_name":"Shinya"},{"first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro","last_name":"Aoki"},{"last_name":"Terai","full_name":"Terai, Kenta","first_name":"Kenta"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"date_published":"2022-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank the members of the Matsuda Laboratory for their helpful discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical assistance. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107 and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no. JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER (no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739 to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO. This work was partly supported by an Extramural Collaborative Research Grant of Cancer Research Institute, Kanazawa University.","status":"public","year":"2022","issue":"19","language":[{"iso":"eng"}],"publication":"Developmental Cell","page":"2290-2304.e7"},{"quality_controlled":"1","date_created":"2023-01-16T10:01:44Z","citation":{"ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 2022;23(7). doi:10.15252/embr.202154163","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” EMBO Reports, vol. 23, no. 7. Embo Press, 2022.","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.","mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23, no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.","apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163."},"scopus_import":"1","day":"05","intvolume":" 23","doi":"10.15252/embr.202154163","ddc":["570"],"abstract":[{"text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.","lang":"eng"}],"oa":1,"article_number":"e54163","article_processing_charge":"No","has_accepted_license":"1","status":"public","acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-07-05T00:00:00Z","volume":23,"external_id":{"pmid":["35586945"],"isi":["000797302700001"]},"author":[{"full_name":"Rahman, Maisha","last_name":"Rahman","first_name":"Maisha"},{"id":"39831956-E4FE-11E9-85DE-0DC7E5697425","last_name":"Ramirez","full_name":"Ramirez, Nelson","first_name":"Nelson"},{"first_name":"Carlos A","last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A"},{"last_name":"Bülow","full_name":"Bülow, Hannes E","first_name":"Hannes E"}],"publication":"EMBO Reports","language":[{"iso":"eng"}],"issue":"7","year":"2022","isi":1,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"_id":"12275","pmid":1,"department":[{"_id":"MaDe"}],"title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","date_updated":"2026-06-18T17:26:25Z","keyword":["Genetics","Molecular Biology","Biochemistry"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.15252/embr.202154163"}],"month":"07","article_type":"original","type":"journal_article","publication_status":"published","publisher":"Embo Press","oa_version":"Published Version"},{"type":"journal_article","publisher":"Elsevier","publication_status":"published","oa_version":"Published Version","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.11.006","open_access":"1"}],"OA_type":"free access","month":"12","article_type":"original","department":[{"_id":"JiFr"}],"title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","date_updated":"2026-06-18T17:23:10Z","OA_place":"publisher","isi":1,"publication_identifier":{"issn":["1534-5807"]},"_id":"12120","pmid":1,"page":"2638-2651.e6","language":[{"iso":"eng"}],"publication":"Developmental Cell","issue":"23","year":"2022","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-05T00:00:00Z","volume":57,"external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"author":[{"last_name":"Xiao","full_name":"Xiao, Huixin","first_name":"Huixin"},{"first_name":"Yumei","last_name":"Hu","full_name":"Hu, Yumei"},{"first_name":"Yaping","full_name":"Wang, Yaping","last_name":"Wang"},{"first_name":"Jinkui","full_name":"Cheng, Jinkui","last_name":"Cheng"},{"last_name":"Wang","full_name":"Wang, Jinyi","first_name":"Jinyi"},{"first_name":"Guojingwei","full_name":"Chen, Guojingwei","last_name":"Chen"},{"first_name":"Qian","last_name":"Li","full_name":"Li, Qian"},{"first_name":"Shuwei","last_name":"Wang","full_name":"Wang, Shuwei"},{"first_name":"Yalu","full_name":"Wang, Yalu","last_name":"Wang"},{"first_name":"Shao-Shuai","full_name":"Wang, Shao-Shuai","last_name":"Wang"},{"first_name":"Yi","last_name":"Wang","full_name":"Wang, Yi"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Li, Zhen","last_name":"Li","first_name":"Zhen"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"first_name":"Zhizhong","full_name":"Gong, Zhizhong","last_name":"Gong"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"Jing","full_name":"Zhang, Jing","last_name":"Zhang"}],"abstract":[{"lang":"eng","text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth."}],"ddc":["580"],"oa":1,"article_processing_charge":"No","quality_controlled":"1","citation":{"ieee":"H. Xiao et al., “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006.","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6."},"date_created":"2023-01-12T11:57:00Z","scopus_import":"1","day":"05","intvolume":" 57","doi":"10.1016/j.devcel.2022.11.006"},{"oa_version":"Published Version","publication_status":"published","publisher":"American Association for the Advancement of Science","type":"journal_article","article_type":"letter_note","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adg0797"}],"date_updated":"2026-06-18T17:22:36Z","department":[{"_id":"FyKo"}],"title":"Remote opportunities for scholars in Ukraine","pmid":1,"_id":"12116","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"isi":1,"year":"2022","issue":"6626","page":"1285-1286","language":[{"iso":"eng"}],"publication":"Science","volume":378,"author":[{"full_name":"Chhugani, Karishma","last_name":"Chhugani","first_name":"Karishma"},{"first_name":"Alina","last_name":"Frolova","full_name":"Frolova, Alina"},{"full_name":"Salyha, Yuriy","last_name":"Salyha","first_name":"Yuriy"},{"first_name":"Andrada","full_name":"Fiscutean, Andrada","last_name":"Fiscutean"},{"first_name":"Oksana","last_name":"Zlenko","full_name":"Zlenko, Oksana"},{"full_name":"Reinsone, Sanita","last_name":"Reinsone","first_name":"Sanita"},{"first_name":"Walter W.","full_name":"Wolfsberger, Walter W.","last_name":"Wolfsberger"},{"first_name":"Oleksandra V.","full_name":"Ivashchenko, Oleksandra V.","last_name":"Ivashchenko"},{"full_name":"Maci, Megi","last_name":"Maci","first_name":"Megi"},{"first_name":"Dmytro","last_name":"Dziuba","full_name":"Dziuba, Dmytro"},{"full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko","first_name":"Andrii"},{"first_name":"Eric","full_name":"Bortz, Eric","last_name":"Bortz"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"full_name":"Romero, Veronika","last_name":"Romero","first_name":"Veronika"},{"full_name":"Hlávka, Jakub","last_name":"Hlávka","first_name":"Jakub"},{"last_name":"Oleksyk","full_name":"Oleksyk, Taras K.","first_name":"Taras K."},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"}],"external_id":{"pmid":["36548425"],"isi":["000963463700023"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-22T00:00:00Z","status":"public","article_processing_charge":"No","oa":1,"ddc":["000"],"abstract":[{"text":"Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.","lang":"eng"}],"doi":"10.1126/science.adg0797","intvolume":" 378","day":"22","quality_controlled":"1","date_created":"2023-01-12T11:56:30Z","citation":{"ama":"Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. Science. 2022;378(6626):1285-1286. doi:10.1126/science.adg0797","short":"K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.","ieee":"K. Chhugani et al., “Remote opportunities for scholars in Ukraine,” Science, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022.","ista":"Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars in Ukraine. Science. 378(6626), 1285–1286.","mla":"Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” Science, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:10.1126/science.adg0797.","apa":"Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg0797","chicago":"Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.adg0797."},"scopus_import":"1"},{"publication":"Journal of Cell Science","language":[{"iso":"eng"}],"issue":"2","year":"2022","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-01-19T00:00:00Z","external_id":{"isi":["000762665200015"]},"author":[{"first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"volume":135,"abstract":[{"lang":"eng","text":"Martin Loose studied chemistry at the University of Heidelberg, Germany. He then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for work on self-organization and pattern formation in the bacterial Min protein system. He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular Biology Organization (EMBO) long-term fellowships; there, he discovered that the bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Martin established his independent research group at the Institute of Science and Technology (IST) Austria in 2015, supported by an European Research Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies the self-organization of bacterial cell division and small GTPase networks."}],"ddc":["570"],"oa":1,"article_processing_charge":"No","article_number":"jcs259715","quality_controlled":"1","citation":{"mla":"Loose, Martin. “Cell Scientist to Watch – Martin Loose.” Journal of Cell Science, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:10.1242/jcs.259715.","apa":"Loose, M. (2022). Cell scientist to watch – Martin Loose. Journal of Cell Science (Vol. 135). The Company of Biologists. https://doi.org/10.1242/jcs.259715","chicago":"Loose, Martin. Cell Scientist to Watch – Martin Loose. Journal of Cell Science. Vol. 135. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.259715.","ista":"Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.","ama":"Loose M. Cell Scientist to Watch – Martin Loose. Vol 135. The Company of Biologists; 2022. doi:10.1242/jcs.259715","short":"M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022.","ieee":"M. Loose, Cell scientist to watch – Martin Loose, vol. 135, no. 2. The Company of Biologists, 2022."},"date_created":"2024-05-28T13:28:30Z","day":"19","intvolume":" 135","doi":"10.1242/jcs.259715","type":"other_academic_publication","publisher":"The Company of Biologists","publication_status":"published","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1242/jcs.259715","open_access":"1"}],"month":"01","title":"Cell scientist to watch – Martin Loose","department":[{"_id":"MaLo"}],"date_updated":"2026-06-18T17:51:26Z","isi":1,"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"_id":"17057"},{"publication":"Model Organisms in Plant Genetics","language":[{"iso":"eng"}],"year":"2022","acknowledgement":"The authors would like to thank Dr. Jeroen de Keijzer and Dr. Tijs Ketelaar for their thoughtful and detailed review of the manuscript. Also, the funding agencies Technology, Knowledge and Innovation, division Horticulture and Propagating Material (TKI T&U) and the Dutch Research Council (NWO) (reference number: TKILWV20.390) for funding JFC and the ERC grant to Prof. J. Friml (reference number: PR1023ERC02) for funding HT. The authors would like to sincerely apologise for the literature not cited that may be relevant for this chapter and is not present due to space constraints.","status":"public","date_published":"2022-06-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Floriach-Clark, Jordi","last_name":"Floriach-Clark","first_name":"Jordi"},{"first_name":"Han","orcid":"0000-0001-6152-6637","full_name":"Tang, Han","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","last_name":"Tang"},{"first_name":"Viola","last_name":"Willemsen","full_name":"Willemsen, Viola"}],"abstract":[{"lang":"eng","text":"Mosses are a cosmopolitan group of land plants, sister to vascular plants, with a high potential for molecular and cell biological research. The species Physcomitrium patens has helped gaining better understanding of the biological processes of the plant cell, and it has become a central system to understand water-to-land plant transition through 2D-to-3D growth transition, regulation of asymmetric cell division, shoot apical cell establishment and maintenance, phyllotaxis and regeneration. P. patens was the first fully sequenced moss in 2008, with the latest annotated release in 2018. It has been shown that many gene functions and networks are conserved in mosses when compared to angiosperms. Importantly, this model organism has a simplified and accessible body structure that facilitates close tracking in time and space with the support of live cell imaging set-ups and multiple reporter lines. This has become possible thanks to its fully established molecular toolkit, with highly efficient PEG-assisted, CRISPR/Cas9 and RNAi transformation and silencing protocols, among others. Here we provide examples on how mosses exhibit advantages over vascular plants to study several processes and their future potential to answer some other outstanding questions in plant cell biology."}],"ddc":["580"],"editor":[{"last_name":"Abdurakhmonov","full_name":"Abdurakhmonov, Ibrokhim Y.","first_name":"Ibrokhim Y."}],"oa":1,"article_processing_charge":"No","quality_controlled":"1","citation":{"ama":"Floriach-Clark J, Tang H, Willemsen V. Mosses: Accessible Systems for Plant Development Studies. In: Abdurakhmonov IY, ed. Model Organisms in Plant Genetics. IntechOpen; 2022. doi:10.5772/intechopen.100535","ieee":"J. Floriach-Clark, H. Tang, and V. Willemsen, “Mosses: Accessible Systems for Plant Development Studies,” in Model Organisms in Plant Genetics, I. Y. Abdurakhmonov, Ed. IntechOpen, 2022.","short":"J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022.","ista":"Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .","apa":"Floriach-Clark, J., Tang, H., & Willemsen, V. (2022). Mosses: Accessible Systems for Plant Development Studies. In I. Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics. IntechOpen. https://doi.org/10.5772/intechopen.100535","mla":"Floriach-Clark, Jordi, et al. “Mosses: Accessible Systems for Plant Development Studies.” Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov, IntechOpen, 2022, doi:10.5772/intechopen.100535.","chicago":"Floriach-Clark, Jordi, Han Tang, and Viola Willemsen. “Mosses: Accessible Systems for Plant Development Studies.” In Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov. IntechOpen, 2022. https://doi.org/10.5772/intechopen.100535."},"date_created":"2024-05-29T06:35:13Z","day":"23","doi":"10.5772/intechopen.100535","publication_status":"published","type":"book_chapter","publisher":"IntechOpen","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5772/intechopen.100535"}],"month":"06","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"department":[{"_id":"JiFr"}],"title":"Mosses: Accessible Systems for Plant Development Studies","date_updated":"2026-06-18T17:52:59Z","publication_identifier":{"isbn":["9781839697500"]},"_id":"17085","ec_funded":1},{"day":"07","corr_author":"1","quality_controlled":"1","date_created":"2024-05-29T05:38:47Z","citation":{"short":"M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting 2022, Fundació Scito, 2022.","ieee":"M. Ibáñez, Y. Liu, and M. Calcabrini, “The importance of surface adsorbates in solution-processed thermoelectric materials,” in Proceedings of the nanoGe Spring Meeting 2022, Spain/Virtual, 2022.","ama":"Ibáñez M, Liu Y, Calcabrini M. The importance of surface adsorbates in solution-processed thermoelectric materials. In: Proceedings of the NanoGe Spring Meeting 2022. Fundació Scito; 2022. doi:10.29363/nanoge.nsm.2022.159","ista":"Ibáñez M, Liu Y, Calcabrini M. 2022. The importance of surface adsorbates in solution-processed thermoelectric materials. Proceedings of the nanoGe Spring Meeting 2022. SNI: Semiconductor Nanocrystals, 159.","mla":"Ibáñez, Maria, et al. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” Proceedings of the NanoGe Spring Meeting 2022, 159, Fundació Scito, 2022, doi:10.29363/nanoge.nsm.2022.159.","chicago":"Ibáñez, Maria, Yu Liu, and Mariano Calcabrini. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” In Proceedings of the NanoGe Spring Meeting 2022. Fundació Scito, 2022. https://doi.org/10.29363/nanoge.nsm.2022.159.","apa":"Ibáñez, M., Liu, Y., & Calcabrini, M. (2022). The importance of surface adsorbates in solution-processed thermoelectric materials. In Proceedings of the nanoGe Spring Meeting 2022. Spain/Virtual: Fundació Scito. https://doi.org/10.29363/nanoge.nsm.2022.159"},"doi":"10.29363/nanoge.nsm.2022.159","related_material":{"record":[{"id":"10123","status":"public","relation":"earlier_version"}]},"oa":1,"ddc":["530"],"conference":{"end_date":"2022-03-11","name":"SNI: Semiconductor Nanocrystals","location":"Spain/Virtual","start_date":"2022-03-07"},"article_number":"159","article_processing_charge":"No","status":"public","acknowledgement":"Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF “Lise Meitner Fellowship”","author":[{"first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"first_name":"Mariano","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-02-07T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the nanoGe Spring Meeting 2022","year":"2022","_id":"17062","title":"The importance of surface adsorbates in solution-processed thermoelectric materials","department":[{"_id":"MaIb"}],"date_updated":"2026-06-18T17:51:51Z","main_file_link":[{"url":"https://doi.org/10.29363/nanoge.nsm.2022.159","open_access":"1"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"month":"02","oa_version":"Published Version","type":"conference_abstract","publication_status":"published","publisher":"Fundació Scito"},{"month":"11","article_type":"original","main_file_link":[{"url":"https://www.doi.org/10.4171/OWR/2021/33","open_access":"1"}],"type":"journal_article","publisher":"European Mathematical Society","publication_status":"published","oa_version":"Published Version","_id":"17063","publication_identifier":{"issn":["1660-8933"],"eissn":["1660-8941"]},"date_updated":"2026-06-18T17:52:19Z","title":"Dynamische Systeme","department":[{"_id":"VaKa"}],"date_published":"2022-11-26T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Arnaud","full_name":"Arnaud, Marie-Claude","first_name":"Marie-Claude"},{"first_name":"Helmut W.","last_name":"Hofer","full_name":"Hofer, Helmut W."},{"first_name":"Michael","last_name":"Hutchings","full_name":"Hutchings, Michael"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim"}],"volume":18,"status":"public","year":"2022","page":"1735-1803","language":[{"iso":"eng"}],"publication":"Oberwolfach Reports","issue":"3","intvolume":" 18","doi":"10.4171/owr/2021/33","scopus_import":"1","quality_controlled":"1","date_created":"2024-05-29T06:01:19Z","citation":{"ista":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. 2022. Dynamische Systeme. Oberwolfach Reports. 18(3), 1735–1803.","mla":"Arnaud, Marie-Claude, et al. “Dynamische Systeme.” Oberwolfach Reports, vol. 18, no. 3, European Mathematical Society, 2022, pp. 1735–803, doi:10.4171/owr/2021/33.","apa":"Arnaud, M.-C., Hofer, H. W., Hutchings, M., & Kaloshin, V. (2022). Dynamische Systeme. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2021/33","chicago":"Arnaud, Marie-Claude, Helmut W. Hofer, Michael Hutchings, and Vadim Kaloshin. “Dynamische Systeme.” Oberwolfach Reports. European Mathematical Society, 2022. https://doi.org/10.4171/owr/2021/33.","ieee":"M.-C. Arnaud, H. W. Hofer, M. Hutchings, and V. Kaloshin, “Dynamische Systeme,” Oberwolfach Reports, vol. 18, no. 3. European Mathematical Society, pp. 1735–1803, 2022.","short":"M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803.","ama":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. Dynamische Systeme. Oberwolfach Reports. 2022;18(3):1735-1803. doi:10.4171/owr/2021/33"},"corr_author":"1","day":"26","article_processing_charge":"No","ddc":["500"],"abstract":[{"text":"This workshop continued a biannual series of workshops at Oberwolfach on dynamical systems that started with a meeting organized by Moser and Zehnder in 1981. Workshops in this series focus on new results and developments in dynamical systems and related areas of mathematics, with symplectic geometry playing an important role in recent years in connection with Hamiltonian dynamics. In this year special emphasis was placed on various kinds of spectra (in contact geometry, in Riemannian geometry, in dynamical systems and in symplectic topology) and their applications to dynamics.","lang":"eng"}],"oa":1},{"oa_version":"Published Version","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","month":"07","project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"date_updated":"2026-06-18T19:02:05Z","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"_id":"11626","ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"OA_place":"publisher","year":"2022","language":[{"iso":"eng"}],"page":"248","author":[{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"}],"file":[{"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","access_level":"open_access","content_type":"application/pdf","date_created":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","file_size":9730864,"creator":"mgallei","file_id":"11645","relation":"main_file","date_updated":"2022-07-25T09:08:47Z"},{"date_updated":"2022-07-25T09:39:58Z","file_id":"11646","creator":"mgallei","relation":"source_file","file_name":"Thesis_Gallei_source.docx","file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","date_created":"2022-07-25T09:09:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"file_size":24542837,"file_name":"Thesis_Gallei_to_print.pdf","content_type":"application/pdf","access_level":"closed","date_created":"2022-07-25T09:09:32Z","checksum":"3994f7f20058941b5bb8a16886b21e71","date_updated":"2022-07-25T09:39:58Z","description":"This is the print version of the thesis including the full appendix","relation":"source_file","creator":"mgallei","file_id":"11647"},{"date_updated":"2022-07-25T11:48:45Z","file_id":"11650","creator":"mgallei","relation":"main_file","file_name":"Thesis_Gallei_Appendix.pdf","file_size":15435966,"checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_created":"2022-07-25T11:48:45Z","content_type":"application/pdf","access_level":"open_access"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2022-07-20T00:00:00Z","status":"public","has_accepted_license":"1","article_processing_charge":"No","oa":1,"file_date_updated":"2022-07-25T11:48:45Z","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"ddc":["575"],"doi":"10.15479/at:ista:11626","related_material":{"record":[{"id":"8138","relation":"part_of_dissertation","status":"public"},{"id":"7142","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10411"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"id":"7465","relation":"part_of_dissertation","status":"public"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6260"}]},"day":"20","corr_author":"1","alternative_title":["ISTA Thesis"],"date_created":"2022-07-20T11:21:53Z","citation":{"ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626."}},{"oa":1,"file_date_updated":"2022-02-22T07:20:12Z","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"ddc":["530"],"has_accepted_license":"1","article_processing_charge":"No","day":"21","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759"},"date_created":"2022-02-16T13:27:37Z","doi":"10.15479/at:ista:10759","related_material":{"record":[{"id":"10762","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"415"},{"relation":"part_of_dissertation","status":"public","id":"8644"},{"relation":"part_of_dissertation","status":"public","id":"7956"}]},"language":[{"iso":"eng"}],"page":"120","year":"2022","status":"public","author":[{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"}],"file":[{"date_updated":"2022-02-22T07:20:12Z","creator":"wrzadkow","file_id":"10785","relation":"source_file","file_name":"Rzadkowski_thesis_final_source.zip","file_size":17668233,"checksum":"0fc54ad1eaede879c665ac9b53c93e22","access_level":"closed","content_type":"application/zip","date_created":"2022-02-21T13:58:16Z"},{"date_created":"2022-02-21T14:02:54Z","access_level":"open_access","content_type":"application/pdf","checksum":"22d2d7af37ca31f6b1730c26cac7bced","file_size":13307331,"success":1,"file_name":"Rzadkowski_thesis_final.pdf","relation":"main_file","file_id":"10786","creator":"wrzadkow","date_updated":"2022-02-21T14:02:54Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2022-02-21T00:00:00Z","title":"Analytic and machine learning approaches to composite quantum impurities","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"date_updated":"2026-06-18T19:29:09Z","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","_id":"10759","ec_funded":1,"degree_awarded":"PhD","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","supervisor":[{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"02"},{"year":"2022","language":[{"iso":"eng"}],"page":"113","author":[{"last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2022-09-29T00:00:00Z","file":[{"date_updated":"2023-01-25T10:52:46Z","creator":"cchlebak","file_id":"12369","relation":"main_file","success":1,"file_name":"THESIS_FINAL_FArslan_pdfa.pdf","file_size":14581024,"checksum":"e54a3e69b83ebf166544164afd25608e","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-25T10:52:46Z"}],"status":"public","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2023-01-25T10:52:46Z","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts."}],"doi":"10.15479/at:ista:12153","related_material":{"record":[{"id":"9350","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"corr_author":"1","day":"29","date_created":"2023-01-25T10:43:24Z","citation":{"apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:10.15479/at:ista:12153"},"oa_version":"Published Version","publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"}],"month":"09","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"date_updated":"2026-06-18T19:47:50Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows","ec_funded":1,"_id":"12368","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-025-1 "]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"OA_place":"publisher"},{"date_updated":"2026-06-18T19:47:28Z","title":"Building and sustaining mentor interactions as a mentee","department":[{"_id":"CaHe"}],"_id":"9336","pmid":1,"isi":1,"publication_identifier":{"eissn":["1742-4658"],"issn":["1742-464X"]},"type":"journal_article","publication_status":"published","publisher":"Wiley","oa_version":"Published Version","month":"03","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/febs.15823"}],"article_processing_charge":"No","ddc":["570"],"abstract":[{"lang":"eng","text":"Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success in careers. Early‐career researchers (ECRs), in particular, can benefit from mentorship to navigate challenges in academic and nonacademic life and careers. Yet, strategies for selecting mentors and maintaining interactions with them are often underdiscussed within research environments. In this Words of Advice, we provide recommendations for ECRs to seek and manage mentorship interactions. Our article draws from our experiences as ECRs and published work, to provide suggestions for mentees to proactively promote beneficial mentorship interactions. The recommended practices highlight the importance of identifying mentorship needs, planning and selecting multiple and diverse mentors, setting goals, and maintaining constructive, and mutually beneficial working relationships with mentors."}],"oa":1,"intvolume":" 289","doi":"10.1111/febs.15823","citation":{"ieee":"S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal, vol. 289, no. 6. Wiley, pp. 1374–1384, 2022.","short":"S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk, N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal 289 (2022) 1374–1384.","ama":"Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions as a mentee. FEBS Journal. 2022;289(6):1374-1384. doi:10.1111/febs.15823","ista":"Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2022. Building and sustaining mentor interactions as a mentee. FEBS Journal. 289(6), 1374–1384.","chicago":"Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal. Wiley, 2022. https://doi.org/10.1111/febs.15823.","apa":"Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E., Bielczyk, N., … Davla, S. (2022). Building and sustaining mentor interactions as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, vol. 289, no. 6, Wiley, 2022, pp. 1374–84, doi:10.1111/febs.15823."},"date_created":"2021-04-18T22:01:43Z","quality_controlled":"1","scopus_import":"1","day":"01","alternative_title":["Words of Advice"],"year":"2022","language":[{"iso":"eng"}],"publication":"FEBS Journal","page":"1374-1384","issue":"6","date_published":"2022-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":289,"external_id":{"pmid":["33818917"],"isi":["000636678800001"]},"author":[{"first_name":"Sarvenaz","last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz"},{"first_name":"Sarah J.","last_name":"Hainer","full_name":"Hainer, Sarah J."},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N"},{"full_name":"De Winde, Charlotte M.","last_name":"De Winde","first_name":"Charlotte M."},{"first_name":"Emily","full_name":"Furlong, Emily","last_name":"Furlong"},{"full_name":"Bielczyk, Natalia","last_name":"Bielczyk","first_name":"Natalia"},{"first_name":"Nafisa M.","full_name":"Jadavji, Nafisa M.","last_name":"Jadavji"},{"full_name":"Shah, Aparna P.","last_name":"Shah","first_name":"Aparna P."},{"full_name":"Davla, Sejal","last_name":"Davla","first_name":"Sejal"}],"acknowledgement":"The authors thank Nicholas Asby of the University of Chicago for valuable comments on an earlier version of this work. A.P.S. was partially supported by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National Institutes of Health grant R35GM133732.","status":"public"},{"ec_funded":1,"_id":"12358","publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"SSU"}],"OA_place":"publisher","date_updated":"2026-06-18T19:57:47Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"month":"09","supervisor":[{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"oa_version":"Published Version","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/at:ista:12103","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8385"},{"id":"11736","relation":"part_of_dissertation","status":"public"},{"id":"9818","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"day":"22","corr_author":"1","date_created":"2023-01-24T10:49:46Z","citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103"},"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2023-02-02T09:39:25Z","oa":1,"abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"ddc":["000","620"],"author":[{"full_name":"Sperl, Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"}],"date_published":"2022-09-22T00:00:00Z","file":[{"creator":"cchlebak","file_id":"12371","relation":"main_file","title":"Thesis","description":"This is the main PDF file of the thesis. 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M.C. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385.","status":"public","external_id":{"isi":["000917837600001"],"pmid":["36248227"]},"author":[{"first_name":"Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","last_name":"Fiedler","full_name":"Fiedler, Christine"},{"orcid":"0000-0003-1537-7436","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"first_name":"Maria","full_name":"Garcia, Maria","id":"6e5c50b8-97dc-11ed-be98-b0a74c84cae0","last_name":"Garcia"},{"last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","first_name":"Seungho"},{"first_name":"Mariano","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria"}],"volume":34,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":10923495,"success":1,"file_name":"2022_ChemistryMaterials_Fiedler.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-30T07:35:09Z","checksum":"f7143e44ab510519d1949099c3558532","date_updated":"2023-01-30T07:35:09Z","relation":"main_file","creator":"dernst","file_id":"12434"}],"date_published":"2022-09-20T00:00:00Z","issue":"19","language":[{"iso":"eng"}],"publication":"Chemistry of Materials","page":"8471-8489","year":"2022","corr_author":"1","day":"20","scopus_import":"1","citation":{"short":"C. Fiedler, T. Kleinhanns, M. Garcia, S. Lee, M. Calcabrini, M. Ibáñez, Chemistry of Materials 34 (2022) 8471–8489.","ieee":"C. Fiedler, T. Kleinhanns, M. Garcia, S. Lee, M. Calcabrini, and M. Ibáñez, “Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇,” Chemistry of Materials, vol. 34, no. 19. American Chemical Society, pp. 8471–8489, 2022.","ama":"Fiedler C, Kleinhanns T, Garcia M, Lee S, Calcabrini M, Ibáñez M. Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. Chemistry of Materials. 2022;34(19):8471-8489. doi:10.1021/acs.chemmater.2c01967","apa":"Fiedler, C., Kleinhanns, T., Garcia, M., Lee, S., Calcabrini, M., & Ibáñez, M. (2022). Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c01967","mla":"Fiedler, Christine, et al. “Solution-Processed Inorganic Thermoelectric Materials: Opportunities and Challenges ∇.” Chemistry of Materials, vol. 34, no. 19, American Chemical Society, 2022, pp. 8471–89, doi:10.1021/acs.chemmater.2c01967.","chicago":"Fiedler, Christine, Tobias Kleinhanns, Maria Garcia, Seungho Lee, Mariano Calcabrini, and Maria Ibáñez. “Solution-Processed Inorganic Thermoelectric Materials: Opportunities and Challenges ∇.” Chemistry of Materials. American Chemical Society, 2022. https://doi.org/10.1021/acs.chemmater.2c01967.","ista":"Fiedler C, Kleinhanns T, Garcia M, Lee S, Calcabrini M, Ibáñez M. 2022. Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. Chemistry of Materials. 34(19), 8471–8489."},"quality_controlled":"1","date_created":"2023-01-16T09:51:26Z","doi":"10.1021/acs.chemmater.2c01967","intvolume":" 34","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20415"},{"id":"12885","relation":"dissertation_contains","status":"public"},{"id":"22017","status":"for_moderation","relation":"dissertation_contains"}]},"file_date_updated":"2023-01-30T07:35:09Z","oa":1,"abstract":[{"lang":"eng","text":"Thermoelectric technology requires synthesizing complex materials where not only the crystal structure but also other structural features such as defects, grain size and orientation, and interfaces must be controlled. To date, conventional solid-state techniques are unable to provide this level of control. Herein, we present a synthetic approach in which dense inorganic thermoelectric materials are produced by the consolidation of well-defined nanoparticle powders. The idea is that controlling the characteristics of the powder allows the chemical transformations that take place during consolidation to be guided, ultimately yielding inorganic solids with targeted features. Different from conventional methods, syntheses in solution can produce particles with unprecedented control over their size, shape, crystal structure, composition, and surface chemistry. However, to date, most works have focused only on the low-cost benefits of this strategy. In this perspective, we first cover the opportunities that solution processing of the powder offers, emphasizing the potential structural features that can be controlled by precisely engineering the inorganic core of the particle, the surface, and the organization of the particles before consolidation. We then discuss the challenges of this synthetic approach and more practical matters related to solution processing. Finally, we suggest some good practices for adequate knowledge transfer and improving reproducibility among different laboratories."}],"ddc":["540"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","keyword":["Materials Chemistry","General Chemical Engineering","General Chemistry"],"article_type":"original","month":"09","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"oa_version":"Published Version","publication_status":"published","type":"journal_article","publisher":"American Chemical Society","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"isi":1,"pmid":1,"ec_funded":1,"_id":"12237","title":"Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"MaIb"}],"date_updated":"2026-06-19T08:16:17Z"},{"language":[{"iso":"eng"}],"page":"2621–2635","publication":"Journal of Ambient Intelligence and Humanized Computing","year":"2022","acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","status":"public","file":[{"relation":"main_file","embargo":"2022-11-12","file_id":"10279","creator":"fkarimip","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-12T19:38:05Z","access_level":"open_access","content_type":"application/pdf","checksum":"0a8961416a9bb2be5a1cebda65468bcf","file_size":1634958,"file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf"}],"date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000712198000001"]},"author":[{"last_name":"Goudarzi","full_name":"Goudarzi, Samira","first_name":"Samira"},{"full_name":"Sharif, Mohammad","last_name":"Sharif","first_name":"Mohammad"},{"first_name":"Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174"}],"volume":13,"ddc":["000"],"abstract":[{"text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively.","lang":"eng"}],"file_date_updated":"2022-12-20T23:30:08Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635.","chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” Journal of Ambient Intelligence and Humanized Computing. Springer Nature, 2022. https://doi.org/10.1007/s12652-021-03569-z.","mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” Journal of Ambient Intelligence and Humanized Computing, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:10.1007/s12652-021-03569-z.","apa":"Goudarzi, S., Sharif, M., & Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. Springer Nature. https://doi.org/10.1007/s12652-021-03569-z","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 2022;13:2621–2635. doi:10.1007/s12652-021-03569-z","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” Journal of Ambient Intelligence and Humanized Computing, vol. 13. Springer Nature, pp. 2621–2635, 2022."},"date_created":"2021-11-02T09:28:55Z","day":"01","intvolume":" 13","doi":"10.1007/s12652-021-03569-z","publisher":"Springer Nature","type":"journal_article","publication_status":"published","oa_version":"Submitted Version","keyword":["general computer science"],"project":[{"name":"Mathematics, Computer Science","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"month":"05","article_type":"original","department":[{"_id":"HeEd"}],"title":"A context-aware dimension reduction framework for trajectory and health signal analyses","date_updated":"2025-04-15T07:16:55Z","isi":1,"publication_identifier":{"issn":["1868-5137"],"eissn":["1868-5145"]},"_id":"10208"},{"intvolume":" 221","doi":"10.1083/jcb.202112138","citation":{"apa":"Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M., … Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202112138","mla":"Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” Journal of Cell Biology, vol. 221, no. 10, e202112138, Rockefeller University Press, 2022, doi:10.1083/jcb.202112138.","chicago":"Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe, Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202112138.","ista":"Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.","ama":"Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 2022;221(10). doi:10.1083/jcb.202112138","ieee":"M. Enshoji et al., “Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway,” Journal of Cell Biology, vol. 221, no. 10. Rockefeller University Press, 2022.","short":"M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022)."},"date_created":"2022-09-11T22:01:54Z","quality_controlled":"1","scopus_import":"1","day":"19","article_number":"e202112138","article_processing_charge":"No","has_accepted_license":"1","abstract":[{"text":"Endocytosis is a multistep process involving the sequential recruitment and action of numerous proteins. This process can be divided into two phases: an early phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated vesicles are formed and internalized into the cytosol, but how these phases link to each other remains unclear. In this study, we demonstrate that anchoring the yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring during the late phase at the peroxisome. At this ectopic location, Pan1p recruits most proteins that function in the late phases—including actin nucleation promoting factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase and actin depolymerizing factors, thereby triggering disassembly immediately after actin assembly and inducing dissociation of endocytic proteins from the peroxisome. These observations suggest that Pan1p is a key regulator for initiating, processing, and completing the late phase of endocytosis.","lang":"eng"}],"ddc":["570"],"oa":1,"file_date_updated":"2023-02-21T23:30:39Z","date_published":"2022-08-19T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"12321","creator":"dernst","relation":"main_file","embargo":"2023-02-20","date_updated":"2023-02-21T23:30:39Z","checksum":"f2e581e66b5cdab9df81b56e850b3eaa","date_created":"2023-01-20T09:32:53Z","content_type":"application/pdf","access_level":"open_access","file_name":"2022_JCB_Enshoji.pdf","file_size":7816875}],"volume":221,"author":[{"first_name":"Mariko","full_name":"Enshoji, Mariko","last_name":"Enshoji"},{"last_name":"Miyano","full_name":"Miyano, Yoshiko","first_name":"Yoshiko"},{"last_name":"Yoshida","full_name":"Yoshida, Nao","first_name":"Nao"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Minami","last_name":"Watanabe","full_name":"Watanabe, Minami"},{"last_name":"Kunihiro","full_name":"Kunihiro, Mayumi","first_name":"Mayumi"},{"first_name":"Daria E","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"external_id":{"isi":["000932770500001"],"pmid":["35984332"]},"status":"public","acknowledgement":"This work was supported by JSPS KAKENHI GRANT #18K062291, and the Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710, the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.","year":"2022","language":[{"iso":"eng"}],"publication":"Journal of Cell Biology","issue":"10","_id":"12080","pmid":1,"isi":1,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"date_updated":"2023-08-03T13:49:07Z","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"department":[{"_id":"DaSi"}],"title":"Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway","month":"08","article_type":"original","publication_status":"published","publisher":"Rockefeller University Press","type":"journal_article","oa_version":"Published Version"},{"related_material":{"record":[{"id":"12248","status":"public","relation":"used_in_publication"}]},"_id":"11653","doi":"10.15479/AT:ISTA:11653","citation":{"ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653","mla":"Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.","short":"M.N. Elkrewi, (2022).","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653"},"date_created":"2022-07-26T11:01:47Z","corr_author":"1","day":"05","date_updated":"2025-04-15T08:34:17Z","article_processing_charge":"No","has_accepted_license":"1","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"ddc":["570"],"oa":1,"file_date_updated":"2022-08-08T22:30:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","date_created":"2022-07-26T12:37:52Z","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Data.zip","file_size":2209382998,"file_id":"11655","creator":"melkrewi","title":"Supplementary Datasets","relation":"main_file","embargo":"2022-08-07","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","date_updated":"2022-08-08T22:30:04Z"}],"date_published":"2022-08-05T00:00:00Z","month":"08","author":[{"first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"status":"public","type":"research_data","publisher":"Institute of Science and Technology Austria","year":"2022","oa_version":"Published Version","contributor":[{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}]},{"scopus_import":"1","citation":{"ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. PRX Quantum. 2022;3(2). doi:10.1103/prxquantum.3.020365","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., & Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.3.020365","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.020365.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” PRX Quantum, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:10.1103/prxquantum.3.020365.","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365."},"date_created":"2022-06-29T20:21:32Z","quality_controlled":"1","corr_author":"1","day":"29","intvolume":" 3","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"},{"id":"14622","relation":"dissertation_contains","status":"public"}]},"doi":"10.1103/prxquantum.3.020365","ddc":["530"],"abstract":[{"text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. ","lang":"eng"}],"file_date_updated":"2022-06-30T07:14:48Z","oa":1,"article_processing_charge":"No","article_number":"020365","has_accepted_license":"1","acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","status":"public","file":[{"relation":"main_file","creator":"dernst","file_id":"11472","date_updated":"2022-06-30T07:14:48Z","content_type":"application/pdf","access_level":"open_access","date_created":"2022-06-30T07:14:48Z","checksum":"a7706b28d24a0e32a55ea04b82a2df43","file_size":4231591,"success":1,"file_name":"2022_PRXQuantum_Sack.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-29T00:00:00Z","external_id":{"isi":["000822564300001"],"arxiv":["2201.08194"]},"author":[{"orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan"},{"first_name":"Raimel A","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"last_name":"Kueng","full_name":"Kueng, Richard","first_name":"Richard"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"volume":3,"language":[{"iso":"eng"}],"publication":"PRX Quantum","issue":"2","year":"2022","isi":1,"publication_identifier":{"issn":["2691-3399"]},"ec_funded":1,"_id":"11471","department":[{"_id":"MaSe"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Avoiding barren plateaus using classical shadows","date_updated":"2026-06-19T22:30:21Z","keyword":["General Medicine"],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"month":"06","article_type":"original","arxiv":1,"type":"journal_article","publication_status":"published","publisher":"American Physical Society","oa_version":"Published Version"},{"status":"public","acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","date_published":"2022-01-01T00:00:00Z","file":[{"file_name":"2020_ApplicAnalysis_Shehu.pdf","file_size":4282586,"checksum":"869efe8cb09505dfa6012f67d20db63d","access_level":"open_access","content_type":"application/pdf","date_created":"2020-10-12T10:42:54Z","date_updated":"2021-03-16T23:30:06Z","creator":"dernst","file_id":"8648","embargo":"2021-03-15","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":101,"author":[{"last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","first_name":"Yekini"},{"first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola"}],"external_id":{"arxiv":["2101.08057"],"isi":["000518364100001"]},"page":"192-216","language":[{"iso":"eng"}],"publication":"Applicable Analysis","issue":"1","year":"2022","citation":{"ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 2022;101(1):192-216. doi:10.1080/00036811.2020.1736287","ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” Applicable Analysis, vol. 101, no. 1. Taylor & Francis, pp. 192–216, 2022.","short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” Applicable Analysis. Taylor & Francis, 2022. https://doi.org/10.1080/00036811.2020.1736287.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” Applicable Analysis, vol. 101, no. 1, Taylor & Francis, 2022, pp. 192–216, doi:10.1080/00036811.2020.1736287.","apa":"Shehu, Y., & Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. Taylor & Francis. https://doi.org/10.1080/00036811.2020.1736287","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216."},"date_created":"2020-03-09T07:06:52Z","quality_controlled":"1","scopus_import":"1","day":"01","corr_author":"1","intvolume":" 101","doi":"10.1080/00036811.2020.1736287","ddc":["510","515","518"],"abstract":[{"lang":"eng","text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods."}],"oa":1,"file_date_updated":"2021-03-16T23:30:06Z","article_processing_charge":"No","has_accepted_license":"1","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"month":"01","article_type":"original","arxiv":1,"publication_status":"published","type":"journal_article","publisher":"Taylor & Francis","oa_version":"Submitted Version","isi":1,"publication_identifier":{"issn":["0003-6811"],"eissn":["1563-504X"]},"_id":"7577","ec_funded":1,"title":"Weak convergence for variational inequalities with inertial-type method","department":[{"_id":"VlKo"}],"date_updated":"2024-11-04T13:52:44Z"}]