--- _id: '12174' abstract: - lang: eng 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." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc 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 article_type: original author: - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: Davide full_name: Mei, Davide last_name: Mei - first_name: Margit Katalin full_name: Szigeti, Margit Katalin id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87 last_name: Szigeti orcid: 0000-0001-9500-8758 - first_name: Sara full_name: Pepe, Sara last_name: Pepe - first_name: Mary Kay full_name: Koenig, Mary Kay last_name: Koenig - first_name: Gretchen full_name: Von Allmen, Gretchen last_name: Von Allmen - first_name: Megan T full_name: Cho, Megan T last_name: Cho - first_name: Kimberly full_name: McDonald, Kimberly last_name: McDonald - first_name: Janice full_name: Baker, Janice last_name: Baker - first_name: Vikas full_name: Bhambhani, Vikas last_name: Bhambhani - first_name: Zöe full_name: Powis, Zöe last_name: Powis - first_name: Lance full_name: Rodan, Lance last_name: Rodan - first_name: Rima full_name: Nabbout, Rima last_name: Nabbout - first_name: Giulia full_name: Barcia, Giulia last_name: Barcia - first_name: Jill A full_name: Rosenfeld, Jill A last_name: Rosenfeld - first_name: Carlos A full_name: Bacino, Carlos A last_name: Bacino - first_name: Cyril full_name: Mignot, Cyril last_name: Mignot - first_name: Lillian H full_name: Power, Lillian H last_name: Power - first_name: Catharine J full_name: Harris, Catharine J last_name: Harris - first_name: Dragan full_name: Marjanovic, Dragan last_name: Marjanovic - first_name: Rikke S full_name: Møller, Rikke S last_name: Møller - first_name: Trine B full_name: Hammer, Trine B last_name: Hammer - first_name: Riikka full_name: Keski Filppula, Riikka last_name: Keski Filppula - first_name: Päivi full_name: Vieira, Päivi last_name: Vieira - first_name: Clara full_name: Hildebrandt, Clara last_name: Hildebrandt - first_name: Stephanie full_name: Sacharow, Stephanie last_name: Sacharow - first_name: Luca full_name: Maragliano, Luca last_name: Maragliano - first_name: Fabio full_name: Benfenati, Fabio last_name: Benfenati - first_name: Katherine full_name: Lachlan, Katherine last_name: Lachlan - first_name: Andreas full_name: Benneche, Andreas last_name: Benneche - first_name: Florence full_name: Petit, Florence last_name: Petit - first_name: Jean Madeleine full_name: de Sainte Agathe, Jean Madeleine last_name: de Sainte Agathe - first_name: Barbara full_name: Hallinan, Barbara last_name: Hallinan - first_name: Yue full_name: Si, Yue last_name: Si - first_name: Ingrid M full_name: Wentzensen, Ingrid M last_name: Wentzensen - first_name: Fanggeng full_name: Zou, Fanggeng last_name: Zou - first_name: Vinodh full_name: Narayanan, Vinodh last_name: Narayanan - first_name: Naomichi full_name: Matsumoto, Naomichi last_name: Matsumoto - first_name: Alessandra full_name: Boncristiano, Alessandra last_name: Boncristiano - first_name: Giancarlo full_name: la Marca, Giancarlo last_name: la Marca - first_name: Mitsuhiro full_name: Kato, Mitsuhiro last_name: Kato - first_name: Kristin full_name: Anderson, Kristin last_name: Anderson - first_name: Carmen full_name: Barba, Carmen last_name: Barba - first_name: Luisa full_name: Sturiale, Luisa last_name: Sturiale - first_name: Domenico full_name: Garozzo, Domenico last_name: Garozzo - first_name: Roberto full_name: Bei, Roberto last_name: Bei - first_name: Laura full_name: Masuelli, Laura last_name: Masuelli - first_name: Valerio full_name: Conti, Valerio last_name: Conti - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Anna full_name: Fassio, Anna last_name: Fassio citation: 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' 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' 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.' 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.' 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.' 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.' 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. date_created: 2023-01-12T12:11:45Z date_published: 2022-08-01T00:00:00Z date_updated: 2026-06-18T17:24:52Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1093/brain/awac145 ec_funded: 1 external_id: isi: - '000807770000001' pmid: - '35675510' intvolume: ' 145' isi: 1 issue: '8' keyword: - Neurology (clinical) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/brain/awac145 month: '08' oa: 1 oa_version: Published Version page: 2687-2703 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2022' ... --- OA_place: publisher OA_type: free access _id: '12238' 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. 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. article_processing_charge: No article_type: original author: - first_name: Naoya full_name: Hino, Naoya id: 5299a9ce-7679-11eb-a7bc-d1e62b936307 last_name: Hino - first_name: Kimiya full_name: Matsuda, Kimiya last_name: Matsuda - first_name: Yuya full_name: Jikko, Yuya last_name: Jikko - first_name: Gembu full_name: Maryu, Gembu last_name: Maryu - first_name: Katsuya full_name: Sakai, Katsuya last_name: Sakai - first_name: Ryu full_name: Imamura, Ryu last_name: Imamura - first_name: Shinya full_name: Tsukiji, Shinya last_name: Tsukiji - first_name: Kazuhiro full_name: Aoki, Kazuhiro last_name: Aoki - first_name: Kenta full_name: Terai, Kenta last_name: Terai - first_name: Tsuyoshi full_name: Hirashima, Tsuyoshi last_name: Hirashima - first_name: Xavier full_name: Trepat, Xavier last_name: Trepat - first_name: Michiyuki full_name: Matsuda, Michiyuki last_name: Matsuda 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 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. 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. 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. corr_author: '1' date_created: 2023-01-16T09:51:39Z date_published: 2022-10-01T00:00:00Z date_updated: 2026-06-18T17:25:21Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1016/j.devcel.2022.09.003 external_id: isi: - '000898428700006' pmid: - '36174555' intvolume: ' 57' isi: 1 issue: '19' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2022.09.003 month: '10' oa: 1 oa_version: Published Version page: 2290-2304.e7 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2022' ... --- _id: '12275' abstract: - lang: eng 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. 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' article_number: e54163 article_processing_charge: No article_type: original author: - first_name: Maisha full_name: Rahman, Maisha last_name: Rahman - first_name: Nelson full_name: Ramirez, Nelson id: 39831956-E4FE-11E9-85DE-0DC7E5697425 last_name: Ramirez - first_name: Carlos A full_name: Diaz‐Balzac, Carlos A last_name: Diaz‐Balzac - first_name: Hannes E full_name: Bülow, Hannes E last_name: Bülow 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 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 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. 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. 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. 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. short: M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022). date_created: 2023-01-16T10:01:44Z date_published: 2022-07-05T00:00:00Z date_updated: 2026-06-18T17:26:25Z day: '05' ddc: - '570' department: - _id: MaDe doi: 10.15252/embr.202154163 external_id: isi: - '000797302700001' pmid: - '35586945' has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '7' keyword: - Genetics - Molecular Biology - Biochemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.15252/embr.202154163 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2022' ... --- OA_place: publisher OA_type: free access _id: '12120' 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. 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). article_processing_charge: No article_type: original author: - first_name: Huixin full_name: Xiao, Huixin last_name: Xiao - first_name: Yumei full_name: Hu, Yumei last_name: Hu - first_name: Yaping full_name: Wang, Yaping last_name: Wang - first_name: Jinkui full_name: Cheng, Jinkui last_name: Cheng - first_name: Jinyi full_name: Wang, Jinyi last_name: Wang - first_name: Guojingwei full_name: Chen, Guojingwei last_name: Chen - first_name: Qian full_name: Li, Qian last_name: Li - first_name: Shuwei full_name: Wang, Shuwei last_name: Wang - 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 full_name: Wang, Yi last_name: Wang - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Zhen full_name: Li, Zhen last_name: Li - first_name: Yan full_name: Guo, Yan last_name: Guo - first_name: Zhizhong full_name: Gong, Zhizhong last_name: Gong - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jing full_name: Zhang, Jing last_name: Zhang citation: 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 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 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. 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. 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. 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. 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. date_created: 2023-01-12T11:57:00Z date_published: 2022-12-05T00:00:00Z date_updated: 2026-06-18T17:23:10Z day: '05' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.devcel.2022.11.006 external_id: isi: - '000919603800005' pmid: - '36473460' intvolume: ' 57' isi: 1 issue: '23' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2022.11.006 month: '12' oa: 1 oa_version: Published Version page: 2638-2651.e6 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2022' ... --- _id: '12116' abstract: - lang: eng 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. article_processing_charge: No article_type: letter_note author: - first_name: Karishma full_name: Chhugani, Karishma last_name: Chhugani - first_name: Alina full_name: Frolova, Alina last_name: Frolova - first_name: Yuriy full_name: Salyha, Yuriy last_name: Salyha - first_name: Andrada full_name: Fiscutean, Andrada last_name: Fiscutean - first_name: Oksana full_name: Zlenko, Oksana last_name: Zlenko - first_name: Sanita full_name: Reinsone, Sanita last_name: Reinsone - first_name: Walter W. full_name: Wolfsberger, Walter W. last_name: Wolfsberger - first_name: Oleksandra V. full_name: Ivashchenko, Oleksandra V. last_name: Ivashchenko - first_name: Megi full_name: Maci, Megi last_name: Maci - first_name: Dmytro full_name: Dziuba, Dmytro last_name: Dziuba - first_name: Andrii full_name: Parkhomenko, Andrii last_name: Parkhomenko - first_name: Eric full_name: Bortz, Eric last_name: Bortz - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Paweł P. full_name: Łabaj, Paweł P. last_name: Łabaj - first_name: Veronika full_name: Romero, Veronika last_name: Romero - first_name: Jakub full_name: Hlávka, Jakub last_name: Hlávka - first_name: Taras K. full_name: Oleksyk, Taras K. last_name: Oleksyk - first_name: Serghei full_name: Mangul, Serghei last_name: Mangul 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 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. 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. 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. date_created: 2023-01-12T11:56:30Z date_published: 2022-12-22T00:00:00Z date_updated: 2026-06-18T17:22:36Z day: '22' ddc: - '000' department: - _id: FyKo doi: 10.1126/science.adg0797 external_id: isi: - '000963463700023' pmid: - '36548425' intvolume: ' 378' isi: 1 issue: '6626' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.adg0797 month: '12' oa: 1 oa_version: Published Version page: 1285-1286 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Remote opportunities for scholars in Ukraine type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 378 year: '2022' ... --- _id: '17057' 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. article_number: jcs259715 article_processing_charge: No author: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Loose M. Cell Scientist to Watch – Martin Loose. Vol 135. 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. ieee: M. Loose, Cell scientist to watch – Martin Loose, vol. 135, no. 2. The Company of Biologists, 2022. ista: Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p. 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. short: M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022. date_created: 2024-05-28T13:28:30Z date_published: 2022-01-19T00:00:00Z date_updated: 2026-06-18T17:51:26Z day: '19' ddc: - '570' department: - _id: MaLo doi: 10.1242/jcs.259715 external_id: isi: - '000762665200015' intvolume: ' 135' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/jcs.259715 month: '01' oa: 1 oa_version: Published Version publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: Cell scientist to watch – Martin Loose type: other_academic_publication user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2022' ... --- _id: '17085' 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. 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.' article_processing_charge: No author: - first_name: Jordi full_name: Floriach-Clark, Jordi last_name: Floriach-Clark - first_name: Han full_name: Tang, Han id: 19BDF720-25A0-11EA-AC6E-928F3DDC885E last_name: Tang orcid: 0000-0001-6152-6637 - first_name: Viola full_name: Willemsen, Viola last_name: Willemsen 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' 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' 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.' 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.' ista: 'Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .' 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.' short: J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022. date_created: 2024-05-29T06:35:13Z date_published: 2022-06-23T00:00:00Z date_updated: 2026-06-18T17:52:59Z day: '23' ddc: - '580' department: - _id: JiFr doi: 10.5772/intechopen.100535 ec_funded: 1 editor: - first_name: Ibrokhim Y. full_name: Abdurakhmonov, Ibrokhim Y. last_name: Abdurakhmonov language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5772/intechopen.100535 month: '06' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Model Organisms in Plant Genetics publication_identifier: isbn: - '9781839697500' publication_status: published publisher: IntechOpen quality_controlled: '1' status: public title: 'Mosses: Accessible Systems for Plant Development Studies' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '17062' acknowledgement: "Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF “Lise Meitner Fellowship”" article_number: '159' article_processing_charge: No author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: 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' 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' 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. 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. 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. short: M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting 2022, Fundació Scito, 2022. conference: end_date: 2022-03-11 location: Spain/Virtual name: 'SNI: Semiconductor Nanocrystals' start_date: 2022-03-07 corr_author: '1' date_created: 2024-05-29T05:38:47Z date_published: 2022-02-07T00:00:00Z date_updated: 2026-06-18T17:51:51Z day: '07' ddc: - '530' department: - _id: MaIb doi: 10.29363/nanoge.nsm.2022.159 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.29363/nanoge.nsm.2022.159 month: '02' oa: 1 oa_version: Published Version project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Proceedings of the nanoGe Spring Meeting 2022 publication_status: published publisher: Fundació Scito quality_controlled: '1' related_material: record: - id: '10123' relation: earlier_version status: public status: public title: The importance of surface adsorbates in solution-processed thermoelectric materials type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '17063' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Marie-Claude full_name: Arnaud, Marie-Claude last_name: Arnaud - first_name: Helmut W. full_name: Hofer, Helmut W. last_name: Hofer - first_name: Michael full_name: Hutchings, Michael last_name: Hutchings - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: 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 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. 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. short: M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803. corr_author: '1' date_created: 2024-05-29T06:01:19Z date_published: 2022-11-26T00:00:00Z date_updated: 2026-06-18T17:52:19Z day: '26' ddc: - '500' department: - _id: VaKa doi: 10.4171/owr/2021/33 intvolume: ' 18' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.4171/OWR/2021/33 month: '11' oa: 1 oa_version: Published Version page: 1735-1803 publication: Oberwolfach Reports publication_identifier: eissn: - 1660-8941 issn: - 1660-8933 publication_status: published publisher: European Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamische Systeme type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2022' ... --- OA_place: publisher _id: '11626' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 citation: ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 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. 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. short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-07-20T11:21:53Z date_published: 2022-07-20T00:00:00Z date_updated: 2026-06-18T19:02:05Z day: '20' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:11626 ec_funded: 1 file: - access_level: open_access checksum: bd7ac35403cf5b4b2607287d2a104b3a content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:08:47Z date_updated: 2022-07-25T09:08:47Z file_id: '11645' file_name: Thesis_Gallei.pdf file_size: 9730864 relation: main_file - access_level: closed checksum: a9e54fe5471ba25dc13c2150c1b8ccbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mgallei date_created: 2022-07-25T09:09:09Z date_updated: 2022-07-25T09:39:58Z file_id: '11646' file_name: Thesis_Gallei_source.docx file_size: 19560720 relation: source_file - access_level: closed checksum: 3994f7f20058941b5bb8a16886b21e71 content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:09:32Z date_updated: 2022-07-25T09:39:58Z description: This is the print version of the thesis including the full appendix file_id: '11647' file_name: Thesis_Gallei_to_print.pdf file_size: 24542837 relation: source_file - access_level: open_access checksum: f24acd3c0d864f4c6676e8b0d7bfa76b content_type: application/pdf creator: mgallei date_created: 2022-07-25T11:48:45Z date_updated: 2022-07-25T11:48:45Z file_id: '11650' file_name: Thesis_Gallei_Appendix.pdf file_size: 15435966 relation: main_file file_date_updated: 2022-07-25T11:48:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '248' project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: isbn: - 978-3-99078-019-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8138' relation: part_of_dissertation status: public - id: '7142' relation: part_of_dissertation status: public - id: '10411' relation: part_of_dissertation status: public - id: '8931' relation: part_of_dissertation status: public - id: '7465' relation: part_of_dissertation status: public - id: '9287' relation: part_of_dissertation status: public - id: '6260' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eilon full_name: Shani, Eilon last_name: Shani title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _id: '10759' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 citation: ama: Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 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 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. ieee: W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022. ista: Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. 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. short: W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-02-16T13:27:37Z date_published: 2022-02-21T00:00:00Z date_updated: 2026-06-18T19:29:09Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MiLe doi: 10.15479/at:ista:10759 ec_funded: 1 file: - access_level: closed checksum: 0fc54ad1eaede879c665ac9b53c93e22 content_type: application/zip creator: wrzadkow date_created: 2022-02-21T13:58:16Z date_updated: 2022-02-22T07:20:12Z file_id: '10785' file_name: Rzadkowski_thesis_final_source.zip file_size: 17668233 relation: source_file - access_level: open_access checksum: 22d2d7af37ca31f6b1730c26cac7bced content_type: application/pdf creator: wrzadkow date_created: 2022-02-21T14:02:54Z date_updated: 2022-02-21T14:02:54Z file_id: '10786' file_name: Rzadkowski_thesis_final.pdf file_size: 13307331 relation: main_file success: 1 file_date_updated: 2022-02-22T07:20:12Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '120' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10762' relation: part_of_dissertation status: public - id: '415' relation: part_of_dissertation status: public - id: '8644' relation: part_of_dissertation status: public - id: '7956' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Analytic and machine learning approaches to composite quantum impurities type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _id: '12368' 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\x02mediated 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\x02cadherin 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." acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 citation: ama: Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:10.15479/at:ista:12153 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 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. ieee: F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022. ista: Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. 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. short: F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2023-01-25T10:43:24Z date_published: 2022-09-29T00:00:00Z date_updated: 2026-06-18T19:47:50Z day: '29' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:12153 ec_funded: 1 file: - access_level: open_access checksum: e54a3e69b83ebf166544164afd25608e content_type: application/pdf creator: cchlebak date_created: 2023-01-25T10:52:46Z date_updated: 2023-01-25T10:52:46Z file_id: '12369' file_name: THESIS_FINAL_FArslan_pdfa.pdf file_size: 14581024 relation: main_file success: 1 file_date_updated: 2023-01-25T10:52:46Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication_identifier: isbn: - '978-3-99078-025-1 ' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9350' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Remodeling of E-cadherin-mediated contacts via cortical flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- _id: '9336' 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. 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. alternative_title: - Words of Advice article_processing_charge: No article_type: original author: - first_name: Sarvenaz full_name: Sarabipour, Sarvenaz last_name: Sarabipour - first_name: Sarah J. full_name: Hainer, Sarah J. last_name: Hainer - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Charlotte M. full_name: De Winde, Charlotte M. last_name: De Winde - first_name: Emily full_name: Furlong, Emily last_name: Furlong - first_name: Natalia full_name: Bielczyk, Natalia last_name: Bielczyk - first_name: Nafisa M. full_name: Jadavji, Nafisa M. last_name: Jadavji - first_name: Aparna P. full_name: Shah, Aparna P. last_name: Shah - first_name: Sejal full_name: Davla, Sejal last_name: Davla citation: 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 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 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. ieee: S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal, vol. 289, no. 6. Wiley, pp. 1374–1384, 2022. 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. 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. 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. date_created: 2021-04-18T22:01:43Z date_published: 2022-03-01T00:00:00Z date_updated: 2026-06-18T19:47:28Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1111/febs.15823 external_id: isi: - '000636678800001' pmid: - '33818917' intvolume: ' 289' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/febs.15823 month: '03' oa: 1 oa_version: Published Version page: 1374-1384 pmid: 1 publication: FEBS Journal publication_identifier: eissn: - 1742-4658 issn: - 1742-464X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Building and sustaining mentor interactions as a mentee type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 289 year: '2022' ... --- OA_place: publisher _id: '12358' 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" acknowledged_ssus: - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl citation: ama: 'Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 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' 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.' ieee: 'G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.' ista: 'Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.' 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.' short: 'G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.' corr_author: '1' date_created: 2023-01-24T10:49:46Z date_published: 2022-09-22T00:00:00Z date_updated: 2026-06-18T19:57:47Z day: '22' ddc: - '000' - '620' degree_awarded: PhD department: - _id: GradSch - _id: ChWo doi: 10.15479/at:ista:12103 ec_funded: 1 file: - access_level: open_access checksum: 083722acbb8115e52e3b0fdec6226769 content_type: application/pdf creator: cchlebak date_created: 2023-01-25T12:04:41Z date_updated: 2023-02-02T09:29:57Z description: 'This is the main PDF file of the thesis. File size: 105 MB' file_id: '12371' file_name: thesis_gsperl.pdf file_size: 104497530 relation: main_file title: Thesis - access_level: open_access checksum: 511f82025e5fcb70bff4731d6896ca07 content_type: application/pdf creator: cchlebak date_created: 2023-02-02T09:33:37Z date_updated: 2023-02-02T09:33:37Z description: This version of the thesis uses stronger image compression for a smaller file size of 23MB. file_id: '12483' file_name: thesis_gsperl_compressed.pdf file_size: 23183710 relation: main_file title: Thesis (compressed 23MB) - access_level: open_access checksum: ed4cb85225eedff761c25bddfc37a2ed content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-02-02T09:39:25Z date_updated: 2023-02-02T09:39:25Z file_id: '12484' file_name: thesis-source.zip file_size: 98382247 relation: source_file file_date_updated: 2023-02-02T09:39:25Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '138' project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales' publication_identifier: isbn: - 978-3-99078-020-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8385' relation: part_of_dissertation status: public - id: '11736' relation: part_of_dissertation status: public - id: '9818' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: 'Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- _id: '12237' 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. acknowledgement: This work was financially supported by ISTA and the Werner Siemens Foundation. 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Christine full_name: Fiedler, Christine id: bd3fceba-dc74-11ea-a0a7-c17f71817366 last_name: Fiedler - first_name: Tobias full_name: Kleinhanns, Tobias id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425 last_name: Kleinhanns orcid: 0000-0003-1537-7436 - first_name: Maria full_name: Garcia, Maria id: 6e5c50b8-97dc-11ed-be98-b0a74c84cae0 last_name: Garcia - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: 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' 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.' 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.' 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.' 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.' short: C. Fiedler, T. Kleinhanns, M. Garcia, S. Lee, M. Calcabrini, M. Ibáñez, Chemistry of Materials 34 (2022) 8471–8489. corr_author: '1' date_created: 2023-01-16T09:51:26Z date_published: 2022-09-20T00:00:00Z date_updated: 2026-06-19T08:16:17Z day: '20' ddc: - '540' department: - _id: MaIb doi: 10.1021/acs.chemmater.2c01967 ec_funded: 1 external_id: isi: - '000917837600001' pmid: - '36248227' file: - access_level: open_access checksum: f7143e44ab510519d1949099c3558532 content_type: application/pdf creator: dernst date_created: 2023-01-30T07:35:09Z date_updated: 2023-01-30T07:35:09Z file_id: '12434' file_name: 2022_ChemistryMaterials_Fiedler.pdf file_size: 10923495 relation: main_file success: 1 file_date_updated: 2023-01-30T07:35:09Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '19' keyword: - Materials Chemistry - General Chemical Engineering - General Chemistry language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 8471-8489 pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '20415' relation: dissertation_contains status: public - id: '12885' relation: dissertation_contains status: public - id: '22017' relation: dissertation_contains status: for_moderation scopus_import: '1' status: public title: 'Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2022' ... --- _id: '10208' abstract: - lang: eng 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. acknowledgement: The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. article_processing_charge: No article_type: original author: - first_name: Samira full_name: Goudarzi, Samira last_name: Goudarzi - first_name: Mohammad full_name: Sharif, Mohammad last_name: Sharif - first_name: Farid full_name: Karimipour, Farid id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425 last_name: Karimipour orcid: 0000-0001-6746-4174 citation: 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 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 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. 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. 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. 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. short: S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635. date_created: 2021-11-02T09:28:55Z date_published: 2022-05-01T00:00:00Z date_updated: 2025-04-15T07:16:55Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s12652-021-03569-z external_id: isi: - '000712198000001' file: - access_level: open_access checksum: 0a8961416a9bb2be5a1cebda65468bcf content_type: application/pdf creator: fkarimip date_created: 2021-11-12T19:38:05Z date_updated: 2022-12-20T23:30:08Z embargo: 2022-11-12 file_id: '10279' file_name: A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf file_size: 1634958 relation: main_file file_date_updated: 2022-12-20T23:30:08Z has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - general computer science language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 2621–2635 project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication: Journal of Ambient Intelligence and Humanized Computing publication_identifier: eissn: - 1868-5145 issn: - 1868-5137 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A context-aware dimension reduction framework for trajectory and health signal analyses type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '12080' abstract: - lang: eng 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.' 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.' article_number: e202112138 article_processing_charge: No article_type: original author: - first_name: Mariko full_name: Enshoji, Mariko last_name: Enshoji - first_name: Yoshiko full_name: Miyano, Yoshiko last_name: Miyano - first_name: Nao full_name: Yoshida, Nao last_name: Yoshida - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Minami full_name: Watanabe, Minami last_name: Watanabe - first_name: Mayumi full_name: Kunihiro, Mayumi last_name: Kunihiro - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Junko Y. full_name: Toshima, Junko Y. last_name: Toshima - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: 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 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 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. 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. 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. 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. 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 date_published: 2022-08-19T00:00:00Z date_updated: 2023-08-03T13:49:07Z day: '19' ddc: - '570' department: - _id: DaSi doi: 10.1083/jcb.202112138 external_id: isi: - '000932770500001' pmid: - '35984332' file: - access_level: open_access checksum: f2e581e66b5cdab9df81b56e850b3eaa content_type: application/pdf creator: dernst date_created: 2023-01-20T09:32:53Z date_updated: 2023-02-21T23:30:39Z embargo: 2023-02-20 file_id: '12321' file_name: 2022_JCB_Enshoji.pdf file_size: 7816875 relation: main_file file_date_updated: 2023-02-21T23:30:39Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 221 year: '2022' ... --- _id: '11653' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: 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 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 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. 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. 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. 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). contributor: - first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Uladzislava last_name: Khauratovich - first_name: Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups - first_name: Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Luca last_name: Sax - first_name: Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans - first_name: Francisco last_name: 'Hontoria ' - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 corr_author: '1' date_created: 2022-07-26T11:01:47Z date_published: 2022-08-05T00:00:00Z date_updated: 2025-04-15T08:34:17Z day: '05' ddc: - '570' department: - _id: GradSch - _id: BeVi doi: 10.15479/AT:ISTA:11653 file: - access_level: open_access checksum: 5f1d7c6d7ab5375ed2564521432bed0c content_type: application/x-zip-compressed creator: melkrewi date_created: 2022-07-26T12:37:52Z date_updated: 2022-08-08T22:30:04Z description: | The folder contains the following datasets (fasta files, and text files): Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan male draft assembly Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and A. parthenogenetica females and rare male. Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window Sup. Dataset 5: FASTA file with candidate W scaffolds Sup. Dataset 6: Candidate W-derived transcripts and alignments Sup. Dataset 7: Gene expression with genomic location Sup. Dataset 8: VCF for asexual female and rare male Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis) Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using A. sp. Kazakhstan as the reference), and inferred ancestry Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their locations in the Artemia sinica male genome. embargo: 2022-08-07 file_id: '11655' file_name: Data.zip file_size: 2209382998 relation: main_file title: Supplementary Datasets file_date_updated: 2022-08-08T22:30:04Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12248' relation: used_in_publication status: public status: public 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 legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11471' abstract: - lang: eng 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. ' 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)." article_number: '020365' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Stefan full_name: Sack, Stefan id: dd622248-f6e0-11ea-865d-ce382a1c81a5 last_name: Sack orcid: 0000-0001-5400-8508 - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Richard full_name: Kueng, Richard last_name: Kueng - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 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 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. 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. ista: Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 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. short: S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022). corr_author: '1' date_created: 2022-06-29T20:21:32Z date_published: 2022-06-29T00:00:00Z date_updated: 2026-06-19T22:30:21Z day: '29' ddc: - '530' department: - _id: MaSe doi: 10.1103/prxquantum.3.020365 ec_funded: 1 external_id: arxiv: - '2201.08194' isi: - '000822564300001' file: - access_level: open_access checksum: a7706b28d24a0e32a55ea04b82a2df43 content_type: application/pdf creator: dernst date_created: 2022-06-30T07:14:48Z date_updated: 2022-06-30T07:14:48Z file_id: '11472' file_name: 2022_PRXQuantum_Sack.pdf file_size: 4231591 relation: main_file success: 1 file_date_updated: 2022-06-30T07:14:48Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '2' keyword: - General Medicine language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: PRX Quantum publication_identifier: issn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '17208' relation: dissertation_contains status: public - id: '14622' relation: dissertation_contains status: public scopus_import: '1' status: public title: Avoiding barren plateaus using classical shadows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 3 year: '2022' ... --- _id: '7577' 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. 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). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Olaniyi S. full_name: Iyiola, Olaniyi S. last_name: Iyiola 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 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 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. 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. ista: Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216. 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. short: Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216. corr_author: '1' date_created: 2020-03-09T07:06:52Z date_published: 2022-01-01T00:00:00Z date_updated: 2024-11-04T13:52:44Z day: '01' ddc: - '510' - '515' - '518' department: - _id: VlKo doi: 10.1080/00036811.2020.1736287 ec_funded: 1 external_id: arxiv: - '2101.08057' isi: - '000518364100001' file: - access_level: open_access checksum: 869efe8cb09505dfa6012f67d20db63d content_type: application/pdf creator: dernst date_created: 2020-10-12T10:42:54Z date_updated: 2021-03-16T23:30:06Z embargo: 2021-03-15 file_id: '8648' file_name: 2020_ApplicAnalysis_Shehu.pdf file_size: 4282586 relation: main_file file_date_updated: 2021-03-16T23:30:06Z has_accepted_license: '1' intvolume: ' 101' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 192-216 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Applicable Analysis publication_identifier: eissn: - 1563-504X issn: - 0003-6811 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Weak convergence for variational inequalities with inertial-type method type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 101 year: '2022' ...