[{"issue":"1","page":"1-382","month":"02","isi":1,"article_processing_charge":"No","volume":17,"language":[{"iso":"eng"}],"ddc":["580","570"],"year":"2021","quality_controlled":"1","intvolume":"        17","type":"journal_article","publisher":"Taylor & Francis","publication_status":"published","abstract":[{"lang":"eng","text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. "}],"citation":{"ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. 2021;17(1):1-382. doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. 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Klionsky <i>et al.</i>, “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” <i>Autophagy</i>, vol. 17, no. 1. Taylor &#38; Francis, pp. 1–382, 2021.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>. Taylor &#38; Francis, 2021. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>, vol. 17, no. 1, Taylor &#38; Francis, 2021, pp. 1–382, doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>."},"doi":"10.1080/15548627.2020.1797280","scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"day":"08","article_type":"review","acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2020.1797280"}],"author":[{"full_name":"Klionsky, Daniel J.","first_name":"Daniel J.","last_name":"Klionsky"},{"first_name":"Amal Kamal","last_name":"Abdel-Aziz","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"first_name":"Mahmoud","last_name":"Abdellatif","full_name":"Abdellatif, Mahmoud"},{"full_name":"Abdoli, Asghar","first_name":"Asghar","last_name":"Abdoli"},{"full_name":"Abel, Steffen","first_name":"Steffen","last_name":"Abel"},{"full_name":"Abeliovich, Hagai","last_name":"Abeliovich","first_name":"Hagai"},{"last_name":"Abildgaard","first_name":"Marie H.","full_name":"Abildgaard, Marie H."},{"last_name":"Abudu","first_name":"Yakubu Princely","full_name":"Abudu, Yakubu Princely"},{"first_name":"Abraham","last_name":"Acevedo-Arozena","full_name":"Acevedo-Arozena, Abraham"},{"full_name":"Adamopoulos, Iannis E.","first_name":"Iannis E.","last_name":"Adamopoulos"},{"full_name":"Adeli, Khosrow","last_name":"Adeli","first_name":"Khosrow"},{"full_name":"Adolph, Timon E.","last_name":"Adolph","first_name":"Timon E."},{"full_name":"Adornetto, Annagrazia","last_name":"Adornetto","first_name":"Annagrazia"},{"full_name":"Aflaki, Elma","first_name":"Elma","last_name":"Aflaki"},{"full_name":"Agam, Galila","first_name":"Galila","last_name":"Agam"},{"last_name":"Agarwal","first_name":"Anupam","full_name":"Agarwal, Anupam"},{"last_name":"Aggarwal","first_name":"Bharat B.","full_name":"Aggarwal, Bharat B."},{"first_name":"Maria","last_name":"Agnello","full_name":"Agnello, Maria"},{"full_name":"Agostinis, Patrizia","first_name":"Patrizia","last_name":"Agostinis"},{"full_name":"Agrewala, Javed N.","first_name":"Javed N.","last_name":"Agrewala"},{"first_name":"Alexander","last_name":"Agrotis","full_name":"Agrotis, Alexander"},{"full_name":"Aguilar, Patricia V.","last_name":"Aguilar","first_name":"Patricia V."},{"full_name":"Ahmad, S. 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Yuting","last_name":"Zhao","first_name":"Yuting"},{"full_name":"Zheng, Guoping","last_name":"Zheng","first_name":"Guoping"},{"full_name":"Zheng, Kai","last_name":"Zheng","first_name":"Kai"},{"last_name":"Zheng","first_name":"Ling","full_name":"Zheng, Ling"},{"last_name":"Zheng","first_name":"Shizhong","full_name":"Zheng, Shizhong"},{"full_name":"Zheng, Xi Long","first_name":"Xi Long","last_name":"Zheng"},{"full_name":"Zheng, Yi","first_name":"Yi","last_name":"Zheng"},{"full_name":"Zheng, Zu Guo","last_name":"Zheng","first_name":"Zu Guo"},{"last_name":"Zhivotovsky","first_name":"Boris","full_name":"Zhivotovsky, Boris"},{"full_name":"Zhong, Qing","first_name":"Qing","last_name":"Zhong"},{"first_name":"Ao","last_name":"Zhou","full_name":"Zhou, Ao"},{"full_name":"Zhou, Ben","last_name":"Zhou","first_name":"Ben"},{"first_name":"Cefan","last_name":"Zhou","full_name":"Zhou, Cefan"},{"first_name":"Gang","last_name":"Zhou","full_name":"Zhou, Gang"},{"first_name":"Hao","last_name":"Zhou","full_name":"Zhou, Hao"},{"full_name":"Zhou, Hong","first_name":"Hong","last_name":"Zhou"},{"full_name":"Zhou, Hongbo","first_name":"Hongbo","last_name":"Zhou"},{"full_name":"Zhou, Jie","last_name":"Zhou","first_name":"Jie"},{"last_name":"Zhou","first_name":"Jing","full_name":"Zhou, Jing"},{"last_name":"Zhou","first_name":"Jing","full_name":"Zhou, Jing"},{"first_name":"Jiyong","last_name":"Zhou","full_name":"Zhou, Jiyong"},{"last_name":"Zhou","first_name":"Kailiang","full_name":"Zhou, Kailiang"},{"last_name":"Zhou","first_name":"Rongjia","full_name":"Zhou, Rongjia"},{"full_name":"Zhou, Xu Jie","last_name":"Zhou","first_name":"Xu Jie"},{"last_name":"Zhou","first_name":"Yanshuang","full_name":"Zhou, Yanshuang"},{"first_name":"Yinghong","last_name":"Zhou","full_name":"Zhou, Yinghong"},{"last_name":"Zhou","first_name":"Yubin","full_name":"Zhou, Yubin"},{"first_name":"Zheng Yu","last_name":"Zhou","full_name":"Zhou, Zheng Yu"},{"full_name":"Zhou, Zhou","last_name":"Zhou","first_name":"Zhou"},{"last_name":"Zhu","first_name":"Binglin","full_name":"Zhu, Binglin"},{"full_name":"Zhu, Changlian","first_name":"Changlian","last_name":"Zhu"},{"first_name":"Guo Qing","last_name":"Zhu","full_name":"Zhu, Guo Qing"},{"full_name":"Zhu, Haining","last_name":"Zhu","first_name":"Haining"},{"last_name":"Zhu","first_name":"Hongxin","full_name":"Zhu, Hongxin"},{"full_name":"Zhu, Hua","first_name":"Hua","last_name":"Zhu"},{"last_name":"Zhu","first_name":"Wei Guo","full_name":"Zhu, Wei Guo"},{"last_name":"Zhu","first_name":"Yanping","full_name":"Zhu, Yanping"},{"first_name":"Yushan","last_name":"Zhu","full_name":"Zhu, Yushan"},{"first_name":"Haixia","last_name":"Zhuang","full_name":"Zhuang, Haixia"},{"full_name":"Zhuang, Xiaohong","last_name":"Zhuang","first_name":"Xiaohong"},{"full_name":"Zientara-Rytter, Katarzyna","first_name":"Katarzyna","last_name":"Zientara-Rytter"},{"full_name":"Zimmermann, Christine M.","last_name":"Zimmermann","first_name":"Christine M."},{"last_name":"Ziviani","first_name":"Elena","full_name":"Ziviani, Elena"},{"last_name":"Zoladek","first_name":"Teresa","full_name":"Zoladek, Teresa"},{"full_name":"Zong, Wei Xing","last_name":"Zong","first_name":"Wei Xing"},{"last_name":"Zorov","first_name":"Dmitry B.","full_name":"Zorov, Dmitry B."},{"first_name":"Antonio","last_name":"Zorzano","full_name":"Zorzano, Antonio"},{"last_name":"Zou","first_name":"Weiping","full_name":"Zou, Weiping"},{"full_name":"Zou, Zhen","first_name":"Zhen","last_name":"Zou"},{"full_name":"Zou, Zhengzhi","last_name":"Zou","first_name":"Zhengzhi"},{"full_name":"Zuryn, Steven","first_name":"Steven","last_name":"Zuryn"},{"last_name":"Zwerschke","first_name":"Werner","full_name":"Zwerschke, Werner"},{"full_name":"Brand-Saberi, Beate","first_name":"Beate","last_name":"Brand-Saberi"},{"first_name":"X. Charlie","last_name":"Dong","full_name":"Dong, X. Charlie"},{"full_name":"Kenchappa, Chandra Shekar","last_name":"Kenchappa","first_name":"Chandra Shekar"},{"first_name":"Zuguo","last_name":"Li","full_name":"Li, Zuguo"},{"last_name":"Lin","first_name":"Yong","full_name":"Lin, Yong"},{"first_name":"Shigeru","last_name":"Oshima","full_name":"Oshima, Shigeru"},{"full_name":"Rong, Yueguang","first_name":"Yueguang","last_name":"Rong"},{"first_name":"Judith C.","last_name":"Sluimer","full_name":"Sluimer, Judith C."},{"last_name":"Stallings","first_name":"Christina L.","full_name":"Stallings, Christina L."},{"first_name":"Chun Kit","last_name":"Tong","full_name":"Tong, Chun Kit"}],"title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","date_updated":"2026-07-28T12:37:19Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Autophagy","pmid":1,"_id":"9298","oa_version":"Published Version","date_created":"2021-03-28T22:01:44Z","external_id":{"isi":["000636121800001"],"pmid":["33634751"]},"oa":1,"publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"OA_type":"free access","date_published":"2021-02-08T00:00:00Z"},{"article_number":"iyaa025","oa_version":"Published Version","date_created":"2021-02-18T14:41:30Z","pmid":1,"project":[{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"_id":"9168","publication":"Genetics","date_published":"2021-02-01T00:00:00Z","publication_identifier":{"issn":["1943-2631"]},"OA_type":"free access","external_id":{"pmid":["33724409"],"isi":["000637218100005"]},"oa":1,"author":[{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"main_file_link":[{"url":"https://doi.org/10.1093/genetics/iyaa025","open_access":"1"}],"title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","article_type":"original","OA_place":"publisher","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","day":"01","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-07-28T12:39:03Z","publication_status":"published","publisher":"Genetics Society of America","type":"journal_article","corr_author":"1","intvolume":"       217","scopus_import":"1","doi":"10.1093/genetics/iyaa025","citation":{"apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021.","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025."},"abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}],"article_processing_charge":"No","isi":1,"month":"02","issue":"2","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"year":"2021","language":[{"iso":"eng"}],"volume":217},{"date_updated":"2026-07-28T12:30:05Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"day":"04","ec_funded":1,"OA_place":"publisher","article_type":"original","acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","author":[{"last_name":"Baldwin","first_name":"Katherine T.","full_name":"Baldwin, Katherine T."},{"full_name":"Tan, Christabel X.","last_name":"Tan","first_name":"Christabel X."},{"full_name":"Strader, Samuel T.","last_name":"Strader","first_name":"Samuel T."},{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"},{"first_name":"Justin T.","last_name":"Savage","full_name":"Savage, Justin T."},{"full_name":"Elorza-Vidal, Xabier","last_name":"Elorza-Vidal","first_name":"Xabier"},{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Estévez","first_name":"Raúl","full_name":"Estévez, Raúl"},{"last_name":"Ji","first_name":"Ru-Rong","full_name":"Ji, Ru-Rong"},{"first_name":"Cagla","last_name":"Eroglu","full_name":"Eroglu, Cagla"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2021.05.025"}],"title":"HepaCAM controls astrocyte self-organization and coupling","external_id":{"pmid":["34171291"],"isi":["000692851900010"]},"oa":1,"OA_type":"free access","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"date_published":"2021-08-04T00:00:00Z","publication":"Neuron","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"pmid":1,"_id":"9793","oa_version":"Published Version","date_created":"2021-08-06T09:08:25Z","volume":109,"language":[{"iso":"eng"}],"year":"2021","ddc":["570"],"quality_controlled":"1","issue":"15","page":"2427-2442.e10","month":"08","isi":1,"article_processing_charge":"No","abstract":[{"text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology.","lang":"eng"}],"citation":{"mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. 2021;109(15):2427-2442.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10.","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","ieee":"K. T. Baldwin <i>et al.</i>, “HepaCAM controls astrocyte self-organization and coupling,” <i>Neuron</i>, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>."},"doi":"10.1016/j.neuron.2021.05.025","scopus_import":"1","intvolume":"       109","type":"journal_article","publisher":"Elsevier","publication_status":"published"},{"main_file_link":[{"url":"https://doi.org/10.1093/protein/gzab025","open_access":"1"}],"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","author":[{"last_name":"Lee","first_name":"Jungmin","full_name":"Lee, Jungmin"},{"full_name":"Vernet, Andyna","first_name":"Andyna","last_name":"Vernet"},{"id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","full_name":"Gruber, Nathalie","last_name":"Gruber","first_name":"Nathalie"},{"first_name":"Kasia M.","last_name":"Kready","full_name":"Kready, Kasia M."},{"first_name":"Devin R.","last_name":"Burrill","full_name":"Burrill, Devin R."},{"full_name":"Way, Jeffrey C.","first_name":"Jeffrey C.","last_name":"Way"},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"department":[{"_id":"CaGu"}],"day":"01","acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T12:27:59Z","status":"public","_id":"10363","pmid":1,"date_created":"2021-11-28T23:01:28Z","oa_version":"Published Version","article_number":"gzab025","publication":"Protein Engineering, Design and Selection","OA_type":"free access","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"date_published":"2021-11-01T00:00:00Z","oa":1,"external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"isi":1,"article_processing_charge":"No","month":"11","year":"2021","ddc":["570"],"quality_controlled":"1","volume":34,"language":[{"iso":"eng"}],"type":"journal_article","publisher":"Oxford University Press","publication_status":"published","intvolume":"        34","doi":"10.1093/protein/gzab025","scopus_import":"1","abstract":[{"text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.","lang":"eng"}],"citation":{"mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>, vol. 34, gzab025, Oxford University Press, 2021, doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., &#38; Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. 2021;34. doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","ieee":"J. Lee <i>et al.</i>, “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” <i>Protein Engineering, Design and Selection</i>, vol. 34. Oxford University Press, 2021.","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>."}},{"article_type":"letter_note","day":"12","department":[{"_id":"MaIb"}],"author":[{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"title":"Tidying up the mess","status":"public","date_updated":"2026-07-28T12:16:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Science","oa_version":"None","date_created":"2022-03-03T09:51:48Z","pmid":1,"_id":"10809","external_id":{"isi":["000617551600027"],"pmid":["33574201"]},"date_published":"2021-02-12T00:00:00Z","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"OA_type":"closed access","month":"02","issue":"6530","page":"678-679","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":371,"quality_controlled":"1","year":"2021","intvolume":"       371","publication_status":"published","type":"journal_article","corr_author":"1","publisher":"American Association for the Advancement of Science","citation":{"ieee":"Y. Liu and M. Ibáñez, “Tidying up the mess,” <i>Science</i>, vol. 371, no. 6530. American Association for the Advancement of Science, pp. 678–679, 2021.","ista":"Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679.","chicago":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abg0886\">https://doi.org/10.1126/science.abg0886</a>.","ama":"Liu Y, Ibáñez M. Tidying up the mess. <i>Science</i>. 2021;371(6530):678-679. doi:<a href=\"https://doi.org/10.1126/science.abg0886\">10.1126/science.abg0886</a>","short":"Y. Liu, M. Ibáñez, Science 371 (2021) 678–679.","mla":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” <i>Science</i>, vol. 371, no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79, doi:<a href=\"https://doi.org/10.1126/science.abg0886\">10.1126/science.abg0886</a>.","apa":"Liu, Y., &#38; Ibáñez, M. (2021). Tidying up the mess. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abg0886\">https://doi.org/10.1126/science.abg0886</a>"},"abstract":[{"text":"Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material.","lang":"eng"}],"scopus_import":"1","doi":"10.1126/science.abg0886"},{"arxiv":1,"publication_identifier":{"eissn":["1879-081X"],"issn":["0925-7721"]},"date_published":"2021-02-01T00:00:00Z","oa":1,"external_id":{"isi":["000579185100004"],"arxiv":["1910.09917"]},"_id":"8317","project":[{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science"}],"date_created":"2020-08-30T22:01:09Z","article_number":"101700","oa_version":"Preprint","publication":"Computational Geometry: Theory and Applications","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-07-28T13:08:48Z","status":"public","title":"Folding polyominoes with holes into a cube","main_file_link":[{"url":"https://arxiv.org/abs/1910.09917v3","open_access":"1"}],"author":[{"first_name":"Oswin","last_name":"Aichholzer","full_name":"Aichholzer, Oswin"},{"last_name":"Akitaya","first_name":"Hugo A.","full_name":"Akitaya, Hugo A."},{"last_name":"Cheung","first_name":"Kenneth C.","full_name":"Cheung, Kenneth C."},{"full_name":"Demaine, Erik D.","first_name":"Erik D.","last_name":"Demaine"},{"last_name":"Demaine","first_name":"Martin L.","full_name":"Demaine, Martin L."},{"last_name":"Fekete","first_name":"Sándor P.","full_name":"Fekete, Sándor P."},{"first_name":"Linda","last_name":"Kleist","full_name":"Kleist, Linda"},{"last_name":"Kostitsyna","first_name":"Irina","full_name":"Kostitsyna, Irina"},{"last_name":"Löffler","first_name":"Maarten","full_name":"Löffler, Maarten"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322"},{"first_name":"Klara","last_name":"Mundilova","full_name":"Mundilova, Klara"},{"first_name":"Christiane","last_name":"Schmidt","full_name":"Schmidt, Christiane"}],"department":[{"_id":"HeEd"}],"day":"01","acknowledgement":"This research was performed in part at the 33rd Bellairs Winter Workshop on Computational Geometry. We thank all other participants for a fruitful atmosphere. H. Akitaya was supported by NSF CCF-1422311 & 1423615. Z. Masárová was partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","article_type":"original","doi":"10.1016/j.comgeo.2020.101700","related_material":{"record":[{"id":"6989","relation":"shorter_version","status":"public"}]},"scopus_import":"1","abstract":[{"text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.","lang":"eng"}],"citation":{"mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>, vol. 93, 101700, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2021). Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. 2021;93. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, Computational Geometry: Theory and Applications 93 (2021).","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” <i>Computational Geometry: Theory and Applications</i>, vol. 93. Elsevier, 2021.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2021. Folding polyominoes with holes into a cube. Computational Geometry: Theory and Applications. 93, 101700.","chicago":"Aichholzer, Oswin, Hugo A. Akitaya, Kenneth C. Cheung, Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>."},"type":"journal_article","corr_author":"1","publisher":"Elsevier","publication_status":"published","intvolume":"        93","year":"2021","quality_controlled":"1","volume":93,"language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"No","month":"02"},{"OA_type":"green","arxiv":1,"date_published":"2021-08-17T00:00:00Z","external_id":{"arxiv":["2108.06686"]},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"_id":"10912","oa_version":"Preprint","article_number":"2108.06686","date_created":"2022-03-21T11:41:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-29T06:53:41Z","status":"public","title":"Quantifying the coexistence of neuronal oscillations and avalanches","main_file_link":[{"url":"https://arxiv.org/abs/2108.06686","open_access":"1"}],"author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Pepic, Selver","last_name":"Pepic","first_name":"Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"},{"full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"}],"day":"17","department":[{"_id":"GaTk"}],"ec_funded":1,"OA_place":"repository","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone Grant\r\nNo. P34015.","related_material":{"record":[{"relation":"later_version","id":"12762","status":"public"}]},"doi":"10.48550/ARXIV.2108.06686","abstract":[{"text":"Brain dynamics display collective phenomena as diverse as neuronal oscillations and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic scale, whereas avalanches are scale-free cascades of neural activity. Here we show that such antithetic features can coexist in a very generic class of adaptive neural networks. In the most simple yet fully microscopic model from this class we make direct contact with human brain resting-state activity recordings via tractable inference of the model's two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor fluctuations, collective behaviors of nearly-synchronous extreme events on multiple sensors, to neuronal avalanches unfolding over multiple sensors across multiple time-bins. Importantly, the inferred parameters correlate with model-independent signatures of \"closeness to criticality\", suggesting that the coexistence of scale-specific (neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"citation":{"mla":"Lombardi, Fabrizio, et al. <i>Quantifying the Coexistence of Neuronal Oscillations and Avalanches</i>. 2108.06686, arXiv, doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (n.d.). Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. 2108.06686.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.)."},"publisher":"arXiv","type":"preprint","publication_status":"submitted","ddc":["570"],"year":"2021","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"08"},{"doi":"10.1101/2021.09.30.462269","date_published":"2021-10-02T00:00:00Z","abstract":[{"text":"Hippocampal and neocortical neural activity is modulated by the position of the individual in space. While hippocampal neurons provide the basis for a spatial map, prefrontal cortical neurons generalize over environmental features. Whether these generalized representations result from a bidirectional interaction with, or are mainly derived from hippocampal spatial representations is not known. By examining simultaneously recorded hippocampal and medial prefrontal neurons, we observed that prefrontal spatial representations show a delayed coherence with hippocampal ones. We also identified subpopulations of cells in the hippocampus and medial prefrontal cortex that formed functional cross-area couplings; these resembled the optimal connections predicted by a probabilistic model of spatial information transfer and generalization. Moreover, cross-area couplings were strongest and had the shortest delay preceding spatial decision-making. Our results suggest that generalized spatial coding in the medial prefrontal cortex is inherited from spatial representations in the hippocampus, and that the routing of information can change dynamically with behavioral demands.","lang":"eng"}],"oa":1,"citation":{"ama":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>","short":"M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.).","ieee":"M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus,” <i>bioRxiv</i>. .","chicago":"Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>.","ista":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","mla":"Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","apa":"Nardin, M., Käfer, K., &#38; Csicsvari, J. L. (n.d.). The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>"},"external_id":{"biorxivid":["10.1101/2021.09.30.462269"]},"type":"preprint","_id":"10080","project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","name":"inter-and intracellular signalling in schizophrenia","call_identifier":"FP7"}],"date_created":"2021-10-04T06:28:32Z","oa_version":"Preprint","publication_status":"submitted","biorxivid":1,"publication":"bioRxiv","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-29T06:33:53Z","status":"public","language":[{"iso":"eng"}],"author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"title":"The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.30.462269"}],"article_processing_charge":"No","das_tickbox":"1","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"day":"02","acknowledgement":"We thank Federico Stella for invaluable suggestions and discussions. We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616).","month":"10"},{"date_published":"2021-07-30T00:00:00Z","publication_identifier":{"eissn":["2045-2322"]},"external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"oa":1,"oa_version":"Published Version","article_number":"15729","date_created":"2021-08-15T22:01:26Z","pmid":1,"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"_id":"9905","publication":"Scientific Reports","file":[{"creator":"asandaue","file_name":"2021_ScientificReports_Rella.pdf","relation":"main_file","file_size":3432001,"date_created":"2021-08-16T11:36:49Z","checksum":"ac86892ed17e6724c7251844da5cef5c","success":1,"content_type":"application/pdf","date_updated":"2021-08-16T11:36:49Z","access_level":"open_access","file_id":"9927"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-07-29T12:57:49Z","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon"},{"first_name":"Yuliya A.","last_name":"Kulikova","full_name":"Kulikova, Yuliya A."},{"last_name":"Dermitzakis","first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","department":[{"_id":"FyKo"}],"day":"30","ec_funded":1,"scopus_import":"1","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}],"record":[{"status":"public","id":"20811","relation":"dissertation_contains"}]},"doi":"10.1038/s41598-021-95025-3","citation":{"ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>."},"abstract":[{"text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period.","lang":"eng"}],"publication_status":"published","publisher":"Springer Nature","type":"journal_article","has_accepted_license":"1","intvolume":"        11","quality_controlled":"1","year":"2021","ddc":["570","610"],"language":[{"iso":"eng"}],"volume":11,"article_processing_charge":"Yes","isi":1,"month":"07","issue":"1","file_date_updated":"2021-08-16T11:36:49Z"},{"publication_identifier":{"issn":["2663-337X"]},"date_published":"2021-05-30T00:00:00Z","oa":1,"_id":"9418","oa_version":"Published Version","date_created":"2021-05-24T13:06:23Z","file":[{"date_created":"2021-05-24T11:22:29Z","checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_size":2673905,"relation":"main_file","file_name":"mph-thesis-v519-pdfimages.pdf","creator":"bphuong","file_id":"9419","access_level":"open_access","date_updated":"2021-05-24T11:22:29Z","success":1,"content_type":"application/pdf"},{"creator":"bphuong","file_name":"thesis.zip","relation":"source_file","file_size":92995100,"checksum":"f5699e876bc770a9b0df8345a77720a2","date_created":"2021-05-24T11:56:02Z","content_type":"application/zip","date_updated":"2021-05-24T11:56:02Z","access_level":"closed","file_id":"9420"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-30T05:33:52Z","status":"public","alternative_title":["ISTA Thesis"],"title":"Underspecification in deep learning","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","first_name":"Phuong"}],"day":"30","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"OA_place":"publisher","degree_awarded":"PhD","related_material":{"record":[{"status":"deleted","relation":"part_of_dissertation","id":"7435"},{"relation":"part_of_dissertation","id":"7481","status":"public"},{"status":"public","id":"9416","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7479","status":"public"}]},"doi":"10.15479/AT:ISTA:9418","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"citation":{"short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>.","apa":"Phuong, M. (2021). <i>Underspecification in deep learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>","mla":"Phuong, Mary. <i>Underspecification in Deep Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>."},"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","doi_confirm":"1","has_accepted_license":"1","year":"2021","ddc":["000"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","page":"125","file_date_updated":"2021-05-24T11:56:02Z","month":"05"},{"file_date_updated":"2021-05-24T11:15:57Z","month":"05","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2021","conference":{"start_date":"2021-05-03","location":"Virtual","name":"ICLR: International Conference on Learning Representations","end_date":"2021-05-07"},"ddc":["000"],"quality_controlled":"1","has_accepted_license":"1","type":"conference","corr_author":"1","publication_status":"published","abstract":[{"lang":"eng","text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time  onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks."}],"citation":{"short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: <i>9th International Conference on Learning Representations</i>. ; 2021.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in <i>9th International Conference on Learning Representations</i>, Virtual, 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In <i>9th International Conference on Learning Representations</i>, 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” <i>9th International Conference on Learning Representations</i>, 2021.","apa":"Phuong, M., &#38; Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In <i>9th International Conference on Learning Representations</i>. Virtual."},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9418"}]},"scopus_import":"1","day":"01","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"author":[{"first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"title":"The inductive bias of ReLU networks on orthogonally separable data","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"date_updated":"2026-07-30T05:33:51Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"9417","date_updated":"2021-05-24T11:15:57Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-24T11:15:57Z","checksum":"f34ff17017527db5ba6927f817bdd125","file_size":502356,"creator":"bphuong","file_name":"iclr2021_conference.pdf"}],"publication":"9th International Conference on Learning Representations","_id":"9416","oa_version":"Published Version","date_created":"2021-05-24T11:16:46Z","oa":1,"date_published":"2021-05-01T00:00:00Z"},{"type":"journal_article","publisher":"Elsevier","publication_status":"published","intvolume":"        58","has_accepted_license":"1","doi":"10.1016/j.ufug.2020.126970","scopus_import":"1","abstract":[{"text":"Increasing urban tree cover is an often proposed mitigation strategy against urban heat as trees are expected to cool cities through evapotranspiration and shade provision. However, trees also modify wind flow and urban aerodynamic roughness, which can potentially limit heat dissipation. Existing studies show a varying cooling potential of urban trees in different climates and times of the day. These differences are so far not systematically explained as partitioning the individual tree effects is challenging and impossible through observations alone. Here, we conduct numerical experiments removing and adding radiation, evapotranspiration, and aerodynamic roughness effects caused by urban trees using a mechanistic urban ecohydrological model. Simulations are presented for four cities in different climates (Phoenix, Singapore, Melbourne, Zurich) considering the seasonal and diurnal cycles of air and surface temperatures.\r\nResults show that evapotranspiration of well-watered trees alone can decrease local 2 m air temperature at maximum by 3.1– 5.8 °C in the four climates during summer. Further cooling is prevented by stomatal closure at peak temperatures as high vapour pressure deficits limit transpiration. While shading reduces surface temperatures, the interaction of a non-transpiring tree with radiation can increase 2 m air temperature by up to 1.6 – 2.1 °C in certain hours of the day at local scale, thus partially counteracting the evapotranspirative cooling effect. Furthermore, in the analysed scenarios, which do not account for tree wind blockage effects, trees lead to a decrease in urban roughness, which inhibits turbulent energy exchange and increases air temperature during daytime. At night, single tree effects are variable likely due to differences in atmospheric stability within the urban canyon. These results explain reported diurnal, seasonal and climatic differences in the cooling effects of urban trees, and can guide future field campaigns, planning strategies, and species selection aimed at improving local microclimate using urban greenery.","lang":"eng"}],"citation":{"apa":"Meili, N., Manoli, G., Burlando, P., Carmeliet, J., Chow, W. T. L., Coutts, A. M., … Fatichi, S. (2021). Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. <i>Urban Forestry &#38; Urban Greening</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">https://doi.org/10.1016/j.ufug.2020.126970</a>","mla":"Meili, Naika, et al. “Tree Effects on Urban Microclimate: Diurnal, Seasonal, and Climatic Temperature Differences Explained by Separating Radiation, Evapotranspiration, and Roughness Effects.” <i>Urban Forestry &#38; Urban Greening</i>, vol. 58, no. 3, 126970, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">10.1016/j.ufug.2020.126970</a>.","ista":"Meili N, Manoli G, Burlando P, Carmeliet J, Chow WTL, Coutts AM, Roth M, Velasco E, Vivoni ER, Fatichi S. 2021. Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. Urban Forestry &#38; Urban Greening. 58(3), 126970.","ieee":"N. Meili <i>et al.</i>, “Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects,” <i>Urban Forestry &#38; Urban Greening</i>, vol. 58, no. 3. Elsevier, 2021.","chicago":"Meili, Naika, Gabriele Manoli, Paolo Burlando, Jan Carmeliet, Winston T.L. Chow, Andrew M. Coutts, Matthias Roth, Erik Velasco, Enrique R. Vivoni, and Simone Fatichi. “Tree Effects on Urban Microclimate: Diurnal, Seasonal, and Climatic Temperature Differences Explained by Separating Radiation, Evapotranspiration, and Roughness Effects.” <i>Urban Forestry &#38; Urban Greening</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">https://doi.org/10.1016/j.ufug.2020.126970</a>.","short":"N. Meili, G. Manoli, P. Burlando, J. Carmeliet, W.T.L. Chow, A.M. Coutts, M. Roth, E. Velasco, E.R. Vivoni, S. Fatichi, Urban Forestry &#38; Urban Greening 58 (2021).","ama":"Meili N, Manoli G, Burlando P, et al. Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. <i>Urban Forestry &#38; Urban Greening</i>. 2021;58(3). doi:<a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">10.1016/j.ufug.2020.126970</a>"},"article_processing_charge":"Yes (in subscription journal)","issue":"3","month":"03","ddc":["550"],"year":"2021","quality_controlled":"1","volume":58,"language":[{"iso":"eng"}],"_id":"22472","date_created":"2026-07-27T12:30:23Z","oa_version":"Published Version","article_number":"126970","publication":"Urban Forestry & Urban Greening","extern":"1","OA_type":"hybrid","publication_identifier":{"eissn":["1610-8167"],"issn":["1618-8667"]},"date_published":"2021-03-01T00:00:00Z","oa":1,"title":"Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects","main_file_link":[{"url":"https://doi.org/10.1016/j.ufug.2020.126970","open_access":"1"}],"author":[{"first_name":"Naika","last_name":"Meili","full_name":"Meili, Naika"},{"last_name":"Manoli","first_name":"Gabriele","full_name":"Manoli, Gabriele"},{"full_name":"Burlando, Paolo","first_name":"Paolo","last_name":"Burlando"},{"full_name":"Carmeliet, Jan","last_name":"Carmeliet","first_name":"Jan"},{"full_name":"Chow, Winston T.L.","first_name":"Winston T.L.","last_name":"Chow"},{"first_name":"Andrew M.","last_name":"Coutts","full_name":"Coutts, Andrew M."},{"last_name":"Roth","first_name":"Matthias","full_name":"Roth, Matthias"},{"last_name":"Velasco","first_name":"Erik","full_name":"Velasco, Erik"},{"last_name":"Vivoni","first_name":"Enrique R.","full_name":"Vivoni, Enrique R."},{"full_name":"Fatichi, Simone","last_name":"Fatichi","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"das_tickbox":"1","day":"01","OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-30T08:40:12Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public"},{"article_processing_charge":"No","month":"09","ddc":["550"],"year":"2021","quality_controlled":"1","volume":39,"language":[{"iso":"eng"}],"type":"journal_article","publisher":"Elsevier","publication_status":"published","intvolume":"        39","has_accepted_license":"1","doi":"10.1016/j.uclim.2021.100939","scopus_import":"1","abstract":[{"lang":"eng","text":"In light of globally increasing temperatures, accentuated in cities by the urban heat island effect, urban planners and designers are looking for new, quantitative methods to assess the performance of their designs in terms of ecosystem services provided by vegetation. Among these ecosystem services, improved microclimate conditions are particularly important for human thermal comfort and health. In this study, an urban scene in the tropical city of Singapore is numerically investigated with a fully-integrated, three-dimensional urban microclimate model implemented in OpenFOAM. Mass and heat transport in air and storage effect in the urban environment are coupled so that the daily turbulent transport in air using steady Reynolds-averaged Navier-Stokes (RANS) can be solved iteratively with the unsteady heat and moisture transfer from urban surfaces. Vegetation is modeled as a porous medium for the flow of moist air and a leaf energy balance model is used to determine the heat fluxes and transpiration at leaf surfaces. The analysis shows the influence of an urban park upon air temperatures and thermal comfort. Cooling intensity of 1 °C is observed downwind of the park within a region of 27 m for an incoming wind speed of 2.3 m s−1, which reduces to 0.6 °C at a distance of 117 m from the park. The Universal Thermal Comfort Index (UTCI) shows a reduction in thermal stress in and around the park. The approach presented here can provide specific guidelines for urban planners and frame expectations on magnitude and spatial extent of local microclimate modifications generated by an urban park in a tropical city."}],"citation":{"apa":"Mughal, M. O., Kubilay, A., Fatichi, S., Meili, N., Carmeliet, J., Edwards, P., &#38; Burlando, P. (2021). Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. <i>Urban Climate</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">https://doi.org/10.1016/j.uclim.2021.100939</a>","mla":"Mughal, Muhammad Omer, et al. “Detailed Investigation of Vegetation Effects on Microclimate by Means of Computational Fluid Dynamics (CFD) in a Tropical Urban Environment.” <i>Urban Climate</i>, vol. 39, 100939, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">10.1016/j.uclim.2021.100939</a>.","ama":"Mughal MO, Kubilay A, Fatichi S, et al. Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. <i>Urban Climate</i>. 2021;39. doi:<a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">10.1016/j.uclim.2021.100939</a>","short":"M.O. Mughal, A. Kubilay, S. Fatichi, N. Meili, J. Carmeliet, P. Edwards, P. Burlando, Urban Climate 39 (2021).","ieee":"M. O. Mughal <i>et al.</i>, “Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment,” <i>Urban Climate</i>, vol. 39. Elsevier, 2021.","chicago":"Mughal, Muhammad Omer, Aytac Kubilay, Simone Fatichi, Naika Meili, Jan Carmeliet, Peter Edwards, and Paolo Burlando. “Detailed Investigation of Vegetation Effects on Microclimate by Means of Computational Fluid Dynamics (CFD) in a Tropical Urban Environment.” <i>Urban Climate</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">https://doi.org/10.1016/j.uclim.2021.100939</a>.","ista":"Mughal MO, Kubilay A, Fatichi S, Meili N, Carmeliet J, Edwards P, Burlando P. 2021. Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. Urban Climate. 39, 100939."},"title":"Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment","main_file_link":[{"url":"https://doi.org/10.1016/j.uclim.2021.100939","open_access":"1"}],"author":[{"full_name":"Mughal, Muhammad Omer","last_name":"Mughal","first_name":"Muhammad Omer"},{"last_name":"Kubilay","first_name":"Aytac","full_name":"Kubilay, Aytac"},{"first_name":"Simone","last_name":"Fatichi","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"first_name":"Naika","last_name":"Meili","full_name":"Meili, Naika"},{"last_name":"Carmeliet","first_name":"Jan","full_name":"Carmeliet, Jan"},{"last_name":"Edwards","first_name":"Peter","full_name":"Edwards, Peter"},{"first_name":"Paolo","last_name":"Burlando","full_name":"Burlando, Paolo"}],"das_tickbox":"1","day":"01","article_type":"original","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-30T09:08:16Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","_id":"22474","date_created":"2026-07-27T12:30:23Z","article_number":"100939","oa_version":"Published Version","extern":"1","publication":"Urban Climate","publication_identifier":{"eissn":["2212-0955"]},"OA_type":"hybrid","date_published":"2021-09-01T00:00:00Z","oa":1},{"abstract":[{"text":"Vegetation establishment, growth and succession in riparian ecosystems are linked to river flow dynamics and groundwater table fluctuations. This is especially true in Alpine gravel-bed rivers with wide floodplains, geomorphically active floods and a strong river-aquifer exchange. The role of short-term groundwater fluctuations is not always clear in these ecosystems, as it is assumed that phreatophytic vegetation close to rivers is adapted to such conditions. Here, we provide data evidence of riparian plant response to short-term groundwater table fluctuations in a braided gravel-bed river (Maggia). We used indirect physiological variables for photosynthesis and transpiration—stomatal conductance gs and daily variation in stem diameter ΔDd—which we measured at six mature riparian trees of the Salicaceae family at two sites with different mean depths to groundwater during two growing seasons. The data demonstrate that (a) short-term variation of the groundwater table affects riparian vegetation—at the site with deeper groundwater, the water table depth was the best predictor of gs variability, while at the site with shallower groundwater, temperature and vapour pressure deficit (VPD) were the best predictors of ΔDd variability; (b) instantaneous stomatal conductance is related to VPD, but conditioned by groundwater levels, with higher stomatal conductance for the same radiative input and VPD when the water table was higher for all trees; and (c) local microclimate measured at tree locations had a stronger predictive power for gs than valley scale climate, suggesting local climate controls on vegetated stands on gravel bars. Our results provide evidence of riparian trees undertaking physiological adjustments to transpiration in response to groundwater stage, depending on their riparian floodplain setting.","lang":"eng"}],"citation":{"mla":"Martinetti, Stefano, et al. “Field Evidence of Riparian Vegetation Response to Groundwater Levels in a Gravel‐bed River.” <i>Ecohydrology</i>, vol. 14, no. 2, e2264, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/eco.2264\">10.1002/eco.2264</a>.","apa":"Martinetti, S., Fatichi, S., Floriancic, M., Burlando, P., &#38; Molnar, P. (2021). Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. <i>Ecohydrology</i>. Wiley. <a href=\"https://doi.org/10.1002/eco.2264\">https://doi.org/10.1002/eco.2264</a>","chicago":"Martinetti, Stefano, Simone Fatichi, Marius Floriancic, Paolo Burlando, and Peter Molnar. “Field Evidence of Riparian Vegetation Response to Groundwater Levels in a Gravel‐bed River.” <i>Ecohydrology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/eco.2264\">https://doi.org/10.1002/eco.2264</a>.","ieee":"S. Martinetti, S. Fatichi, M. Floriancic, P. Burlando, and P. Molnar, “Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river,” <i>Ecohydrology</i>, vol. 14, no. 2. Wiley, 2021.","ista":"Martinetti S, Fatichi S, Floriancic M, Burlando P, Molnar P. 2021. Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. Ecohydrology. 14(2), e2264.","ama":"Martinetti S, Fatichi S, Floriancic M, Burlando P, Molnar P. Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. <i>Ecohydrology</i>. 2021;14(2). doi:<a href=\"https://doi.org/10.1002/eco.2264\">10.1002/eco.2264</a>","short":"S. Martinetti, S. Fatichi, M. Floriancic, P. Burlando, P. Molnar, Ecohydrology 14 (2021)."},"doi":"10.1002/eco.2264","scopus_import":"1","intvolume":"        14","type":"journal_article","publisher":"Wiley","publication_status":"published","volume":14,"language":[{"iso":"eng"}],"year":"2021","quality_controlled":"1","issue":"2","month":"03","article_processing_charge":"No","publication_identifier":{"issn":["1936-0584"],"eissn":["1936-0592"]},"OA_type":"closed access","date_published":"2021-03-01T00:00:00Z","publication":"Ecohydrology","extern":"1","_id":"22468","oa_version":"None","article_number":"e2264","date_created":"2026-07-27T12:30:23Z","date_updated":"2026-07-30T08:46:20Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","das_tickbox":"1","article_type":"original","author":[{"last_name":"Martinetti","first_name":"Stefano","full_name":"Martinetti, Stefano"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"},{"full_name":"Floriancic, Marius","last_name":"Floriancic","first_name":"Marius"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"first_name":"Peter","last_name":"Molnar","full_name":"Molnar, Peter"}],"title":"Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river"},{"title":"A review of studies on observed precipitation trends in Italy","author":[{"last_name":"Caporali","first_name":"Enrica","full_name":"Caporali, Enrica"},{"full_name":"Lompi, Marco","first_name":"Marco","last_name":"Lompi"},{"first_name":"Tommaso","last_name":"Pacetti","full_name":"Pacetti, Tommaso"},{"first_name":"Valentina","last_name":"Chiarello","full_name":"Chiarello, Valentina"},{"last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"day":"01","das_tickbox":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-30T09:04:34Z","status":"public","_id":"22430","oa_version":"None","date_created":"2026-07-27T12:30:23Z","publication":"International Journal of Climatology","extern":"1","OA_type":"closed access","publication_identifier":{"eissn":["1097-0088"],"issn":["0899-8418"]},"date_published":"2021-01-01T00:00:00Z","article_processing_charge":"No","page":"E1-E25","issue":"S1","month":"01","year":"2021","quality_controlled":"1","volume":41,"language":[{"iso":"eng"}],"publisher":"Wiley","type":"journal_article","publication_status":"published","intvolume":"        41","doi":"10.1002/joc.6741","scopus_import":"1","abstract":[{"lang":"eng","text":"Research to detect changes in precipitation variables has become a topic of particular interest to understand modifications in water resources availability. The review is focused on the Italian territory, outlining the “state of the art” of changes in precipitation regime through a review of 54 published studies on observed rainfall trend analyses, in the period 1999–2018. The aim is to combine a large body of knowledge in a single review and to explain the main patterns of rainfall changes occurred in Italy over the last decades. The analysis focused on the Total Precipitation (TP) and the number of Wet Days (WDs) indices at the annual and seasonal scale. A weight factor is introduced to take into account the differences among studies in geographical area, time series length, and number of stations. The review is accompanied by the discussion of other rainfall related variables, that is, precipitation intensity, extreme rainfall events and meteorological droughts, which are useful to provide a broader picture of rainfall changes. Overall, there is an agreement about the tendency of a decrease in wet days on the entire Italy, with limited discrepancies in the various regions. A decrease in wet days is accompanied by a negative trend (although less evident) in total precipitation, especially in winter. Nevertheless, a univocal direction of trends (or lack of thereof) in annual total precipitation and mostly hydrological extreme events is difficult to achieve."}],"citation":{"mla":"Caporali, Enrica, et al. “A Review of Studies on Observed Precipitation Trends in Italy.” <i>International Journal of Climatology</i>, vol. 41, no. S1, Wiley, 2021, pp. E1–25, doi:<a href=\"https://doi.org/10.1002/joc.6741\">10.1002/joc.6741</a>.","apa":"Caporali, E., Lompi, M., Pacetti, T., Chiarello, V., &#38; Fatichi, S. (2021). A review of studies on observed precipitation trends in Italy. <i>International Journal of Climatology</i>. Wiley. <a href=\"https://doi.org/10.1002/joc.6741\">https://doi.org/10.1002/joc.6741</a>","short":"E. Caporali, M. Lompi, T. Pacetti, V. Chiarello, S. Fatichi, International Journal of Climatology 41 (2021) E1–E25.","ama":"Caporali E, Lompi M, Pacetti T, Chiarello V, Fatichi S. A review of studies on observed precipitation trends in Italy. <i>International Journal of Climatology</i>. 2021;41(S1):E1-E25. doi:<a href=\"https://doi.org/10.1002/joc.6741\">10.1002/joc.6741</a>","chicago":"Caporali, Enrica, Marco Lompi, Tommaso Pacetti, Valentina Chiarello, and Simone Fatichi. “A Review of Studies on Observed Precipitation Trends in Italy.” <i>International Journal of Climatology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/joc.6741\">https://doi.org/10.1002/joc.6741</a>.","ista":"Caporali E, Lompi M, Pacetti T, Chiarello V, Fatichi S. 2021. A review of studies on observed precipitation trends in Italy. International Journal of Climatology. 41(S1), E1–E25.","ieee":"E. Caporali, M. Lompi, T. Pacetti, V. Chiarello, and S. Fatichi, “A review of studies on observed precipitation trends in Italy,” <i>International Journal of Climatology</i>, vol. 41, no. S1. Wiley, pp. E1–E25, 2021."}},{"extern":"1","publication":"Building and Environment","_id":"22457","date_created":"2026-07-27T12:30:23Z","article_number":"107733","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["0360-1323"]},"OA_type":"hybrid","date_published":"2021-05-01T00:00:00Z","das_tickbox":"1","day":"01","article_type":"original","OA_place":"publisher","title":"Vegetation cover and plant-trait effects on outdoor thermal comfort in a tropical city","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.buildenv.2021.107733"}],"author":[{"first_name":"Naika","last_name":"Meili","full_name":"Meili, Naika"},{"first_name":"Juan Angel","last_name":"Acero","full_name":"Acero, Juan Angel"},{"full_name":"Peleg, Nadav","first_name":"Nadav","last_name":"Peleg"},{"full_name":"Manoli, Gabriele","first_name":"Gabriele","last_name":"Manoli"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"}],"date_updated":"2026-07-30T09:12:50Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       195","has_accepted_license":"1","type":"journal_article","publisher":"Elsevier","publication_status":"published","abstract":[{"text":"An increase in urban vegetation is an often proposed mitigation strategy to reduce urban heat and improve outdoor thermal comfort (OTC). Vegetation can alter urban microclimate through changes in air temperature, mean radiant temperature, humidity, and wind speed. In this study, we model how street tree and ground vegetation cover and their structural, optical, interception, and physiological traits control the diurnal cycle of OTC in different urban densities in a tropical city (Singapore). For this purpose, we perform a variance based sensitivity analysis of the urban ecohydrological model UT&C. Model performance is evaluated through a comparison with local microclimate measurements and OTC is assessed with the Universal Thermal Climate Index (UTCI).\r\nWe find a pronounced daily cycle of vegetation effects on UTCI. Tree cover fraction is more efficient in decreasing UTCI during daytime, while a higher vegetated ground fraction provides more cooling during night. Generally, increasing vegetation cover fractions do not deter OTC, except in certain urban densities during some periods of the day. An increase in tree and ground vegetation fractions provides a higher average UTCI reduction compared to a change in vegetation traits (0.9 – 2.9  °C vs. 0.7 – 1.1  °C during midday, 10 month average). The increase in humidity related to plant transpiration prevents further reduction of UTCI. However, the choice of vegetation traits enhancing tree transpiration can decrease UTCI during hot periods. These results can inform urban planners on the selection of vegetation amount and traits to achieve feasible OTC improvements in tropical cities.","lang":"eng"}],"citation":{"mla":"Meili, Naika, et al. “Vegetation Cover and Plant-Trait Effects on Outdoor Thermal Comfort in a Tropical City.” <i>Building and Environment</i>, vol. 195, 107733, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.buildenv.2021.107733\">10.1016/j.buildenv.2021.107733</a>.","apa":"Meili, N., Acero, J. A., Peleg, N., Manoli, G., Burlando, P., &#38; Fatichi, S. (2021). Vegetation cover and plant-trait effects on outdoor thermal comfort in a tropical city. <i>Building and Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.buildenv.2021.107733\">https://doi.org/10.1016/j.buildenv.2021.107733</a>","ama":"Meili N, Acero JA, Peleg N, Manoli G, Burlando P, Fatichi S. Vegetation cover and plant-trait effects on outdoor thermal comfort in a tropical city. <i>Building and Environment</i>. 2021;195. doi:<a href=\"https://doi.org/10.1016/j.buildenv.2021.107733\">10.1016/j.buildenv.2021.107733</a>","short":"N. Meili, J.A. Acero, N. Peleg, G. Manoli, P. Burlando, S. Fatichi, Building and Environment 195 (2021).","chicago":"Meili, Naika, Juan Angel Acero, Nadav Peleg, Gabriele Manoli, Paolo Burlando, and Simone Fatichi. “Vegetation Cover and Plant-Trait Effects on Outdoor Thermal Comfort in a Tropical City.” <i>Building and Environment</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.buildenv.2021.107733\">https://doi.org/10.1016/j.buildenv.2021.107733</a>.","ieee":"N. Meili, J. A. Acero, N. Peleg, G. Manoli, P. Burlando, and S. Fatichi, “Vegetation cover and plant-trait effects on outdoor thermal comfort in a tropical city,” <i>Building and Environment</i>, vol. 195. Elsevier, 2021.","ista":"Meili N, Acero JA, Peleg N, Manoli G, Burlando P, Fatichi S. 2021. Vegetation cover and plant-trait effects on outdoor thermal comfort in a tropical city. Building and Environment. 195, 107733."},"doi":"10.1016/j.buildenv.2021.107733","scopus_import":"1","month":"05","article_processing_charge":"No","volume":195,"language":[{"iso":"eng"}],"ddc":["550"],"year":"2021","quality_controlled":"1"},{"has_accepted_license":"1","intvolume":"         7","PlanS_conform":"1","publication_status":"published","publisher":"American Association for the Advancement of Science","type":"journal_article","citation":{"apa":"Fatichi, S., Peleg, N., Mastrotheodoros, T., Pappas, C., &#38; Manoli, G. (2021). An ecohydrological journey of 4500 years reveals a stable but threatened precipitation–groundwater recharge relation around Jerusalem. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abe6303\">https://doi.org/10.1126/sciadv.abe6303</a>","mla":"Fatichi, Simone, et al. “An Ecohydrological Journey of 4500 Years Reveals a Stable but Threatened Precipitation–Groundwater Recharge Relation around Jerusalem.” <i>Science Advances</i>, vol. 7, no. 37, eabe6303, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abe6303\">10.1126/sciadv.abe6303</a>.","ista":"Fatichi S, Peleg N, Mastrotheodoros T, Pappas C, Manoli G. 2021. An ecohydrological journey of 4500 years reveals a stable but threatened precipitation–groundwater recharge relation around Jerusalem. Science Advances. 7(37), eabe6303.","chicago":"Fatichi, Simone, Nadav Peleg, Theodoros Mastrotheodoros, Christoforos Pappas, and Gabriele Manoli. “An Ecohydrological Journey of 4500 Years Reveals a Stable but Threatened Precipitation–Groundwater Recharge Relation around Jerusalem.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abe6303\">https://doi.org/10.1126/sciadv.abe6303</a>.","ieee":"S. Fatichi, N. Peleg, T. Mastrotheodoros, C. Pappas, and G. Manoli, “An ecohydrological journey of 4500 years reveals a stable but threatened precipitation–groundwater recharge relation around Jerusalem,” <i>Science Advances</i>, vol. 7, no. 37. American Association for the Advancement of Science, 2021.","short":"S. Fatichi, N. Peleg, T. Mastrotheodoros, C. Pappas, G. Manoli, Science Advances 7 (2021).","ama":"Fatichi S, Peleg N, Mastrotheodoros T, Pappas C, Manoli G. An ecohydrological journey of 4500 years reveals a stable but threatened precipitation–groundwater recharge relation around Jerusalem. <i>Science Advances</i>. 2021;7(37). doi:<a href=\"https://doi.org/10.1126/sciadv.abe6303\">10.1126/sciadv.abe6303</a>"},"abstract":[{"lang":"eng","text":"Groundwater is a key water resource in semiarid and seasonally dry regions around the world, which is replenished by intermittent precipitation events and mediated by vegetation, soil, and regolith properties. Here, a climate reconstruction of 4500 years for the Jerusalem region was used to determine the relation between climate, vegetation, and groundwater recharge. Despite changes in air temperature and vegetation characteristics, simulated recharge remained linearly related to precipitation over the entire analyzed period, with drier decades having lower rates of recharge for a given annual precipitation due to soil memory effects. We show that in recent decades, the lack of changes in the precipitation–groundwater recharge relation results from the compensating responses of vegetation to increasing CO2, i.e., increased leaf area and reduced stomatal conductance. This multicentury relation is expected to be modified by climate change, with changes up to −20% in recharge for unchanged precipitation, potentially jeopardizing water resource availability."}],"scopus_import":"1","doi":"10.1126/sciadv.abe6303","month":"09","issue":"37","article_processing_charge":"Yes","language":[{"iso":"eng"}],"volume":7,"quality_controlled":"1","ddc":["550"],"year":"2021","publication":"Science Advances","extern":"1","oa_version":"Published Version","article_number":"eabe6303","date_created":"2026-07-27T12:30:23Z","_id":"22448","oa":1,"date_published":"2021-09-01T00:00:00Z","DOAJ_listed":"1","OA_type":"gold","publication_identifier":{"eissn":["2375-2548"]},"OA_place":"publisher","article_type":"original","day":"01","das_tickbox":"1","main_file_link":[{"url":"https://doi.org/10.1126/sciadv.abe6303","open_access":"1"}],"title":"An ecohydrological journey of 4500 years reveals a stable but threatened precipitation–groundwater recharge relation around Jerusalem","author":[{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone","last_name":"Fatichi","first_name":"Simone"},{"first_name":"Nadav","last_name":"Peleg","full_name":"Peleg, Nadav"},{"full_name":"Mastrotheodoros, Theodoros","first_name":"Theodoros","last_name":"Mastrotheodoros"},{"last_name":"Pappas","first_name":"Christoforos","full_name":"Pappas, Christoforos"},{"last_name":"Manoli","first_name":"Gabriele","full_name":"Manoli, Gabriele"}],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-07-30T09:24:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Advancing process representation in hydrological models: Integrating new concepts, knowledge, and data","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2021WR030661"}],"author":[{"full_name":"Guse, Björn","last_name":"Guse","first_name":"Björn"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi","full_name":"Fatichi, Simone"},{"full_name":"Gharari, Shervan","last_name":"Gharari","first_name":"Shervan"},{"full_name":"Melsen, Lieke A.","last_name":"Melsen","first_name":"Lieke A."}],"article_type":"original","OA_place":"publisher","day":"01","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-07-30T09:15:11Z","article_number":"e2021WR030661","oa_version":"Published Version","date_created":"2026-07-27T12:30:23Z","_id":"22452","extern":"1","publication":"Water Resources Research","date_published":"2021-11-01T00:00:00Z","OA_type":"free access","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"oa":1,"article_processing_charge":"No","month":"11","issue":"11","quality_controlled":"1","year":"2021","language":[{"iso":"eng"}],"volume":57,"publication_status":"published","publisher":"American Geophysical Union","type":"journal_article","intvolume":"        57","scopus_import":"1","doi":"10.1029/2021wr030661","citation":{"apa":"Guse, B., Fatichi, S., Gharari, S., &#38; Melsen, L. A. (2021). Advancing process representation in hydrological models: Integrating new concepts, knowledge, and data. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2021wr030661\">https://doi.org/10.1029/2021wr030661</a>","mla":"Guse, Björn, et al. “Advancing Process Representation in Hydrological Models: Integrating New Concepts, Knowledge, and Data.” <i>Water Resources Research</i>, vol. 57, no. 11, e2021WR030661, American Geophysical Union, 2021, doi:<a href=\"https://doi.org/10.1029/2021wr030661\">10.1029/2021wr030661</a>.","ieee":"B. Guse, S. Fatichi, S. Gharari, and L. A. Melsen, “Advancing process representation in hydrological models: Integrating new concepts, knowledge, and data,” <i>Water Resources Research</i>, vol. 57, no. 11. American Geophysical Union, 2021.","ista":"Guse B, Fatichi S, Gharari S, Melsen LA. 2021. Advancing process representation in hydrological models: Integrating new concepts, knowledge, and data. Water Resources Research. 57(11), e2021WR030661.","chicago":"Guse, Björn, Simone Fatichi, Shervan Gharari, and Lieke A. Melsen. “Advancing Process Representation in Hydrological Models: Integrating New Concepts, Knowledge, and Data.” <i>Water Resources Research</i>. American Geophysical Union, 2021. <a href=\"https://doi.org/10.1029/2021wr030661\">https://doi.org/10.1029/2021wr030661</a>.","ama":"Guse B, Fatichi S, Gharari S, Melsen LA. Advancing process representation in hydrological models: Integrating new concepts, knowledge, and data. <i>Water Resources Research</i>. 2021;57(11). doi:<a href=\"https://doi.org/10.1029/2021wr030661\">10.1029/2021wr030661</a>","short":"B. Guse, S. Fatichi, S. Gharari, L.A. Melsen, Water Resources Research 57 (2021)."},"abstract":[{"lang":"eng","text":"Model fidelity and accuracy in process representations have been the crux of scientific hydrological modeling, creating a pressing need for a better linkage between the development of hydrological models and the growing number of data sources and measurement techniques. Improved representation of process dynamics in hydrological models can provide new insights into complex hydrological systems and point out less understood natural phenomena that need further investigation. This special issue includes contributions that offer potential solutions and strategies to improve and test the representation of hydrological processes. We have organized the special issue contributions into four topical categories: (a) Beyond streamflow, which looks into the power of complementary data sources in addition to traditionally used streamflow for process inference. (b) Challenge of subsurface hydrology, that reflects on lesser understood processes under the surface and their impact on the model structure. (c) Evaporation in hydrological modeling, linking ecological aspects to the hydrological functioning of the natural system. Finally, (d) top down vs. bottom up modeling approaches, relied upon for process representation analysis. The special issue and our reflection on the contributions present a snapshot of ongoing efforts for integrating new concepts, knowledge, and data in process representation in hydrological models."}]},{"date_published":"2021-12-27T00:00:00Z","arxiv":1,"external_id":{"arxiv":["2112.13558"]},"oa":1,"oa_version":"Preprint","article_number":"2112.13558","date_created":"2021-12-28T06:52:09Z","_id":"10579","publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2026-08-04T08:34:23Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2112.13558"}],"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Token-driven totally asymmetric simple exclusion process","acknowledgement":"B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for their help with the usage of the cluster. B.K. additionally thanks Călin Guet and his group for help and advice. We thank M. Hennessey-Wesen for constructive comments on the manuscript. We thank Ankita Gupta (Indian Institute of Technology) for spotting a typographical error in Eq. (49) in the preprint version of this paper.","day":"27","department":[{"_id":"GaTk"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"19785"}]},"doi":"10.48550/arXiv.2112.13558","citation":{"ieee":"B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion process,” <i>arXiv</i>. .","ista":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv, 2112.13558.","chicago":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2112.13558\">https://doi.org/10.48550/arXiv.2112.13558</a>.","short":"B. Kavcic, G. Tkačik, ArXiv (n.d.).","ama":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2112.13558\">10.48550/arXiv.2112.13558</a>","mla":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” <i>ArXiv</i>, 2112.13558, doi:<a href=\"https://doi.org/10.48550/arXiv.2112.13558\">10.48550/arXiv.2112.13558</a>.","apa":"Kavcic, B., &#38; Tkačik, G. (n.d.). Token-driven totally asymmetric simple exclusion process. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2112.13558\">https://doi.org/10.48550/arXiv.2112.13558</a>"},"abstract":[{"lang":"eng","text":"We consider a totally asymmetric simple exclusion process (TASEP) consisting of particles on a lattice that require binding by a \"token\" to move. Using a combination of theory and simulations, we address the following questions: (i) How token binding kinetics affects the current-density relation; (ii) How the current-density relation depends on the scarcity of tokens; (iii) How tokens propagate the effects of the locally-imposed disorder (such a slow site) over the entire lattice; (iv) How a shared pool of tokens couples concurrent TASEPs running on multiple lattices; (v) How our results translate to TASEPs with open boundaries that exchange particles with the reservoir. Since real particle motion (including in systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations."}],"publication_status":"submitted","type":"preprint","corr_author":"1","has_accepted_license":"1","ddc":["530"],"year":"2021","language":[{"iso":"eng"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"12"},{"oa":1,"date_published":"2021-11-01T00:00:00Z","publication_identifier":{"issn":["0169-2046"],"eissn":["1872-6062"]},"OA_type":"green","publication":"Landscape and Urban Planning","extern":"1","oa_version":"Preprint","article_number":"104198","date_created":"2026-07-27T12:30:24Z","_id":"22546","status":"public","date_updated":"2026-08-06T08:20:58Z","keyword":["Urban green spaces","Remnant vegetation","Irrigation","Stormwater harvesting","Ecohydrological modeling"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","OA_place":"repository","day":"01","das_tickbox":"1","main_file_link":[{"open_access":"1","url":"https://discovery.ucl.ac.uk/id/eprint/10133304/1/REVISED_Manuscript_Marchionni.pdf"}],"title":"Assessing vegetation response to irrigation strategies and soil properties in an urban reserve in southeast Australia","author":[{"last_name":"Marchionni","first_name":"V.","full_name":"Marchionni, V."},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi","full_name":"Fatichi, Simone"},{"full_name":"Tapper, N.","first_name":"N.","last_name":"Tapper"},{"full_name":"Walker, J.P.","first_name":"J.P.","last_name":"Walker"},{"full_name":"Manoli, G.","last_name":"Manoli","first_name":"G."},{"last_name":"Daly","first_name":"E.","full_name":"Daly, E."}],"citation":{"short":"V. Marchionni, S. Fatichi, N. Tapper, J.P. Walker, G. Manoli, E. Daly, Landscape and Urban Planning 215 (2021).","ama":"Marchionni V, Fatichi S, Tapper N, Walker JP, Manoli G, Daly E. Assessing vegetation response to irrigation strategies and soil properties in an urban reserve in southeast Australia. <i>Landscape and Urban Planning</i>. 2021;215. doi:<a href=\"https://doi.org/10.1016/j.landurbplan.2021.104198\">10.1016/j.landurbplan.2021.104198</a>","ieee":"V. Marchionni, S. Fatichi, N. Tapper, J. P. Walker, G. Manoli, and E. Daly, “Assessing vegetation response to irrigation strategies and soil properties in an urban reserve in southeast Australia,” <i>Landscape and Urban Planning</i>, vol. 215. Elsevier, 2021.","ista":"Marchionni V, Fatichi S, Tapper N, Walker JP, Manoli G, Daly E. 2021. Assessing vegetation response to irrigation strategies and soil properties in an urban reserve in southeast Australia. Landscape and Urban Planning. 215, 104198.","chicago":"Marchionni, V., Simone Fatichi, N. Tapper, J.P. Walker, G. Manoli, and E. Daly. “Assessing Vegetation Response to Irrigation Strategies and Soil Properties in an Urban Reserve in Southeast Australia.” <i>Landscape and Urban Planning</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.landurbplan.2021.104198\">https://doi.org/10.1016/j.landurbplan.2021.104198</a>.","apa":"Marchionni, V., Fatichi, S., Tapper, N., Walker, J. P., Manoli, G., &#38; Daly, E. (2021). Assessing vegetation response to irrigation strategies and soil properties in an urban reserve in southeast Australia. <i>Landscape and Urban Planning</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.landurbplan.2021.104198\">https://doi.org/10.1016/j.landurbplan.2021.104198</a>","mla":"Marchionni, V., et al. “Assessing Vegetation Response to Irrigation Strategies and Soil Properties in an Urban Reserve in Southeast Australia.” <i>Landscape and Urban Planning</i>, vol. 215, 104198, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.landurbplan.2021.104198\">10.1016/j.landurbplan.2021.104198</a>."},"abstract":[{"text":"Increasing urban green spaces and canopy cover requires careful planning of irrigation strategies, especially in arid and semiarid areas. This study investigates how vegetation cover and irrigation affect the water balance and vegetation productivity of a small urban reserve in the Melbourne metropolitan area, Australia. Using a mechanistic ecohydrological model, a series of numerical experiments were carried out for the period 1999–2018, which included a prolonged drought. Results indicated that irrigation played an essential role in helping both trees and grass productivity by increasing soil moisture and vegetation water access during the drought. With 10% tree cover, grass benefitted more than trees by increasing irrigation, and trees coped well with drought even without additional water. However, trees strongly relied on irrigation to maintain productivity when tree cover increased, highlighting the need for a sustainable balance between increasing urban greening and water conservation. Differences in soil properties and rooting strategies were also found to strongly modify the need for irrigation and the competition for water. These results provide quantitative insights on how increasing tree cover and vegetation diversity may impact irrigation requirements, highlighting the key role of mechanistic numerical models to support urban planners in the evaluation and design of urban green spaces.","lang":"eng"}],"scopus_import":"1","doi":"10.1016/j.landurbplan.2021.104198","intvolume":"       215","publication_status":"published","type":"journal_article","publisher":"Elsevier","language":[{"iso":"eng"}],"volume":215,"quality_controlled":"1","year":"2021","month":"11","article_processing_charge":"No"}]