[{"oa":1,"publisher":"Lobachevsky State University of Nizhny Novgorod","publication":"Opera Medica et Physiologica","title":"Diffraction-unlimited optical imaging for synaptic physiology","date_created":"2021-03-07T23:01:25Z","main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-03T07:31:05Z","language":[{"iso":"eng"}],"quality_controlled":"1","alternative_title":["Molecular and cellular neuroscience"],"citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod, 2018. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. 2018;4(S1):11. doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11."},"status":"public","publication_status":"published","year":"2018","date_published":"2018-06-30T00:00:00Z","author":[{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"issue":"S1","intvolume":"         4","page":"11","department":[{"_id":"JoDa"}],"scopus_import":"1","article_processing_charge":"No","month":"06","type":"journal_article","oa_version":"Published Version","day":"30","doi":"10.20388/omp2018.00s1.001","publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"volume":4,"_id":"9229","article_type":"letter_note"},{"article_processing_charge":"No","scopus_import":"1","ddc":["580"],"department":[{"_id":"DaZi"}],"page":"E4720-E4729","oa_version":"Published Version","type":"journal_article","month":"05","_id":"9471","volume":115,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"doi":"10.1073/pnas.1713333115","day":"15","article_type":"original","publisher":"National Academy of Sciences","oa":1,"abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}],"file":[{"creator":"asandaue","file_name":"2018_PNAS_Frost.pdf","file_size":3045260,"relation":"main_file","content_type":"application/pdf","checksum":"810260dc0e3cc3033e15c19ad0dc123e","date_updated":"2021-06-07T06:16:38Z","access_level":"open_access","date_created":"2021-06-07T06:16:38Z","success":1,"file_id":"9472"}],"pmid":1,"date_updated":"2021-12-14T07:53:40Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-06-07T06:11:28Z","title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","keyword":["Multidisciplinary"],"publication":"Proceedings of the National Academy of Sciences","related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"year":"2018","date_published":"2018-05-15T00:00:00Z","status":"public","extern":"1","publication_status":"published","citation":{"ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>."},"file_date_updated":"2021-06-07T06:16:38Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["29712855"]},"intvolume":"       115","issue":"20","author":[{"first_name":"Jennifer M.","full_name":"Frost, Jennifer M.","last_name":"Frost"},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"last_name":"Park","full_name":"Park, Guen Tae","first_name":"Guen Tae"},{"first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung","last_name":"Hsieh"},{"first_name":"Miyuki","full_name":"Nakamura, Miyuki","last_name":"Nakamura"},{"last_name":"Lin","full_name":"Lin, Samuel J. H.","first_name":"Samuel J. H."},{"first_name":"Hyunjin","full_name":"Yoo, Hyunjin","last_name":"Yoo"},{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"first_name":"Yoko","full_name":"Ikeda, Yoko","last_name":"Ikeda"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"last_name":"Choi","first_name":"Yeonhee","full_name":"Choi, Yeonhee"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."}],"has_accepted_license":"1"},{"doi":"10.1103/PhysRevMaterials.2.035602","day":"29","volume":2,"_id":"95","publist_id":"7959","article_number":"035602","month":"03","type":"journal_article","oa_version":"Preprint","external_id":{"arxiv":["1801.09278"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Lee, Victor, et al. “Collisional Charging of Individual Submillimeter Particles: Using Ultrasonic Levitation to Initiate and Track Charge Transfer.” <i>Physical Review Materials</i>, vol. 2, no. 3, 035602, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.2.035602\">10.1103/PhysRevMaterials.2.035602</a>.","ista":"Lee V, James N, Waitukaitis SR, Jaeger H. 2018. Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. Physical Review Materials. 2(3), 035602.","apa":"Lee, V., James, N., Waitukaitis, S. R., &#38; Jaeger, H. (2018). Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.2.035602\">https://doi.org/10.1103/PhysRevMaterials.2.035602</a>","ama":"Lee V, James N, Waitukaitis SR, Jaeger H. Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer. <i>Physical Review Materials</i>. 2018;2(3). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.2.035602\">10.1103/PhysRevMaterials.2.035602</a>","ieee":"V. Lee, N. James, S. R. Waitukaitis, and H. Jaeger, “Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer,” <i>Physical Review Materials</i>, vol. 2, no. 3. American Physical Society, 2018.","chicago":"Lee, Victor, Nicole James, Scott R Waitukaitis, and Heinrich Jaeger. “Collisional Charging of Individual Submillimeter Particles: Using Ultrasonic Levitation to Initiate and Track Charge Transfer.” <i>Physical Review Materials</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevMaterials.2.035602\">https://doi.org/10.1103/PhysRevMaterials.2.035602</a>.","short":"V. Lee, N. James, S.R. Waitukaitis, H. Jaeger, Physical Review Materials 2 (2018)."},"extern":"1","publication_status":"published","status":"public","date_published":"2018-03-29T00:00:00Z","year":"2018","author":[{"first_name":"Victor","full_name":"Lee, Victor","last_name":"Lee"},{"last_name":"James","first_name":"Nicole","full_name":"James, Nicole"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"},{"last_name":"Jaeger","full_name":"Jaeger, Heinrich","first_name":"Heinrich"}],"issue":"3","intvolume":"         2","abstract":[{"text":"Electrostatic charging of insulating fine particles can be responsible for numerous phenomena ranging from lightning in volcanic plumes to dust explosions. However, even basic aspects of how fine particles become charged are still unclear. Studying particle charging is challenging because it usually involves the complexities associated with many-particle collisions. To address these issues, we introduce a method based on acoustic levitation, which makes it possible to initiate sequences of repeated collisions of a single submillimeter particle with a flat plate, and to precisely measure the particle charge in situ after each collision. We show that collisional charge transfer between insulators is dependent on the hydrophobicity of the contacting surfaces. We use glass, which we modify by attaching nonpolar molecules to the particle, the plate, or both. We find that hydrophilic surfaces develop significant positive charges after contacting hydrophobic surfaces. Moreover, we demonstrate that charging between a hydrophilic and a hydrophobic surface is suppressed in an acidic environment and enhanced in a basic one. Application of an electric field during each collision is found to modify the charge transfer, again depending on surface hydrophobicity. We discuss these results within the context of contact charging due to ion transfer, and we show that they lend strong support to OH− ions as the charge carriers.","lang":"eng"}],"oa":1,"publisher":"American Physical Society","publication":"Physical Review Materials","title":"Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer","date_created":"2018-12-11T11:44:36Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:22:09Z","main_file_link":[{"url":"https://arxiv.org/abs/1801.09278","open_access":"1"}]},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["1708.07746"]},"quality_controlled":"1","citation":{"ista":"Ferber A, Kwan MA, Sudakov B. 2018. Counting Hamilton cycles in sparse random directed graphs. Random Structures and Algorithms. 53(4), 592–603.","ieee":"A. Ferber, M. A. Kwan, and B. Sudakov, “Counting Hamilton cycles in sparse random directed graphs,” <i>Random Structures and Algorithms</i>, vol. 53, no. 4. Wiley, pp. 592–603, 2018.","apa":"Ferber, A., Kwan, M. A., &#38; Sudakov, B. (2018). Counting Hamilton cycles in sparse random directed graphs. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.20815\">https://doi.org/10.1002/rsa.20815</a>","ama":"Ferber A, Kwan MA, Sudakov B. Counting Hamilton cycles in sparse random directed graphs. <i>Random Structures and Algorithms</i>. 2018;53(4):592-603. doi:<a href=\"https://doi.org/10.1002/rsa.20815\">10.1002/rsa.20815</a>","mla":"Ferber, Asaf, et al. “Counting Hamilton Cycles in Sparse Random Directed Graphs.” <i>Random Structures and Algorithms</i>, vol. 53, no. 4, Wiley, 2018, pp. 592–603, doi:<a href=\"https://doi.org/10.1002/rsa.20815\">10.1002/rsa.20815</a>.","short":"A. Ferber, M.A. Kwan, B. Sudakov, Random Structures and Algorithms 53 (2018) 592–603.","chicago":"Ferber, Asaf, Matthew Alan Kwan, and Benny Sudakov. “Counting Hamilton Cycles in Sparse Random Directed Graphs.” <i>Random Structures and Algorithms</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/rsa.20815\">https://doi.org/10.1002/rsa.20815</a>."},"extern":"1","status":"public","publication_status":"published","date_published":"2018-12-01T00:00:00Z","year":"2018","author":[{"full_name":"Ferber, Asaf","first_name":"Asaf","last_name":"Ferber"},{"last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"issue":"4","intvolume":"        53","abstract":[{"text":"Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n directed Hamilton cycles.","lang":"eng"}],"oa":1,"publisher":"Wiley","publication":"Random Structures and Algorithms","title":"Counting Hamilton cycles in sparse random directed graphs","date_created":"2021-06-18T12:06:28Z","arxiv":1,"date_updated":"2023-02-23T14:01:03Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.07746"}],"doi":"10.1002/rsa.20815","day":"01","publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"volume":53,"_id":"9565","article_type":"original","page":"592-603","scopus_import":"1","article_processing_charge":"No","month":"12","type":"journal_article","oa_version":"Preprint"},{"quality_controlled":"1","external_id":{"arxiv":["1708.01054"]},"language":[{"iso":"eng"}],"extern":"1","publication_status":"published","status":"public","year":"2018","date_published":"2018-12-01T00:00:00Z","citation":{"short":"M. Krivelevich, M.A. Kwan, P. Loh, B. Sudakov, Random Structures and Algorithms 53 (2018) 692–716.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, Po‐Shen Loh, and Benny Sudakov. “The Random K‐matching‐free Process.” <i>Random Structures and Algorithms</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/rsa.20814\">https://doi.org/10.1002/rsa.20814</a>.","ista":"Krivelevich M, Kwan MA, Loh P, Sudakov B. 2018. The random k‐matching‐free process. Random Structures and Algorithms. 53(4), 692–716.","apa":"Krivelevich, M., Kwan, M. A., Loh, P., &#38; Sudakov, B. (2018). The random k‐matching‐free process. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.20814\">https://doi.org/10.1002/rsa.20814</a>","ieee":"M. Krivelevich, M. A. Kwan, P. Loh, and B. Sudakov, “The random k‐matching‐free process,” <i>Random Structures and Algorithms</i>, vol. 53, no. 4. Wiley, pp. 692–716, 2018.","ama":"Krivelevich M, Kwan MA, Loh P, Sudakov B. The random k‐matching‐free process. <i>Random Structures and Algorithms</i>. 2018;53(4):692-716. doi:<a href=\"https://doi.org/10.1002/rsa.20814\">10.1002/rsa.20814</a>","mla":"Krivelevich, Michael, et al. “The Random K‐matching‐free Process.” <i>Random Structures and Algorithms</i>, vol. 53, no. 4, Wiley, 2018, pp. 692–716, doi:<a href=\"https://doi.org/10.1002/rsa.20814\">10.1002/rsa.20814</a>."},"issue":"4","intvolume":"        53","author":[{"last_name":"Krivelevich","full_name":"Krivelevich, Michael","first_name":"Michael"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Loh, Po‐Shen","first_name":"Po‐Shen","last_name":"Loh"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"oa":1,"abstract":[{"lang":"eng","text":"Let P be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty n-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the constraint that P is not violated. These types of random processes have been the subject of extensive research over the last 20 years, having striking applications in extremal combinatorics, and leading to the discovery of important probabilistic tools. In this paper we consider the k-matching-free process, where P is the property of not containing a matching of size k. We are able to analyse the behaviour of this process for a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn) then this process is likely to terminate in a k-matching-free graph with the maximum possible number of edges, as characterised by Erdős and Gallai. We also show that these bounds on k are essentially best possible, and we make a first step towards understanding the behaviour of the process in the intermediate regime."}],"publisher":"Wiley","date_created":"2021-06-18T12:37:40Z","publication":"Random Structures and Algorithms","title":"The random k‐matching‐free process","arxiv":1,"date_updated":"2023-02-23T14:01:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01054"}],"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"day":"01","doi":"10.1002/rsa.20814","volume":53,"_id":"9567","article_type":"original","scopus_import":"1","page":"692-716","article_processing_charge":"No","oa_version":"Preprint","month":"12","type":"journal_article"},{"publisher":"Wiley","oa":1,"abstract":[{"lang":"eng","text":"An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number of intercalates in a uniformly random n×n Latin square. We prove that asymptotically almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically almost surely N≤fn2 for any f→∞). This significantly improves the previous best lower and upper bounds. We also give an upper tail bound for the number of intercalates in two fixed rows of a random Latin square. In addition, we discuss a problem of Linial and Luria on low-discrepancy Latin squares."}],"date_updated":"2023-02-23T14:01:09Z","main_file_link":[{"url":"https://arxiv.org/abs/1607.04981","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","arxiv":1,"date_created":"2021-06-18T12:47:25Z","publication":"Random Structures and Algorithms","title":"Intercalates and discrepancy in random Latin squares","publication_status":"published","status":"public","extern":"1","year":"2018","date_published":"2018-03-01T00:00:00Z","citation":{"chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in Random Latin Squares.” <i>Random Structures and Algorithms</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/rsa.20742\">https://doi.org/10.1002/rsa.20742</a>.","short":"M.A. Kwan, B. Sudakov, Random Structures and Algorithms 52 (2018) 181–196.","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in Random Latin Squares.” <i>Random Structures and Algorithms</i>, vol. 52, no. 2, Wiley, 2018, pp. 181–96, doi:<a href=\"https://doi.org/10.1002/rsa.20742\">10.1002/rsa.20742</a>.","ama":"Kwan MA, Sudakov B. Intercalates and discrepancy in random Latin squares. <i>Random Structures and Algorithms</i>. 2018;52(2):181-196. doi:<a href=\"https://doi.org/10.1002/rsa.20742\">10.1002/rsa.20742</a>","ieee":"M. A. Kwan and B. Sudakov, “Intercalates and discrepancy in random Latin squares,” <i>Random Structures and Algorithms</i>, vol. 52, no. 2. Wiley, pp. 181–196, 2018.","apa":"Kwan, M. A., &#38; Sudakov, B. (2018). Intercalates and discrepancy in random Latin squares. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.20742\">https://doi.org/10.1002/rsa.20742</a>","ista":"Kwan MA, Sudakov B. 2018. Intercalates and discrepancy in random Latin squares. Random Structures and Algorithms. 52(2), 181–196."},"quality_controlled":"1","external_id":{"arxiv":["1607.04981"]},"language":[{"iso":"eng"}],"issue":"2","intvolume":"        52","author":[{"last_name":"Kwan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"}],"article_processing_charge":"No","scopus_import":"1","page":"181-196","oa_version":"Preprint","month":"03","type":"journal_article","volume":52,"_id":"9568","publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"day":"01","doi":"10.1002/rsa.20742","article_type":"original"},{"publication_identifier":{"issn":["0097-3165"]},"day":"01","doi":"10.1016/j.jcta.2017.12.001","_id":"9587","volume":156,"article_type":"original","scopus_import":"1","page":"44-60","article_processing_charge":"No","oa_version":"Preprint","type":"journal_article","month":"05","quality_controlled":"1","external_id":{"arxiv":["1703.09946"]},"language":[{"iso":"eng"}],"year":"2018","date_published":"2018-05-01T00:00:00Z","publication_status":"published","status":"public","extern":"1","citation":{"chicago":"Kwan, Matthew Alan, Benny Sudakov, and Pedro Vieira. “Non-Trivially Intersecting Multi-Part Families.” <i>Journal of Combinatorial Theory Series A</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jcta.2017.12.001\">https://doi.org/10.1016/j.jcta.2017.12.001</a>.","short":"M.A. Kwan, B. Sudakov, P. Vieira, Journal of Combinatorial Theory Series A 156 (2018) 44–60.","mla":"Kwan, Matthew Alan, et al. “Non-Trivially Intersecting Multi-Part Families.” <i>Journal of Combinatorial Theory Series A</i>, vol. 156, Elsevier, 2018, pp. 44–60, doi:<a href=\"https://doi.org/10.1016/j.jcta.2017.12.001\">10.1016/j.jcta.2017.12.001</a>.","ieee":"M. A. Kwan, B. Sudakov, and P. Vieira, “Non-trivially intersecting multi-part families,” <i>Journal of Combinatorial Theory Series A</i>, vol. 156. Elsevier, pp. 44–60, 2018.","apa":"Kwan, M. A., Sudakov, B., &#38; Vieira, P. (2018). Non-trivially intersecting multi-part families. <i>Journal of Combinatorial Theory Series A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcta.2017.12.001\">https://doi.org/10.1016/j.jcta.2017.12.001</a>","ama":"Kwan MA, Sudakov B, Vieira P. Non-trivially intersecting multi-part families. <i>Journal of Combinatorial Theory Series A</i>. 2018;156:44-60. doi:<a href=\"https://doi.org/10.1016/j.jcta.2017.12.001\">10.1016/j.jcta.2017.12.001</a>","ista":"Kwan MA, Sudakov B, Vieira P. 2018. Non-trivially intersecting multi-part families. Journal of Combinatorial Theory Series A. 156, 44–60."},"intvolume":"       156","author":[{"full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","last_name":"Kwan"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"last_name":"Vieira","first_name":"Pedro","full_name":"Vieira, Pedro"}],"oa":1,"abstract":[{"text":"We say a family of sets is intersecting if any two of its sets intersect, and we say it is trivially intersecting if there is an element which appears in every set of the family. In this paper we study the maximum size of a non-trivially intersecting family in a natural “multi-part” setting. Here the ground set is divided into parts, and one considers families of sets whose intersection with each part is of a prescribed size. Our work is motivated by classical results in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and by a theorem of Frankl concerning intersecting families in this multi-part setting. In the case where the part sizes are sufficiently large we determine the maximum size of a non-trivially intersecting multi-part family, disproving a conjecture of Alon and Katona.","lang":"eng"}],"publisher":"Elsevier","date_created":"2021-06-22T11:42:48Z","title":"Non-trivially intersecting multi-part families","publication":"Journal of Combinatorial Theory Series A","main_file_link":[{"url":"https://arxiv.org/abs/1703.09946","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T14:01:55Z","arxiv":1},{"oa_version":"Submitted Version","type":"journal_article","month":"06","article_processing_charge":"No","scopus_import":"1","article_number":"231102","article_type":"original","_id":"9659","volume":148,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"day":"21","doi":"10.1063/1.5038396","pmid":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T14:03:57Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5038396"}],"date_created":"2021-07-15T07:51:42Z","title":"Communication: Computing the Tolman length for solid-liquid interfaces","publication":"The Journal of Chemical Physics","publisher":"AIP Publishing","oa":1,"abstract":[{"lang":"eng","text":"The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account."}],"intvolume":"       148","issue":"23","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"year":"2018","date_published":"2018-06-21T00:00:00Z","status":"public","extern":"1","publication_status":"published","citation":{"ieee":"B. Cheng and M. Ceriotti, “Communication: Computing the Tolman length for solid-liquid interfaces,” <i>The Journal of Chemical Physics</i>, vol. 148, no. 23. AIP Publishing, 2018.","ama":"Cheng B, Ceriotti M. Communication: Computing the Tolman length for solid-liquid interfaces. <i>The Journal of Chemical Physics</i>. 2018;148(23). doi:<a href=\"https://doi.org/10.1063/1.5038396\">10.1063/1.5038396</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2018). Communication: Computing the Tolman length for solid-liquid interfaces. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5038396\">https://doi.org/10.1063/1.5038396</a>","ista":"Cheng B, Ceriotti M. 2018. Communication: Computing the Tolman length for solid-liquid interfaces. The Journal of Chemical Physics. 148(23), 231102.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>, vol. 148, no. 23, 231102, AIP Publishing, 2018, doi:<a href=\"https://doi.org/10.1063/1.5038396\">10.1063/1.5038396</a>.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2018. <a href=\"https://doi.org/10.1063/1.5038396\">https://doi.org/10.1063/1.5038396</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.09140"],"pmid":["29935495"]}},{"type":"journal_article","month":"06","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","article_type":"review","article_number":"225901","doi":"10.1103/physrevlett.120.225901","day":"01","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"_id":"9665","volume":120,"title":"Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations","publication":"Physical Review Letters","date_created":"2021-07-15T12:22:41Z","pmid":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2021-08-09T12:36:22Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.00600"}],"arxiv":1,"abstract":[{"lang":"eng","text":"We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments."}],"oa":1,"publisher":"American Physical Society","author":[{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"Paxton, Anthony T.","first_name":"Anthony T.","last_name":"Paxton"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"intvolume":"       120","issue":"22","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.00600"],"pmid":["29906144"]},"quality_controlled":"1","citation":{"chicago":"Cheng, Bingqing, Anthony T. Paxton, and Michele Ceriotti. “Hydrogen Diffusion and Trapping in α-Iron: The Role of Quantum and Anharmonic Fluctuations.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevlett.120.225901\">https://doi.org/10.1103/physrevlett.120.225901</a>.","short":"B. Cheng, A.T. Paxton, M. Ceriotti, Physical Review Letters 120 (2018).","mla":"Cheng, Bingqing, et al. “Hydrogen Diffusion and Trapping in α-Iron: The Role of Quantum and Anharmonic Fluctuations.” <i>Physical Review Letters</i>, vol. 120, no. 22, 225901, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevlett.120.225901\">10.1103/physrevlett.120.225901</a>.","ista":"Cheng B, Paxton AT, Ceriotti M. 2018. Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. Physical Review Letters. 120(22), 225901.","ama":"Cheng B, Paxton AT, Ceriotti M. Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. <i>Physical Review Letters</i>. 2018;120(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.120.225901\">10.1103/physrevlett.120.225901</a>","ieee":"B. Cheng, A. T. Paxton, and M. Ceriotti, “Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations,” <i>Physical Review Letters</i>, vol. 120, no. 22. American Physical Society, 2018.","apa":"Cheng, B., Paxton, A. T., &#38; Ceriotti, M. (2018). Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.120.225901\">https://doi.org/10.1103/physrevlett.120.225901</a>"},"year":"2018","date_published":"2018-06-01T00:00:00Z","extern":"1","publication_status":"published","status":"public"},{"arxiv":1,"date_updated":"2021-08-09T12:36:47Z","main_file_link":[{"url":"https://arxiv.org/abs/1807.05551","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","publication":"Physical Chemistry Chemical Physics","date_created":"2021-07-15T12:51:44Z","publisher":"Royal Society of Chemistry","abstract":[{"lang":"eng","text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods."}],"oa":1,"author":[{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng"},{"first_name":"Christoph","full_name":"Dellago, Christoph","last_name":"Dellago"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"intvolume":"        20","issue":"45","citation":{"short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740.","chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry, 2018. <a href=\"https://doi.org/10.1039/c8cp04561e\">https://doi.org/10.1039/c8cp04561e</a>.","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. <i>Physical Chemistry Chemical Physics</i>. 2018;20(45):28732-28740. doi:<a href=\"https://doi.org/10.1039/c8cp04561e\">10.1039/c8cp04561e</a>","ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” <i>Physical Chemistry Chemical Physics</i>, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018.","apa":"Cheng, B., Dellago, C., &#38; Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8cp04561e\">https://doi.org/10.1039/c8cp04561e</a>","ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.","mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” <i>Physical Chemistry Chemical Physics</i>, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:<a href=\"https://doi.org/10.1039/c8cp04561e\">10.1039/c8cp04561e</a>."},"date_published":"2018-12-07T00:00:00Z","year":"2018","publication_status":"published","extern":"1","status":"public","external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","month":"12","oa_version":"Preprint","article_processing_charge":"No","page":"28732-28740","scopus_import":"1","article_type":"original","_id":"9668","volume":20,"day":"07","doi":"10.1039/c8cp04561e","publication_identifier":{"issn":["1463-9076"],"eissn":["1463-9084"]}},{"publisher":"American Physical Society","abstract":[{"lang":"eng","text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures."}],"oa":1,"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02815"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2021-08-09T12:38:26Z","publication":"Physical Review B","title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","date_created":"2021-07-19T09:39:48Z","citation":{"ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” <i>Physical Review B</i>, vol. 97, no. 5. American Physical Society, 2018.","ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. <i>Physical Review B</i>. 2018;97(5). doi:<a href=\"https://doi.org/10.1103/physrevb.97.054102\">10.1103/physrevb.97.054102</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.97.054102\">https://doi.org/10.1103/physrevb.97.054102</a>","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical Review B</i>, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.054102\">10.1103/physrevb.97.054102</a>.","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevb.97.054102\">https://doi.org/10.1103/physrevb.97.054102</a>."},"extern":"1","status":"public","publication_status":"published","year":"2018","date_published":"2018-02-01T00:00:00Z","external_id":{"arxiv":["1710.02815"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"issue":"5","intvolume":"        97","article_processing_charge":"No","scopus_import":"1","month":"02","type":"journal_article","oa_version":"Preprint","volume":97,"_id":"9687","doi":"10.1103/physrevb.97.054102","day":"01","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_number":"054102","article_type":"original"},{"related_material":{"record":[{"relation":"used_in_publication","id":"20","status":"public"}]},"month":"11","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-06T12:26:53Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:10:47Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"department":[{"_id":"SiHi"}],"oa":1,"publisher":"Springer Nature","article_processing_charge":"No","author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"first_name":"Michael","full_name":"Karbiener, Michael","last_name":"Karbiener"},{"last_name":"Giroud","full_name":"Giroud, Maude","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"first_name":"Marcel","full_name":"Scheideler, Marcel","last_name":"Scheideler"}],"doi":"10.6084/m9.figshare.7295339.v1","day":"03","citation":{"short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>."},"status":"public","date_published":"2018-11-03T00:00:00Z","_id":"9807","year":"2018"},{"date_created":"2021-08-06T12:31:57Z","oa_version":"Published Version","type":"research_data_reference","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","month":"11","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-09-13T09:10:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"oa":1,"department":[{"_id":"SiHi"}],"abstract":[{"lang":"eng","text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb)."}],"article_processing_charge":"No","publisher":"Springer Nature","author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"last_name":"Giroud","full_name":"Giroud, Maude","first_name":"Maude"},{"last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"day":"03","doi":"10.6084/m9.figshare.7295369.v1","date_published":"2018-11-03T00:00:00Z","_id":"9808","year":"2018","status":"public","citation":{"short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. 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Pickup, (2018).","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. 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N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","date_created":"2018-12-11T11:44:20Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.08316"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T12:55:03Z","abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"oa":1,"publisher":"American Physical Society","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"first_name":"Norman","full_name":"Yao, Norman","last_name":"Yao"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym"},{"last_name":"Pollmann","full_name":"Pollmann, Frank","first_name":"Frank"},{"first_name":"Björn","full_name":"Trauzettel, Björn","last_name":"Trauzettel"}],"issue":"16","intvolume":"        98","external_id":{"isi":["000448596500002"],"arxiv":["1806.08316"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>.","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., &#38; Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” <i>Physical Review B</i>, vol. 98, no. 16. American Physical Society, 2018.","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. 2018;98(16). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>","ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018)."},"status":"public","publication_status":"published","date_published":"2018-10-15T00:00:00Z","year":"2018"},{"volume":41,"_id":"462","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.1111/pce.13153","day":"01","publist_id":"7359","article_type":"original","article_processing_charge":"No","page":"850 - 864","department":[{"_id":"JiFr"}],"isi":1,"ddc":["580"],"scopus_import":"1","month":"05","type":"journal_article","oa_version":"Submitted Version","citation":{"chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” <i>Plant, Cell and Environment</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” <i>Plant, Cell and Environment</i>, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>.","ieee":"L. Fan <i>et al.</i>, “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” <i>Plant, Cell and Environment</i>, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. <i>Plant, Cell and Environment</i>. 2018;41:850-864. doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. <i>Plant, Cell and Environment</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864."},"file_date_updated":"2020-07-14T12:46:32Z","status":"public","publication_status":"published","year":"2018","date_published":"2018-05-01T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000426870500012"],"pmid":["29360148"]},"quality_controlled":"1","author":[{"last_name":"Fan","first_name":"Ligang","full_name":"Fan, Ligang"},{"last_name":"Zhao","full_name":"Zhao, Lei","first_name":"Lei"},{"last_name":"Hu","full_name":"Hu, Wei","first_name":"Wei"},{"first_name":"Weina","full_name":"Li, Weina","last_name":"Li"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml"},{"full_name":"Shen, Jinbo","first_name":"Jinbo","last_name":"Shen"},{"last_name":"Jiang","first_name":"Liwen","full_name":"Jiang, Liwen"},{"last_name":"Qiu","full_name":"Qiu, Quan","first_name":"Quan"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"        41","has_accepted_license":"1","publisher":"Wiley-Blackwell","file":[{"date_created":"2019-11-18T16:22:22Z","file_id":"7042","date_updated":"2020-07-14T12:46:32Z","access_level":"open_access","checksum":"6a20f843565f962cb20281cdf5e40914","content_type":"application/pdf","relation":"main_file","file_size":1937976,"file_name":"2018_PlantCellEnv_Fan.pdf","creator":"dernst"}],"abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"oa":1,"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T09:03:18Z","publication":"Plant, Cell and Environment","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","date_created":"2018-12-11T11:46:36Z"},{"doi":"10.1016/j.jbiotec.2018.01.008","day":"20","volume":268,"_id":"503","publist_id":"7317","isi":1,"scopus_import":"1","page":"40 - 52","department":[{"_id":"CaGu"}],"article_processing_charge":"No","oa_version":"None","month":"02","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000425715100006"]},"acknowledged_ssus":[{"_id":"Bio"}],"publication_status":"published","status":"public","year":"2018","date_published":"2018-02-20T00:00:00Z","corr_author":"1","citation":{"ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>."},"intvolume":"       268","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"publisher":"Elsevier","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","date_created":"2018-12-11T11:46:50Z","publication":"Journal of Biotechnology","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","date_updated":"2024-10-09T20:58:29Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]