--- _id: '10926' abstract: - lang: eng text: Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity. article_number: eyab049 article_processing_charge: No article_type: original author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Rogerk full_name: Butlin, Rogerk last_name: Butlin - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson citation: ama: Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 2022;88(1). doi:10.1093/mollus/eyab049 apa: Perini, S., Butlin, R., Westram, A. M., & Johannesson, K. (2022). Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. Oxford Academic. https://doi.org/10.1093/mollus/eyab049 chicago: Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” Journal of Molluscan Studies. Oxford Academic, 2022. https://doi.org/10.1093/mollus/eyab049. ieee: S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings are enough for sperm transfer in Littorina saxatilis,” Journal of Molluscan Studies, vol. 88, no. 1. Oxford Academic, 2022. ista: Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 88(1), eyab049. mla: Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” Journal of Molluscan Studies, vol. 88, no. 1, eyab049, Oxford Academic, 2022, doi:10.1093/mollus/eyab049. short: S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022). date_created: 2022-03-27T22:01:46Z date_published: 2022-03-01T00:00:00Z date_updated: 2023-08-03T06:23:13Z day: '01' department: - _id: BeVi doi: 10.1093/mollus/eyab049 external_id: isi: - '000759081600002' intvolume: ' 88' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprints.whiterose.ac.uk/187332/ month: '03' oa: 1 oa_version: Submitted Version publication: Journal of Molluscan Studies publication_identifier: eissn: - 1464-3766 issn: - 0260-1230 publication_status: published publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: Very short mountings are enough for sperm transfer in Littorina saxatilis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 88 year: '2022' ... --- _id: '10927' abstract: - lang: eng text: "Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes." acknowledgement: "The authors thank the 2020 student class of the Bioinformatics Institute, who\r\nused the first versions of the tool and provided many valuable suggestions to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript proofreading\r\nThis work was supported by the National Center for Cognitive Research of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements." article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Zabelkin, Alexey last_name: Zabelkin - first_name: Yulia full_name: Yakovleva, Yulia last_name: Yakovleva - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Nikita full_name: Alexeev, Nikita last_name: Alexeev citation: ama: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 2022;38(2):357-363. doi:10.1093/bioinformatics/btab691' apa: 'Zabelkin, A., Yakovleva, Y., Bochkareva, O., & Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btab691' chicago: 'Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics. Oxford Academic, 2022. https://doi.org/10.1093/bioinformatics/btab691.' ieee: 'A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” Bioinformatics, vol. 38, no. 2. Oxford Academic, pp. 357–363, 2022.' ista: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.' mla: 'Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics, vol. 38, no. 2, Oxford Academic, 2022, pp. 357–63, doi:10.1093/bioinformatics/btab691.' short: A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363. date_created: 2022-03-27T22:01:46Z date_published: 2022-01-15T00:00:00Z date_updated: 2023-08-03T06:21:46Z day: '15' ddc: - '000' department: - _id: FyKo doi: 10.1093/bioinformatics/btab691 ec_funded: 1 external_id: isi: - '000743380100008' file: - access_level: open_access checksum: 4b5688ff9ac86180ccdf7f82fa33d926 content_type: application/pdf creator: dernst date_created: 2022-03-28T08:07:46Z date_updated: 2022-03-28T08:07:46Z file_id: '10930' file_name: 2022_Bioinformatics_Zabelkin.pdf file_size: 3425744 relation: main_file success: 1 file_date_updated: 2022-03-28T08:07:46Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 357-363 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Bioinformatics publication_identifier: eissn: - 1460-2059 issn: - 1367-4803 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ctlab/parallel-rearrangements scopus_import: '1' status: public title: 'PaReBrick: PArallel REarrangements and BReaks identification toolkit' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2022' ... --- _id: '10934' abstract: - lang: eng text: 'FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. ' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_processing_charge: No author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: ' 0000-0001-9198-2182 ' citation: ama: Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:10.15479/AT:ISTA:10934 apa: Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934 chicago: Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934. ieee: P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022. ista: Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934. mla: Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934. short: P. Radler, (2022). contributor: - contributor_type: supervisor first_name: Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - contributor_type: researcher first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer - contributor_type: researcher first_name: Paulo last_name: Caldas - contributor_type: researcher first_name: David id: B9577E20-AA38-11E9-AC9A-0930E6697425 last_name: Michalik - contributor_type: researcher first_name: Natalia last_name: Baranova date_created: 2022-03-31T11:32:32Z date_published: 2022-04-05T00:00:00Z date_updated: 2024-02-21T12:35:18Z day: '05' ddc: - '572' department: - _id: GradSch - _id: MaLo doi: 10.15479/AT:ISTA:10934 ec_funded: 1 file: - access_level: open_access checksum: 52d50202e04e9daa618a58e686d8ab58 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pradler date_created: 2022-04-22T10:15:19Z date_updated: 2022-04-22T10:15:19Z file_id: '11328' file_name: Inventory for Data repository.docx file_size: 13469 relation: main_file success: 1 - access_level: open_access checksum: 3e1518dd9fe9266b9bcc67695cb5015c content_type: application/x-zip-compressed creator: pradler date_created: 2022-03-31T12:57:36Z date_updated: 2022-03-31T12:57:36Z file_id: '10935' file_name: Raw Data Micrographs.zip file_size: 2406478929 relation: main_file success: 1 - access_level: open_access checksum: 78049c82785fcdded36327f3845cb05f content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-04T08:23:52Z date_updated: 2022-04-04T08:23:52Z file_id: '10941' file_name: Supplementary Movie S1-S5.zip file_size: 3790894919 relation: main_file success: 1 - access_level: open_access checksum: cc3aaa1495aedac66d0779f8fe89493e content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-04T08:25:41Z date_updated: 2022-04-04T08:25:41Z file_id: '10942' file_name: Supplementary Movie S6-S9.zip file_size: 3542799490 relation: main_file success: 1 - access_level: open_access checksum: 8341953226720c711712f9be6f8f77c6 content_type: application/x-zip-compressed creator: pradler date_created: 2022-03-31T19:20:03Z date_updated: 2022-03-31T19:20:03Z file_id: '10936' file_name: Supplementary Movie S10-S18.zip file_size: 4116732289 relation: main_file success: 1 - access_level: open_access checksum: 233015f762973a85802a6a28628a7616 content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-01T10:21:44Z date_updated: 2022-04-01T10:21:44Z file_id: '10937' file_name: FtsA Paper Plots.zip file_size: 917234506 relation: main_file success: 1 - access_level: open_access checksum: a922adee96726cd6a6770afaf12fc5f7 content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-04T08:50:36Z date_updated: 2022-04-04T08:50:36Z file_id: '10943' file_name: Analysis Part 1.zip file_size: 3586995691 relation: main_file success: 1 - access_level: open_access checksum: b231ea0569141979bd4dbbea463df516 content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-04T08:50:01Z date_updated: 2022-04-04T08:50:01Z file_id: '10944' file_name: Analysis Part 2.zip file_size: 3064310102 relation: main_file success: 1 - access_level: open_access checksum: 73b256fc0e7f30645c101d932bbc261f content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-05T08:35:27Z date_updated: 2022-04-05T08:35:27Z file_id: '10951' file_name: Raw Microscopy_FtsZ Autocorrelation.zip file_size: 1730933828 relation: main_file success: 1 - access_level: open_access checksum: 176958b80a4aa344c56a62ccfda56100 content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-05T08:37:02Z date_updated: 2022-04-05T08:37:02Z file_id: '10952' file_name: Raw Microscopy_FtsZ FRAP.zip file_size: 2000482316 relation: main_file success: 1 - access_level: open_access checksum: fe0872b72fd7d50d9c1ae955f1e4bafb content_type: application/x-zip-compressed creator: pradler date_created: 2022-04-05T15:06:08Z date_updated: 2022-04-05T15:06:08Z file_id: '10981' file_name: Single Molecule Measurements FtsZ CTP TAMRA.zip file_size: 1215169392 relation: main_file success: 1 - access_level: open_access checksum: e3cfe2e4d06f52391f8d48571d05f2fc content_type: application/zip creator: pradler date_created: 2022-04-15T09:32:32Z date_updated: 2022-04-15T09:32:32Z file_id: '11168' file_name: Single Molecule Measurements FtsN.zip file_size: 269524347 relation: main_file success: 1 - access_level: open_access checksum: 92724115b8f923cfcd7e908dd50f7416 content_type: application/octet-stream creator: pradler date_created: 2022-04-15T09:55:09Z date_updated: 2022-04-15T09:55:09Z file_id: '11171' file_name: Single Molecule Measurements FtsN.z01 file_size: '4294960000' relation: main_file success: 1 - access_level: open_access checksum: 52ffe8af0ce2eec4aebe1b0eea222b3c content_type: application/zip creator: pradler date_created: 2022-04-20T10:20:40Z date_updated: 2022-04-20T10:20:40Z file_id: '11200' file_name: Single Molecule Measurements FtsAs.zip file_size: 1371864760 relation: main_file success: 1 - access_level: open_access checksum: 61fdd102fd7b887bf1802c5ee63ff0c2 content_type: application/octet-stream creator: pradler date_created: 2022-04-20T14:07:38Z date_updated: 2022-04-20T14:07:38Z file_id: '11219' file_name: Single Molecule Measurements FtsAs.z01 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: e9e05ad8b134caefbd0ec3e4fc5f685a content_type: application/octet-stream creator: pradler date_created: 2022-04-21T12:21:00Z date_updated: 2022-04-21T12:21:00Z file_id: '11269' file_name: Single Molecule Measurements FtsAs.z02 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: 41378ea941cfbccb3b78534a7886fc8f content_type: application/zip creator: pradler date_created: 2022-04-20T14:12:13Z date_updated: 2022-04-20T14:12:13Z file_id: '11223' file_name: Single Molecule Measurements FtsZ_WT vs R286W.zip file_size: 3711833563 relation: main_file success: 1 - access_level: open_access checksum: 5b3932e5607c8e2044d4df5b3e81acc5 content_type: application/octet-stream creator: pradler date_created: 2022-04-21T12:11:12Z date_updated: 2022-04-21T12:11:12Z file_id: '11268' file_name: Single Molecule Measurements FtsZ_WT vs R286W.z01 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: 06d7d5b0598b3ecb44847531ce2db1f7 content_type: application/zip creator: pradler date_created: 2022-04-20T14:04:53Z date_updated: 2022-04-20T14:04:53Z file_id: '11218' file_name: FRET_His SUMO control.zip file_size: 1518826810 relation: main_file success: 1 - access_level: open_access checksum: d96213f721099c8ce629e5b5ab9d2e2d content_type: application/octet-stream creator: pradler date_created: 2022-04-21T12:49:52Z date_updated: 2022-04-21T12:49:52Z file_id: '11271' file_name: FRET_His SUMO control.z01 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: 50dcc9a8034765e7962bed82f7190dc0 content_type: application/octet-stream creator: pradler date_created: 2022-04-21T12:29:11Z date_updated: 2022-04-21T12:29:11Z file_id: '11270' file_name: FRET_His SUMO control.z02 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: b4fa965877982dacf97392c7dbf13acf content_type: application/zip creator: pradler date_created: 2022-04-21T13:00:13Z date_updated: 2022-04-21T13:00:13Z file_id: '11273' file_name: Dual Color FtsA & FtsN.zip file_size: 3406044099 relation: main_file success: 1 - access_level: open_access checksum: 9d24d9c120ac5b1784892bbe286de01a content_type: application/octet-stream creator: pradler date_created: 2022-04-21T13:24:37Z date_updated: 2022-04-21T13:24:37Z file_id: '11275' file_name: Dual Color FtsA & FtsN.z01 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: 7f02cefe490ab1defc518130beb251b0 content_type: application/octet-stream creator: pradler date_created: 2022-04-21T13:20:31Z date_updated: 2022-04-21T13:20:31Z file_id: '11274' file_name: Dual Color FtsA & FtsN.z02 file_size: 4294960000 relation: main_file success: 1 - access_level: open_access checksum: 0baccbc4760abd06b363c3520bdc6a0d content_type: application/octet-stream creator: pradler date_created: 2022-04-21T12:58:08Z date_updated: 2022-04-21T12:58:08Z file_id: '11272' file_name: Dual Color FtsA & FtsN.z03 file_size: 4294960000 relation: main_file success: 1 - 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Written by Christoph Sommer. relation: software url: https://doi.org/10.5281/zenodo.6400639 record: - id: '11373' relation: used_in_publication status: public - id: '14280' relation: used_in_publication status: public status: public title: In vitro reconstitution of Escherichia coli divisome activation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '10939' abstract: - lang: eng text: Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system. acknowledgement: We thank Virgile Andreani for useful discussions about the model and parameter inference. We thank Johan Paulsson and Jeffrey J Tabor for kind gifts of plasmids. R was supported by the ANR grant CyberCircuits (ANR-18-CE91-0002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_number: e1009950 article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Davidović, Anđela last_name: Davidović - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Gregory full_name: Batt, Gregory last_name: Batt - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: Davidović A, Chait RP, Batt G, Ruess J. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. 2022;18(3). doi:10.1371/journal.pcbi.1009950 apa: Davidović, A., Chait, R. P., Batt, G., & Ruess, J. (2022). Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009950 chicago: Davidović, Anđela, Remy P Chait, Gregory Batt, and Jakob Ruess. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” PLoS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1009950. ieee: A. Davidović, R. P. Chait, G. Batt, and J. Ruess, “Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level,” PLoS Computational Biology, vol. 18, no. 3. Public Library of Science, 2022. ista: Davidović A, Chait RP, Batt G, Ruess J. 2022. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. 18(3), e1009950. mla: Davidović, Anđela, et al. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” PLoS Computational Biology, vol. 18, no. 3, e1009950, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1009950. short: A. Davidović, R.P. Chait, G. Batt, J. Ruess, PLoS Computational Biology 18 (2022). date_created: 2022-04-03T22:01:42Z date_published: 2022-03-18T00:00:00Z date_updated: 2022-04-04T10:21:53Z day: '18' ddc: - '570' - '000' department: - _id: CaGu doi: 10.1371/journal.pcbi.1009950 file: - access_level: open_access checksum: 458ef542761fb714ced214f240daf6b2 content_type: application/pdf creator: dernst date_created: 2022-04-04T10:14:39Z date_updated: 2022-04-04T10:14:39Z file_id: '10947' file_name: 2022_PLoSCompBio_Davidovic.pdf file_size: 2958642 relation: main_file success: 1 file_date_updated: 2022-04-04T10:14:39Z has_accepted_license: '1' intvolume: ' 18' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://gitlab.pasteur.fr/adavidov/inferencelnakf scopus_import: '1' status: public title: Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2022' ... --- _id: '10940' abstract: - lang: eng text: 'Magnetic-field-resilient superconducting circuits enable sensing applications and hybrid quantum computing architectures involving spin or topological qubits and electromechanical elements, as well as studying flux noise and quasiparticle loss. We investigate the effect of in-plane magnetic fields up to 1 T on the spectrum and coherence times of thin-film three-dimensional aluminum transmons. Using a copper cavity, unaffected by strong magnetic fields, we can probe solely the effect of magnetic fields on the transmons. We present data on a single-junction and a superconducting-quantum-interference-device (SQUID) transmon that are cooled down in the same cavity. As expected, the transmon frequencies decrease with increasing field, due to suppression of the superconducting gap and a geometric Fraunhofer-like contribution. Nevertheless, the thin-film transmons show strong magnetic field resilience: both transmons display microsecond coherence up to at least 0.65 T, and T1 remains above 1μs over the entire measurable range. SQUID spectroscopy is feasible up to 1 T, the limit of our magnet. We conclude that thin-film aluminum Josephson junctions are suitable hardware for superconducting circuits in the high-magnetic-field regime.' acknowledgement: "We would like to thank Ida Milow for her internship in the laboratory and contributions to our code base. We thank T. Zent and L. Hamdan for technical assistance, and D. Fan for help with setting up the aluminum evaporator. We thank A. Salari, M. Rößler, S. Barzanjeh, M. Zemlicka, F. Hassani, and M. Peruzzo for contributions in the early stages of the experiments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 741121) and was also funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under CRC 1238 – 277146847 (Subproject B01), as well as under Germany’s Excellence Strategy – Cluster of Excellence Matter and Light for Quantum Computing (ML4Q), EXC 2004/1\r\n– 390534769." article_number: '034032' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: J. full_name: Krause, J. last_name: Krause - first_name: C. full_name: Dickel, C. last_name: Dickel - first_name: E. full_name: Vaal, E. last_name: Vaal - first_name: M. full_name: Vielmetter, M. last_name: Vielmetter - first_name: J. full_name: Feng, J. last_name: Feng - first_name: R. full_name: Bounds, R. last_name: Bounds - first_name: G. full_name: Catelani, G. last_name: Catelani - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Yoichi full_name: Ando, Yoichi last_name: Ando citation: ama: Krause J, Dickel C, Vaal E, et al. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied. 2022;17(3). doi:10.1103/PhysRevApplied.17.034032 apa: Krause, J., Dickel, C., Vaal, E., Vielmetter, M., Feng, J., Bounds, R., … Ando, Y. (2022). Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.17.034032 chicago: Krause, J., C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, Johannes M Fink, and Yoichi Ando. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” Physical Review Applied. American Physical Society, 2022. https://doi.org/10.1103/PhysRevApplied.17.034032. ieee: J. Krause et al., “Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T,” Physical Review Applied, vol. 17, no. 3. American Physical Society, 2022. ista: Krause J, Dickel C, Vaal E, Vielmetter M, Feng J, Bounds R, Catelani G, Fink JM, Ando Y. 2022. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied. 17(3), 034032. mla: Krause, J., et al. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” Physical Review Applied, vol. 17, no. 3, 034032, American Physical Society, 2022, doi:10.1103/PhysRevApplied.17.034032. short: J. Krause, C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, J.M. Fink, Y. Ando, Physical Review Applied 17 (2022). date_created: 2022-04-03T22:01:43Z date_published: 2022-03-11T00:00:00Z date_updated: 2023-08-03T06:23:58Z day: '11' department: - _id: JoFi doi: 10.1103/PhysRevApplied.17.034032 external_id: arxiv: - '2111.01115' isi: - '000770371400003' intvolume: ' 17' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2111.01115 month: '03' oa: 1 oa_version: Preprint publication: Physical Review Applied publication_identifier: eissn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2022' ... --- _id: '10945' abstract: - lang: eng text: Mica-titania pearlescent pigments (MTs) were previously coated with organic molecules to obtain combination pigments (CPs) for achieving certain improvements or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from natural resources and exhibit color changes via pH modifications of the enclosing medium. The purpose of the study was to produce a new series of CPs by depositing ACNs on MTs at different pH values, to observe the changes in color, and to associate these changes to thermogravimetrically determined deposition efficiencies in light of spectral differences. The extraction and deposition methods were based on aqueous chemistry and were straightforward. The ACN deposition generally increased with increasing pH and correlated with the consistency between the charges of the MT surfaces and the dominant ACN species at a specific pH value. The fluorescence of the CPs was inversely correlated with the deposition quantities invoking the possibility of a quenching effect. acknowledgement: "This research was partly funded by Hacettepe University (Bilimsel Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra and the decision of excitation wavelengths. The authors also acknowledge use of the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent University and mica donation from Sabuncular Mining Co." article_processing_charge: Yes article_type: original author: - first_name: Mehmet Orkun full_name: Çoruh, Mehmet Orkun id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef last_name: Çoruh orcid: 0000-0002-3219-2022 - first_name: Güngör full_name: Gündüz, Güngör last_name: Gündüz - first_name: Üner full_name: Çolak, Üner last_name: Çolak - first_name: Bora full_name: Maviş, Bora last_name: Maviş citation: ama: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 2022;1(2):149-164. doi:10.3390/colorants1020010 apa: Çoruh, M. O., Gündüz, G., Çolak, Ü., & Maviş, B. (2022). pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. MDPI. https://doi.org/10.3390/colorants1020010 chicago: Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants. MDPI, 2022. https://doi.org/10.3390/colorants1020010. ieee: M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra,” Colorants, vol. 1, no. 2. MDPI, pp. 149–164, 2022. ista: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 1(2), 149–164. mla: Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants, vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:10.3390/colorants1020010. short: M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164. date_created: 2022-04-04T09:03:54Z date_published: 2022-04-01T00:00:00Z date_updated: 2023-08-09T10:12:22Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.3390/colorants1020010 file: - access_level: open_access checksum: 2c15c8d3041ebc36bc64870247081758 content_type: application/pdf creator: dernst date_created: 2022-04-04T10:39:24Z date_updated: 2022-04-04T10:39:24Z file_id: '10949' file_name: 2022_Colorants_Coruh.pdf file_size: 2437988 relation: main_file success: 1 file_date_updated: 2022-04-04T10:39:24Z has_accepted_license: '1' intvolume: ' 1' issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 149-164 publication: Colorants publication_identifier: issn: - 2079-6447 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2022' ... --- _id: '11128' abstract: - lang: eng text: "Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline." acknowledged_ssus: - _id: ScienComp - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lenka full_name: Matejovicova, Lenka id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87 last_name: Matejovicova citation: ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128 apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128 chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128. ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022. ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128. short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022. date_created: 2022-04-07T08:19:54Z date_published: 2022-04-06T00:00:00Z date_updated: 2023-06-23T06:26:41Z day: '06' ddc: - '576' - '582' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11128 file: - access_level: open_access checksum: e9609bc4e8f8e20146fc1125fd4f1bf7 content_type: application/pdf creator: cchlebak date_created: 2022-04-07T08:11:34Z date_updated: 2022-04-07T08:11:34Z file_id: '11129' file_name: LenkaPhD_Official_PDFA.pdf file_size: 11906472 relation: main_file - access_level: closed checksum: 99d67040432fd07a225643a212ee8588 content_type: application/x-zip-compressed creator: cchlebak date_created: 2022-04-07T08:11:51Z date_updated: 2022-04-07T08:11:51Z file_id: '11130' file_name: LenkaPhD Official_source.zip file_size: 23036766 relation: source_file file_date_updated: 2022-04-07T08:11:51Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '112' publication_identifier: isbn: - 978-3-99078-016-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Genetic basis of flower colour as a model for adaptive evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11135' abstract: - lang: eng text: We consider a correlated NxN Hermitian random matrix with a polynomially decaying metric correlation structure. By calculating the trace of the moments of the matrix and using the summable decay of the cumulants, we show that its operator norm is stochastically dominated by one. article_number: '2250036' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker citation: ama: 'Reker J. On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. 2022;11(4). doi:10.1142/s2010326322500368' apa: 'Reker, J. (2022). On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. World Scientific. https://doi.org/10.1142/s2010326322500368' chicago: 'Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” Random Matrices: Theory and Applications. World Scientific, 2022. https://doi.org/10.1142/s2010326322500368.' ieee: 'J. Reker, “On the operator norm of a Hermitian random matrix with correlated entries,” Random Matrices: Theory and Applications, vol. 11, no. 4. World Scientific, 2022.' ista: 'Reker J. 2022. On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. 11(4), 2250036.' mla: 'Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” Random Matrices: Theory and Applications, vol. 11, no. 4, 2250036, World Scientific, 2022, doi:10.1142/s2010326322500368.' short: 'J. Reker, Random Matrices: Theory and Applications 11 (2022).' date_created: 2022-04-08T07:11:12Z date_published: 2022-10-01T00:00:00Z date_updated: 2023-08-03T06:32:22Z day: '01' department: - _id: GradSch - _id: LaEr doi: 10.1142/s2010326322500368 external_id: arxiv: - '2103.03906' isi: - '000848873800001' intvolume: ' 11' isi: 1 issue: '4' keyword: - Discrete Mathematics and Combinatorics - Statistics - Probability and Uncertainty - Statistics and Probability - Algebra and Number Theory language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2103.03906' month: '10' oa: 1 oa_version: Preprint publication: 'Random Matrices: Theory and Applications' publication_identifier: eissn: - 2010-3271 issn: - 2010-3263 publication_status: published publisher: World Scientific quality_controlled: '1' scopus_import: '1' status: public title: On the operator norm of a Hermitian random matrix with correlated entries type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2022' ... --- _id: '11142' abstract: - lang: eng text: SnTe is a promising Pb-free thermoelectric (TE) material with high electrical conductivity. We discovered the synergistic effect of Bi2O3 on enhancing the average power factor (PF) and overall ZT value of the SnTe-based thermoelectric material. The introduction of Bi2O3 forms plenty of SnO2, Bi2O3, and Bi-rich nanoprecipitates. These interfaces between the SnTe matrix and the nanoprecipitates can enhance the average PF through the energy filtering effect. On the other hand, abundant and diverse nanoprecipitates can significantly diminish the lattice thermal conductivity (κlat) through enhanced phonon scattering. The synergistic effect of Bi2O3 resulted in a maximum ZT (ZTmax) value of 0.9 at SnTe-2% Bi2O3 and an average ZT (ZTave) value of 0.4 for SnTe-4% Bi2O3 from 300 K to 823 K. The work provides an excellent reference to develop non-toxic high-performance TE materials. acknowledgement: This work was supported by National Natural Science Foundation of China (52002042), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), 111 Project (B17002) and Lise Meitner Project M 2889-N. This work was also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the high-performance computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM and TEM measurements. article_number: '100985' article_processing_charge: No article_type: original author: - first_name: Tao full_name: Hong, Tao last_name: Hong - first_name: Changrong full_name: Guo, Changrong last_name: Guo - first_name: Dongyang full_name: Wang, Dongyang last_name: Wang - first_name: Bingchao full_name: Qin, Bingchao last_name: Qin - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Xiang full_name: Gao, Xiang last_name: Gao - first_name: Li Dong full_name: Zhao, Li Dong last_name: Zhao citation: ama: Hong T, Guo C, Wang D, et al. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. 2022;25. doi:10.1016/j.mtener.2022.100985 apa: Hong, T., Guo, C., Wang, D., Qin, B., Chang, C., Gao, X., & Zhao, L. D. (2022). Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. Elsevier. https://doi.org/10.1016/j.mtener.2022.100985 chicago: Hong, Tao, Changrong Guo, Dongyang Wang, Bingchao Qin, Cheng Chang, Xiang Gao, and Li Dong Zhao. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” Materials Today Energy. Elsevier, 2022. https://doi.org/10.1016/j.mtener.2022.100985. ieee: T. Hong et al., “Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3,” Materials Today Energy, vol. 25. Elsevier, 2022. ista: Hong T, Guo C, Wang D, Qin B, Chang C, Gao X, Zhao LD. 2022. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. 25, 100985. mla: Hong, Tao, et al. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” Materials Today Energy, vol. 25, 100985, Elsevier, 2022, doi:10.1016/j.mtener.2022.100985. short: T. Hong, C. Guo, D. Wang, B. Qin, C. Chang, X. Gao, L.D. Zhao, Materials Today Energy 25 (2022). date_created: 2022-04-10T22:01:39Z date_published: 2022-04-01T00:00:00Z date_updated: 2023-08-03T06:28:16Z day: '01' department: - _id: MaIb doi: 10.1016/j.mtener.2022.100985 external_id: isi: - '000798679100010' intvolume: ' 25' isi: 1 language: - iso: eng month: '04' oa_version: None project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Materials Today Energy publication_identifier: eissn: - 2468-6069 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2022' ... --- _id: '11143' abstract: - lang: eng text: 'Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology.' acknowledgement: We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com). article_number: '110580' article_processing_charge: No article_type: original author: - first_name: Keisuke full_name: Kaneko, Keisuke last_name: Kaneko - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Kevin M. full_name: Goff, Kevin M. last_name: Goff - first_name: Eric R. full_name: Wengert, Eric R. last_name: Wengert - first_name: Ala full_name: Somarowthu, Ala last_name: Somarowthu - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Ethan M. full_name: Goldberg, Ethan M. last_name: Goldberg citation: ama: Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 2022;38(13). doi:10.1016/j.celrep.2022.110580 apa: Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., & Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110580 chicago: Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110580. ieee: K. Kaneko et al., “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” Cell Reports, vol. 38, no. 13. Elsevier, 2022. ista: Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580. mla: Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” Cell Reports, vol. 38, no. 13, 110580, Elsevier, 2022, doi:10.1016/j.celrep.2022.110580. short: K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022). date_created: 2022-04-10T22:01:39Z date_published: 2022-03-29T00:00:00Z date_updated: 2023-08-03T06:32:55Z day: '29' ddc: - '570' department: - _id: TiVo doi: 10.1016/j.celrep.2022.110580 ec_funded: 1 external_id: isi: - '000779794000001' file: - access_level: open_access checksum: 49105c6c27c9af0f37f50a8bbb4d380d content_type: application/pdf creator: dernst date_created: 2022-04-15T11:00:58Z date_updated: 2022-04-15T11:00:58Z file_id: '11172' file_name: 2022_CellReports_Kaneko.pdf file_size: 4774216 relation: main_file success: 1 file_date_updated: 2022-04-15T11:00:58Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '13' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Cell Reports publication_identifier: eissn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome tmp: 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2022' ... --- _id: '11144' abstract: - lang: eng text: Thermoelectric materials allow for direct conversion between heat and electricity, offering the potential for power generation. The average dimensionless figure of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit outstanding three-dimensional charge and two-dimensional phonon transport along the out-of-plane direction, contributing to a high maximum figure of merit Zmax of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to 773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron decoupling. The chlorine-induced low deformation potential improved the carrier mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance thermoelectrics. acknowledgement: This work was supported by the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Key Research and Development Program of China (2018YFA0702100), the National Science Fund for Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner Project (M2889-N), and the National Key Research and Development Program of China (2018YFB0703600). This work is also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance computing resources at Beihang University. article_processing_charge: No article_type: original author: - first_name: Lizhong full_name: Su, Lizhong last_name: Su - first_name: Dongyang full_name: Wang, Dongyang last_name: Wang - first_name: Sining full_name: Wang, Sining last_name: Wang - first_name: Bingchao full_name: Qin, Bingchao last_name: Qin - first_name: Yuping full_name: Wang, Yuping last_name: Wang - first_name: Yongxin full_name: Qin, Yongxin last_name: Qin - first_name: Yang full_name: Jin, Yang last_name: Jin - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Li Dong full_name: Zhao, Li Dong last_name: Zhao citation: ama: Su L, Wang D, Wang S, et al. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. 2022;375(6587):1385-1389. doi:10.1126/science.abn8997 apa: Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022). High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abn8997 chicago: Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abn8997. ieee: L. Su et al., “High thermoelectric performance realized through manipulating layered phonon-electron decoupling,” Science, vol. 375, no. 6587. American Association for the Advancement of Science, pp. 1385–1389, 2022. ista: Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. 375(6587), 1385–1389. mla: Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” Science, vol. 375, no. 6587, American Association for the Advancement of Science, 2022, pp. 1385–89, doi:10.1126/science.abn8997. short: L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D. Zhao, Science 375 (2022) 1385–1389. date_created: 2022-04-10T22:01:40Z date_published: 2022-03-25T00:00:00Z date_updated: 2023-10-16T09:10:36Z day: '25' department: - _id: MaIb doi: 10.1126/science.abn8997 external_id: isi: - '000778894800038' pmid: - '35324303' intvolume: ' 375' isi: 1 issue: '6587' language: - iso: eng month: '03' oa_version: None page: 1385-1389 pmid: 1 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: High thermoelectric performance realized through manipulating layered phonon-electron decoupling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 375 year: '2022' ... --- _id: '11145' abstract: - lang: eng text: List-decodability of Reed-Solomon codes has re-ceived a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance. article_processing_charge: No arxiv: 1 author: - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Lisa full_name: Sauermann, Lisa last_name: Sauermann citation: ama: 'Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. In: 62nd Annual IEEE Symposium on Foundations of Computer Science. Vol 2022. IEEE; 2022:720-726. doi:10.1109/FOCS52979.2021.00075' apa: 'Ferber, A., Kwan, M. A., & Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. In 62nd Annual IEEE Symposium on Foundations of Computer Science (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE. https://doi.org/10.1109/FOCS52979.2021.00075' chicago: Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” In 62nd Annual IEEE Symposium on Foundations of Computer Science, 2022:720–26. IEEE, 2022. https://doi.org/10.1109/FOCS52979.2021.00075. ieee: A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” in 62nd Annual IEEE Symposium on Foundations of Computer Science, Denver, CO, United States, 2022, vol. 2022, pp. 720–726. ista: 'Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science vol. 2022, 720–726.' mla: Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” 62nd Annual IEEE Symposium on Foundations of Computer Science, vol. 2022, IEEE, 2022, pp. 720–26, doi:10.1109/FOCS52979.2021.00075. short: A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2022, pp. 720–726. conference: end_date: 2022-02-10 location: Denver, CO, United States name: 'FOCS: Symposium on Foundations of Computer Science' start_date: 2022-02-07 date_created: 2022-04-10T22:01:40Z date_published: 2022-02-01T00:00:00Z date_updated: 2023-08-03T06:57:02Z day: '01' department: - _id: MaKw doi: 10.1109/FOCS52979.2021.00075 external_id: arxiv: - '2012.10584' isi: - '000802209600065' intvolume: ' 2022' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2012.10584' month: '02' oa: 1 oa_version: Preprint page: 720-726 publication: 62nd Annual IEEE Symposium on Foundations of Computer Science publication_identifier: isbn: - '9781665420556' issn: - 0272-5428 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '10775' relation: later_version status: public scopus_import: '1' status: public title: List-decodability with large radius for Reed-Solomon codes type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2022 year: '2022' ... --- _id: '11155' abstract: - lang: eng text: The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes. acknowledged_ssus: - _id: LifeSc - _id: ScienComp - _id: EM-Fac acknowledgement: This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback. article_number: '107852' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Wim J.H. full_name: Hagen, Wim J.H. last_name: Hagen - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick - first_name: Lingbo full_name: Yu, Lingbo last_name: Yu - first_name: Abhay full_name: Kotecha, Abhay last_name: Kotecha - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852 apa: Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852 chicago: Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.jsb.2022.107852. ieee: M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022. ista: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852. mla: Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol. 214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852. short: M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022). date_created: 2022-04-15T07:10:26Z date_published: 2022-06-01T00:00:00Z date_updated: 2023-08-03T06:25:23Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.1016/j.jsb.2022.107852 external_id: isi: - '000790733600001' pmid: - '35351542' file: - access_level: open_access checksum: 0b1eb53447aae8e95ae4c12d193b0b00 content_type: application/pdf creator: dernst date_created: 2022-08-02T11:07:58Z date_updated: 2022-08-02T11:07:58Z file_id: '11722' file_name: 2022_JourStructuralBiology_Obr.pdf file_size: 7080863 relation: main_file success: 1 file_date_updated: 2022-08-02T11:07:58Z has_accepted_license: '1' intvolume: ' 214' isi: 1 issue: '2' keyword: - Structural Biology language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 214 year: '2022' ... --- _id: '11160' abstract: - lang: eng text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com. article_number: '110615' article_processing_charge: Yes article_type: original author: - first_name: Carlo Emanuele full_name: Villa, Carlo Emanuele last_name: Villa - first_name: Cristina full_name: Cheroni, Cristina last_name: Cheroni - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Alejandro full_name: López-Tóbon, Alejandro last_name: López-Tóbon - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Aysan Çerağ full_name: Yahya, Aysan Çerağ id: 365A65F8-F248-11E8-B48F-1D18A9856A87 last_name: Yahya - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Michele full_name: Gabriele, Michele last_name: Gabriele - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Mariano full_name: Gabitto, Mariano last_name: Gabitto - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Giuseppe full_name: Testa, Giuseppe last_name: Testa - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 2022;39(1). doi:10.1016/j.celrep.2022.110615 apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615 chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615. ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” Cell Reports, vol. 39, no. 1. Elsevier, 2022. ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615. mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol. 39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615. short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022). date_created: 2022-04-15T09:03:10Z date_published: 2022-04-05T00:00:00Z date_updated: 2024-03-25T23:30:25Z day: '05' ddc: - '570' department: - _id: JoDa - _id: GaNo doi: 10.1016/j.celrep.2022.110615 ec_funded: 1 external_id: isi: - '000785983900003' pmid: - '35385734' file: - access_level: open_access checksum: b4e8d68f0268dec499af333e6fd5d8e1 content_type: application/pdf creator: dernst date_created: 2022-04-15T09:06:25Z date_updated: 2022-04-15T09:06:25Z file_id: '11164' file_name: 2022_CellReports_Villa.pdf file_size: '7808644' relation: main_file success: 1 file_date_updated: 2022-04-15T09:06:25Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2690FEAC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I04205 name: Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy publication: Cell Reports publication_identifier: issn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '12364' relation: dissertation_contains status: public status: public title: CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2022' ... --- _id: '11167' abstract: - lang: eng text: Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I. article_number: '102350' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350 apa: Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350 chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350. ieee: D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” Current Opinion in Structural Biology, vol. 74. Elsevier, 2022. ista: Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350. mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology, vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350. short: D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022). date_created: 2022-04-15T09:32:35Z date_published: 2022-06-01T00:00:00Z date_updated: 2023-08-03T06:31:06Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.sbi.2022.102350 external_id: isi: - '000829029500020' pmid: - '35316665' file: - access_level: open_access checksum: 72bdde48853643a32d42b75f54965c44 content_type: application/pdf creator: dernst date_created: 2022-08-05T05:56:03Z date_updated: 2022-08-05T05:56:03Z file_id: '11725' file_name: 2022_CurrentOpStructBiology_Kampjut.pdf file_size: 815607 relation: main_file success: 1 file_date_updated: 2022-08-05T05:56:03Z has_accepted_license: '1' intvolume: ' 74' isi: 1 keyword: - Molecular Biology - Structural Biology language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Structure of respiratory complex I – An emerging blueprint for the mechanism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 74 year: '2022' ... --- _id: '11179' abstract: - lang: eng text: Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution. acknowledgement: "We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.)." article_number: '1927' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Duccio full_name: Malinverni, Duccio last_name: Malinverni - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Matteo full_name: Paloni, Matteo last_name: Paloni - first_name: Iva full_name: Sučec, Iva last_name: Sučec - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Juan Pablo full_name: Bustamante, Juan Pablo last_name: Bustamante - first_name: Alessandro full_name: Barducci, Alessandro last_name: Barducci - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 2022;13. doi:10.1038/s41467-022-29423-0 apa: Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-29423-0 chicago: Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-29423-0. ieee: D. F. Gauto et al., “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927. mla: Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” Nature Communications, vol. 13, 1927, Springer Nature, 2022, doi:10.1038/s41467-022-29423-0. short: D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022). date_created: 2022-04-17T22:01:45Z date_published: 2022-04-08T00:00:00Z date_updated: 2023-08-03T06:54:56Z day: '08' ddc: - '570' department: - _id: PaSc doi: 10.1038/s41467-022-29423-0 external_id: isi: - '000781498700009' file: - access_level: open_access checksum: db61d5534e988743d6266d3675d77b08 content_type: application/pdf creator: dernst date_created: 2022-05-02T08:48:00Z date_updated: 2022-05-02T08:48:00Z file_id: '11348' file_name: 2022_NatureCommunications_Gauto.pdf file_size: 2637590 relation: main_file success: 1 file_date_updated: 2022-05-02T08:48:00Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-022-31243-1 scopus_import: '1' status: public title: Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '11180' abstract: - lang: eng text: "Designing and implementing efficient parallel priority schedulers is an active research area. An intriguing proposed design is the Multi-Queue: given n threads and m ≥ n distinct priority queues, task insertions are performed uniformly at random, while, to delete, a thread picks two queues uniformly at random, and removes the observed task of higher priority. This approach scales well, and has probabilistic rank guarantees: roughly, the rank of each task removed, relative to remaining tasks in all other queues, is O (m) in expectation. Yet, the performance of this pattern is below that of well-engineered schedulers, which eschew theoretical guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible to design and implement a Multi-Queue-based task scheduler that is both highly-efficient and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue (SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue affinity---each thread has a local queue, from which tasks are usually removed; but, with some probability, threads also attempt to steal higher-priority tasks from the other queues---and task batching, that is, the processing of several tasks in a single insert / remove step. These ideas are well-known for task scheduling without priorities; our theoretical contribution is showing that, despite relaxations, this design can still provide rank guarantees, which in turn implies bounds on total work performed. We provide a general SMQ implementation which can surpass state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular graph-processing benchmarks. Notably, the performance improvement comes mainly from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned approaches can still provide performance improvements for priority task scheduling." acknowledgement: We would like to thank the anonymous reviewers for their useful comments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). article_processing_charge: No arxiv: 1 author: - first_name: Anastasiia full_name: Postnikova, Anastasiia last_name: Postnikova - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. In: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2022:353-367. doi:10.1145/3503221.3508432' apa: 'Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. In Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 353–367). Seoul, Republic of Korea: Association for Computing Machinery. https://doi.org/10.1145/3503221.3508432' chicago: Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 353–67. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508432. ieee: A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers,” in Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Seoul, Republic of Korea, 2022, pp. 353–367. ista: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 353–367.' mla: Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 353–67, doi:10.1145/3503221.3508432. short: A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 353–367. conference: end_date: 2022-04-06 location: Seoul, Republic of Korea name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming' start_date: 2022-04-02 date_created: 2022-04-17T22:01:46Z date_published: 2022-04-02T00:00:00Z date_updated: 2023-08-03T06:48:35Z day: '02' department: - _id: DaAl doi: 10.1145/3503221.3508432 ec_funded: 1 external_id: arxiv: - '2109.00657' isi: - '000883318200025' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2109.00657' month: '04' oa: 1 oa_version: Preprint page: 353-367 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming publication_identifier: isbn: - '9781450392044' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '13076' relation: research_data status: public scopus_import: '1' status: public title: Multi-queues can be state-of-the-art priority schedulers type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2022' ... --- _id: '11181' abstract: - lang: eng text: 'To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance.' acknowledgement: "This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant: CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048, NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018, and the University of Waterloo. We would also like to thank the reviewers for their insightful comments." article_processing_charge: No author: - first_name: Trevor A full_name: Brown, Trevor A id: 3569F0A0-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: William full_name: Sigouin, William last_name: Sigouin - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for concurrent search data structures. In: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2022:385-399. doi:10.1145/3503221.3508410' apa: 'Brown, T. A., Sigouin, W., & Alistarh, D.-A. (2022). PathCAS: An efficient middle ground for concurrent search data structures. In Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery. https://doi.org/10.1145/3503221.3508410' chicago: 'Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” In Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 385–99. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508410.' ieee: 'T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle ground for concurrent search data structures,” in Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Seoul, Republic of Korea, 2022, pp. 385–399.' ista: 'Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 385–399.' mla: 'Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 385–99, doi:10.1145/3503221.3508410.' short: T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 385–399. conference: end_date: 2022-04-06 location: Seoul, Republic of Korea name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming' start_date: 2022-04-02 date_created: 2022-04-17T22:01:46Z date_published: 2022-04-02T00:00:00Z date_updated: 2023-08-03T06:49:20Z day: '02' ddc: - '000' department: - _id: DaAl doi: 10.1145/3503221.3508410 external_id: isi: - '000883318200027' file: - access_level: open_access checksum: 8ceea411fa133795cd4903529498eb6b content_type: application/pdf creator: dernst date_created: 2022-08-05T09:19:29Z date_updated: 2022-08-05T09:19:29Z file_id: '11731' file_name: 2022_PPoPP_Brown.pdf file_size: 1128343 relation: main_file success: 1 file_date_updated: 2022-08-05T09:19:29Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 385-399 publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming publication_identifier: isbn: - '9781450392044' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'PathCAS: An efficient middle ground for concurrent search data structures' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2022' ... --- _id: '11182' abstract: - lang: eng text: Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity. acknowledgement: "We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL." article_number: e407 article_processing_charge: No article_type: original author: - first_name: Janina full_name: Kroll, Janina last_name: Kroll - first_name: Mauricio J.A. full_name: Ruiz-Fernandez, Mauricio J.A. last_name: Ruiz-Fernandez - first_name: Malte B. full_name: Braun, Malte B. last_name: Braun - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 citation: ama: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2022;2(4). doi:10.1002/cpz1.407 apa: Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407 chicago: Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407. ieee: J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022. ista: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407. mla: Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407, Wiley, 2022, doi:10.1002/cpz1.407. short: J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022). date_created: 2022-04-17T22:01:46Z date_published: 2022-04-05T00:00:00Z date_updated: 2022-05-02T08:18:00Z day: '05' ddc: - '570' department: - _id: NanoFab doi: 10.1002/cpz1.407 external_id: pmid: - '35384410' file: - access_level: open_access checksum: 72152d005c367777f6cf2f6a477f0d52 content_type: application/pdf creator: dernst date_created: 2022-05-02T08:16:10Z date_updated: 2022-05-02T08:16:10Z file_id: '11347' file_name: 2022_CurrentProtocols_Kroll.pdf file_size: 2142703 relation: main_file success: 1 file_date_updated: 2022-05-02T08:16:10Z has_accepted_license: '1' intvolume: ' 2' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Current Protocols publication_identifier: eissn: - 2691-1299 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the probing and selection of microenvironmental pores by motile immune cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2022' ... --- _id: '11183' abstract: - lang: eng text: "Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:\r\n- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.\r\n- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems." acknowledgement: "Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070) of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced subgraph detection [36]." alternative_title: - LIPIcs article_number: '15' article_processing_charge: No author: - first_name: Amir full_name: Nikabadi, Amir last_name: Nikabadi - first_name: Janne full_name: Korhonen, Janne id: C5402D42-15BC-11E9-A202-CA2BE6697425 last_name: Korhonen citation: ama: 'Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A, eds. 25th International Conference on Principles of Distributed Systems. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.OPODIS.2021.15' apa: 'Nikabadi, A., & Korhonen, J. (2022). Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V. Gramoli, & A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15' chicago: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” In 25th International Conference on Principles of Distributed Systems, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15.' ieee: 'A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters,” in 25th International Conference on Principles of Distributed Systems, Strasbourg, France, 2022, vol. 217.' ista: 'Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15.' mla: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” 25th International Conference on Principles of Distributed Systems, edited by Quentin Bramas et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.OPODIS.2021.15.' short: A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. conference: end_date: 2021-12-15 location: Strasbourg, France name: OPODIS start_date: 2021-12-13 date_created: 2022-04-17T22:01:47Z date_published: 2022-02-01T00:00:00Z date_updated: 2022-05-02T07:56:35Z day: '01' ddc: - '510' department: - _id: DaAl doi: 10.4230/LIPIcs.OPODIS.2021.15 ec_funded: 1 editor: - first_name: Quentin full_name: Bramas, Quentin last_name: Bramas - first_name: Vincent full_name: Gramoli, Vincent last_name: Gramoli - first_name: Alessia full_name: Milani, Alessia last_name: Milani file: - access_level: open_access checksum: 626551c14de5d4091573200ed0535752 content_type: application/pdf creator: dernst date_created: 2022-05-02T07:53:00Z date_updated: 2022-05-02T07:53:00Z file_id: '11345' file_name: 2022_LIPICs_Nikabadi.pdf file_size: 790396 relation: main_file success: 1 file_date_updated: 2022-05-02T07:53:00Z has_accepted_license: '1' intvolume: ' 217' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: 25th International Conference on Principles of Distributed Systems publication_identifier: isbn: - '9783959772198' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: 'Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 217 year: '2022' ...