@article{12111, abstract = {Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up.}, author = {Stocker, Lidia and Sack, Stefan and Ferguson, Michael S. and Zilberberg, Oded}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Entanglement-based observables for quantum impurities}}, doi = {10.1103/PhysRevResearch.4.043177}, volume = {4}, year = {2022}, } @article{12116, abstract = {Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.}, author = {Chhugani, Karishma and Frolova, Alina and Salyha, Yuriy and Fiscutean, Andrada and Zlenko, Oksana and Reinsone, Sanita and Wolfsberger, Walter W. and Ivashchenko, Oleksandra V. and Maci, Megi and Dziuba, Dmytro and Parkhomenko, Andrii and Bortz, Eric and Kondrashov, Fyodor and Łabaj, Paweł P. and Romero, Veronika and Hlávka, Jakub and Oleksyk, Taras K. and Mangul, Serghei}, issn = {1095-9203}, journal = {Science}, number = {6626}, pages = {1285--1286}, publisher = {American Association for the Advancement of Science}, title = {{Remote opportunities for scholars in Ukraine}}, doi = {10.1126/science.adg0797}, volume = {378}, year = {2022}, } @article{12117, abstract = {To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia. For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1}, author = {Hübschmann, Verena and Korkut, Medina and Siegert, Sandra}, issn = {2666-1667}, journal = {STAR Protocols}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {4}, publisher = {Elsevier}, title = {{Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay}}, doi = {10.1016/j.xpro.2022.101866}, volume = {3}, year = {2022}, } @article{12118, abstract = {Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes.}, author = {Valentini, Marco and Borovkov, Maksim and Prada, Elsa and Martí-Sánchez, Sara and Botifoll, Marc and Hofmann, Andrea C and Arbiol, Jordi and Aguado, Ramón and San-Jose, Pablo and Katsaros, Georgios}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7940}, pages = {442--447}, publisher = {Springer Nature}, title = {{Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks}}, doi = {10.1038/s41586-022-05382-w}, volume = {612}, year = {2022}, } @article{12119, abstract = {Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events.}, author = {Petzold, Tobias and Zhang, Zhe and Ballesteros, Iván and Saleh, Inas and Polzin, Amin and Thienel, Manuela and Liu, Lulu and Ul Ain, Qurrat and Ehreiser, Vincent and Weber, Christian and Kilani, Badr and Mertsch, Pontus and Götschke, Jeremias and Cremer, Sophie and Fu, Wenwen and Lorenz, Michael and Ishikawa-Ankerhold, Hellen and Raatz, Elisabeth and El-Nemr, Shaza and Görlach, Agnes and Marhuenda, Esther and Stark, Konstantin and Pircher, Joachim and Stegner, David and Gieger, Christian and Schmidt-Supprian, Marc and Gärtner, Florian R and Almendros, Isaac and Kelm, Malte and Schulz, Christian and Hidalgo, Andrés and Massberg, Steffen}, issn = {1074-7613}, journal = {Immunity}, keywords = {Infectious Diseases, Immunology, Immunology and Allergy}, number = {12}, pages = {2285--2299.e7}, publisher = {Elsevier}, title = {{Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease}}, doi = {10.1016/j.immuni.2022.10.001}, volume = {55}, year = {2022}, } @article{12120, abstract = {Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.}, author = {Xiao, Huixin and Hu, Yumei and Wang, Yaping and Cheng, Jinkui and Wang, Jinyi and Chen, Guojingwei and Li, Qian and Wang, Shuwei and Wang, Yalu and Wang, Shao-Shuai and Wang, Yi and Xuan, Wei and Li, Zhen and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing}, issn = {1534-5807}, journal = {Developmental Cell}, keywords = {Developmental Biology, Cell Biology, General Biochemistry, Genetics and Molecular Biology, Molecular Biology}, number = {23}, pages = {2638--2651.e6}, publisher = {Elsevier}, title = {{Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth}}, doi = {10.1016/j.devcel.2022.11.006}, volume = {57}, year = {2022}, } @article{12121, abstract = {Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.}, author = {Zhao, Jierui and Bui, Mai Thu and Ma, Juncai and Künzl, Fabian and Picchianti, Lorenzo and De La Concepcion, Juan Carlos and Chen, Yixuan and Petsangouraki, Sofia and Mohseni, Azadeh and García-Leon, Marta and Gomez, Marta Salas and Giannini, Caterina and Gwennogan, Dubois and Kobylinska, Roksolana and Clavel, Marion and Schellmann, Swen and Jaillais, Yvon and Friml, Jiří and Kang, Byung-Ho and Dagdas, Yasin}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {12}, publisher = {Rockefeller University Press}, title = {{Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole}}, doi = {10.1083/jcb.202203139}, volume = {221}, year = {2022}, } @article{12122, abstract = {Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.}, author = {Weier, Ann-Kathrin and Homrich, Mirka and Ebbinghaus, Stephanie and Juda, Pavel and Miková, Eliška and Hauschild, Robert and Zhang, Lili and Quast, Thomas and Mass, Elvira and Schlitzer, Andreas and Kolanus, Waldemar and Burgdorf, Sven and Gruß, Oliver J. and Hons, Miroslav and Wieser, Stefan and Kiermaier, Eva}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {12}, publisher = {Rockefeller University Press}, title = {{Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells}}, doi = {10.1083/jcb.202107134}, volume = {221}, year = {2022}, } @article{12128, abstract = {We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.}, author = {Poelking, Carl and Faber, Felix A and Cheng, Bingqing}, issn = {2632-2153}, journal = {Machine Learning: Science and Technology}, keywords = {Artificial Intelligence, Human-Computer Interaction, Software}, number = {4}, publisher = {IOP Publishing}, title = {{BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale}}, doi = {10.1088/2632-2153/ac4d11}, volume = {3}, year = {2022}, } @article{12129, abstract = {Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations.}, author = {Wagner, Uli and Welzl, Emo}, issn = {1432-0444}, journal = {Discrete & Computational Geometry}, keywords = {Computational Theory and Mathematics, Discrete Mathematics and Combinatorics, Geometry and Topology, Theoretical Computer Science}, number = {4}, pages = {1227--1284}, publisher = {Springer Nature}, title = {{Connectivity of triangulation flip graphs in the plane}}, doi = {10.1007/s00454-022-00436-2}, volume = {68}, year = {2022}, } @article{12130, abstract = {Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.}, author = {Huang, Jian and Zhao, Lei and Malik, Shikha and Gentile, Benjamin R. and Xiong, Va and Arazi, Tzahi and Owen, Heather A. and Friml, Jiří and Zhao, Dazhong}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis}}, doi = {10.1038/s41467-022-34723-6}, volume = {13}, year = {2022}, } @article{12131, abstract = {Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines.}, author = {Byazrova, Maria G. and Astakhova, Ekaterina A. and Minnegalieva, Aygul and Sukhova, Maria M. and Mikhailov, Artem A. and Prilipov, Alexey G. and Gorchakov, Andrey A. and Filatov, Alexander V.}, issn = {2059-0105}, journal = {npj Vaccines}, keywords = {Pharmacology (medical), Infectious Diseases, Pharmacology, Immunology, SARS-COV-2, COVID}, publisher = {Springer Nature}, title = {{Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination}}, doi = {10.1038/s41541-022-00566-x}, volume = {7}, year = {2022}, } @article{12133, abstract = {Social distancing is an effective way to prevent the spread of disease in societies, whereas infection elimination is a key element of organismal immunity. Here, we discuss how the study of social insects such as ants — which form a superorganism of unconditionally cooperative individuals and thus represent a level of organization that is intermediate between a classical society of individuals and an organism of cells — can help to determine common principles of disease defence across levels of organization.}, author = {Cremer, Sylvia and Sixt, Michael K}, issn = {1474-1741}, journal = {Nature Reviews Immunology}, keywords = {Energy Engineering and Power Technology, Fuel Technology}, number = {12}, pages = {713--714}, publisher = {Springer Nature}, title = {{Principles of disease defence in organisms, superorganisms and societies}}, doi = {10.1038/s41577-022-00797-y}, volume = {22}, year = {2022}, } @article{12134, abstract = {Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the type of phase transition. In particular, we uncover three distinct types of explosive phase transitions for epidemic dynamics with capacity-limited interventions. Depending on the capacity limit, interventions may (i) leave the standard second order phase transition unchanged but exponentially suppress the probability of large outbreaks, (ii) induce a first-order discontinuous transition to macroscopic outbreaks, or (iii) cause a secondary explosive yet continuous third-order transition. These insights highlight inherent limitations in predicting and containing epidemic outbreaks. More generally our study offers a cornerstone example of a third-order explosive phase transition in complex systems.}, author = {Börner, Georg and Schröder, Malte and Scarselli, Davide and Budanur, Nazmi B and Hof, Björn and Timme, Marc}, issn = {2632-072X}, journal = {Journal of Physics: Complexity}, keywords = {Artificial Intelligence, Computer Networks and Communications, Computer Science Applications, Information Systems}, number = {4}, publisher = {IOP Publishing}, title = {{Explosive transitions in epidemic dynamics}}, doi = {10.1088/2632-072x/ac99cd}, volume = {3}, year = {2022}, } @inproceedings{12135, abstract = {A good match of material appearance between real-world objects and their digital on-screen representations is critical for many applications such as fabrication, design, and e-commerce. However, faithful appearance reproduction is challenging, especially for complex phenomena, such as gloss. In most cases, the view-dependent nature of gloss and the range of luminance values required for reproducing glossy materials exceeds the current capabilities of display devices. As a result, appearance reproduction poses significant problems even with accurately rendered images. This paper studies the gap between the gloss perceived from real-world objects and their digital counterparts. Based on our psychophysical experiments on a wide range of 3D printed samples and their corresponding photographs, we derive insights on the influence of geometry, illumination, and the display’s brightness and measure the change in gloss appearance due to the display limitations. Our evaluation experiments demonstrate that using the prediction to correct material parameters in a rendering system improves the match of gloss appearance between real objects and their visualization on a display device.}, author = {Chen, Bin and Piovarci, Michael and Wang, Chao and Seidel, Hans-Peter and Didyk, Piotr and Myszkowski, Karol and Serrano, Ana}, booktitle = {SIGGRAPH Asia 2022 Conference Papers}, isbn = {9781450394703}, location = {Daegu, South Korea}, publisher = {Association for Computing Machinery}, title = {{Gloss management for consistent reproduction of real and virtual objects}}, doi = {10.1145/3550469.3555406}, volume = {2022}, year = {2022}, } @article{12137, abstract = {We investigate the local self-sustained process underlying spiral turbulence in counter-rotating Taylor–Couette flow using a periodic annular domain, shaped as a parallelogram, two of whose sides are aligned with the cylindrical helix described by the spiral pattern. The primary focus of the study is placed on the emergence of drifting–rotating waves (DRW) that capture, in a relatively small domain, the main features of coherent structures typically observed in developed turbulence. The transitional dynamics of the subcritical region, far below the first instability of the laminar circular Couette flow, is determined by the upper and lower branches of DRW solutions originated at saddle-node bifurcations. The mechanism whereby these solutions self-sustain, and the chaotic dynamics they induce, are conspicuously reminiscent of other subcritical shear flows. Remarkably, the flow properties of DRW persist even as the Reynolds number is increased beyond the linear stability threshold of the base flow. Simulations in a narrow parallelogram domain stretched in the azimuthal direction to revolve around the apparatus a full turn confirm that self-sustained vortices eventually concentrate into a localised pattern. The resulting statistical steady state satisfactorily reproduces qualitatively, and to a certain degree also quantitatively, the topology and properties of spiral turbulence as calculated in a large periodic domain of sufficient aspect ratio that is representative of the real system.}, author = {Wang, B. and Ayats López, Roger and Deguchi, K. and Mellibovsky, F. and Meseguer, A.}, issn = {1469-7645}, journal = {Journal of Fluid Mechanics}, keywords = {Mechanical Engineering, Mechanics of Materials, Condensed Matter Physics, Applied Mathematics}, publisher = {Cambridge University Press}, title = {{Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow}}, doi = {10.1017/jfm.2022.828}, volume = {951}, year = {2022}, } @article{12138, abstract = {Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.}, author = {Kravchuk, Vladyslav and Petrova, Olga and Kampjut, Domen and Wojciechowska-Bason, Anna and Breese, Zara and Sazanov, Leonid A}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7928}, pages = {808--814}, publisher = {Springer Nature}, title = {{A universal coupling mechanism of respiratory complex I}}, doi = {10.1038/s41586-022-05199-7}, volume = {609}, year = {2022}, } @article{12139, abstract = {We demonstrate the formation of robust zero-energy modes close to magnetic impurities in the iron-based superconductor FeSe1-z Tez. We find that the Zeeman field generated by the impurity favors a spin-triplet interorbital pairing as opposed to the spin-singlet intraorbital pairing prevalent in the bulk. The preferred spin-triplet pairing preserves time-reversal symmetry and is topological, as robust, topologically protected zero modes emerge at the boundary between regions with different pairing states. Moreover, the zero modes form Kramers doublets that are insensitive to the direction of the spin polarization or to the separation between impurities. We argue that our theoretical results are consistent with recent experimental measurements on FeSe1-z Tez.}, author = {Ghazaryan, Areg and Kirmani, Ammar and Fernandes, Rafael M. and Ghaemi, Pouyan}, issn = {2469-9969}, journal = {Physical Review B}, number = {20}, publisher = {American Physical Society}, title = {{Anomalous Shiba states in topological iron-based superconductors}}, doi = {10.1103/physrevb.106.l201107}, volume = {106}, year = {2022}, } @article{12140, abstract = {Microglia are dynamic cells, constantly surveying their surroundings and interacting with neurons and synapses. Indeed, a wealth of knowledge has revealed a critical role of microglia in modulating synaptic transmission and plasticity in the developing brain. In the past decade, novel pharmacological and genetic strategies have allowed the acute removal of microglia, opening the possibility to explore and understand the role of microglia also in the adult brain. In this review, we summarized and discussed the contribution of microglia depletion strategies to the current understanding of the role of microglia on synaptic function, learning and memory, and behavior both in physiological and pathological conditions. We first described the available microglia depletion methods highlighting their main strengths and weaknesses. We then reviewed the impact of microglia depletion on structural and functional synaptic plasticity. Next, we focused our analysis on the effects of microglia depletion on behavior, including general locomotor activity, sensory perception, motor function, sociability, learning and memory both in healthy animals and animal models of disease. Finally, we integrated the findings from the reviewed studies and discussed the emerging roles of microglia on the maintenance of synaptic function, learning, memory strength and forgetfulness, and the implications of microglia depletion in models of brain disease.}, author = {Basilico, Bernadette and Ferrucci, Laura and Khan, Azka and Di Angelantonio, Silvia and Ragozzino, Davide and Reverte, Ingrid}, issn = {1662-5102}, journal = {Frontiers in Cellular Neuroscience}, keywords = {Cellular and Molecular Neuroscience}, publisher = {Frontiers Media}, title = {{What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior}}, doi = {10.3389/fncel.2022.1022431}, volume = {16}, year = {2022}, } @article{12142, abstract = {Theory for liability-scale models of the underlying genetic basis of complex disease provides an important way to interpret, compare, and understand results generated from biological studies. In particular, through estimation of the liability-scale heritability (LSH), liability models facilitate an understanding and comparison of the relative importance of genetic and environmental risk factors that shape different clinically important disease outcomes. Increasingly, large-scale biobank studies that link genetic information to electronic health records, containing hundreds of disease diagnosis indicators that mostly occur infrequently within the sample, are becoming available. Here, we propose an extension of the existing liability-scale model theory suitable for estimating LSH in biobank studies of low-prevalence disease. In a simulation study, we find that our derived expression yields lower mean square error (MSE) and is less sensitive to prevalence misspecification as compared to previous transformations for diseases with =< 2% population prevalence and LSH of =< 0.45, especially if the biobank sample prevalence is less than that of the wider population. Applying our expression to 13 diagnostic outcomes of =< 3% prevalence in the UK Biobank study revealed important differences in LSH obtained from the different theoretical expressions that impact the conclusions made when comparing LSH across disease outcomes. This demonstrates the importance of careful consideration for estimation and prediction of low-prevalence disease outcomes and facilitates improved inference of the underlying genetic basis of =< 2% population prevalence diseases, especially where biobank sample ascertainment results in a healthier sample population.}, author = {Ojavee, Sven E. and Kutalik, Zoltan and Robinson, Matthew Richard}, issn = {0002-9297}, journal = {The American Journal of Human Genetics}, keywords = {Genetics (clinical), Genetics}, number = {11}, pages = {2009--2017}, publisher = {Elsevier}, title = {{Liability-scale heritability estimation for biobank studies of low-prevalence disease}}, doi = {10.1016/j.ajhg.2022.09.011}, volume = {109}, year = {2022}, }