@article{15179, abstract = {The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.}, author = {Palkina, Kseniia A. and Karataeva, Tatiana A. and Perfilov, Maxim M. and Fakhranurova, Liliia I. and Markina, Nadezhda M. and Gonzalez Somermeyer, Louisa and Garcia-Perez, Elena and Vazquez-Vilar, Marta and Rodriguez-Rodriguez, Marta and Vazquez-Vilriales, Victor and Shakhova, Ekaterina S. and Mitiouchkina, Tatiana and Belozerova, Olga A. and Kovalchuk, Sergey I. and Alekberova, Anna and Malyshevskaia, Alena K. and Bugaeva, Evgenia N. and Guglya, Elena B. and Balakireva, Anastasia and Sytov, Nikita and Bezlikhotnova, Anastasia and Boldyreva, Daria I. and Babenko, Vladislav V. and Kondrashov, Fyodor and Choob, Vladimir V. and Orzaez, Diego and Yampolsky, Ilia V. and Mishin, Alexander S. and Sarkisyan, Karen S.}, issn = {2375-2548}, journal = {Science Advances}, number = {10}, publisher = {American Association for the Advancement of Science}, title = {{A hybrid pathway for self-sustained luminescence}}, doi = {10.1126/sciadv.adk1992}, volume = {10}, year = {2024}, } @article{15181, abstract = {We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.}, author = {Becker, A. and Koutentakis, Georgios and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {1}, publisher = {American Physical Society}, title = {{Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions}}, doi = {10.1103/physrevresearch.6.013257}, volume = {6}, year = {2024}, } @article{15186, abstract = {The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain.}, author = {Hwong, Yi-Ling and Muller, Caroline J}, issn = {1944-8007}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {6}, publisher = {Wiley}, title = {{The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation}}, doi = {10.1029/2023gl106523}, volume = {51}, year = {2024}, } @article{15247, abstract = {Extending the notion of sunflowers, we call a family of at least two sets an odd-sunflower if every element of the underlying set is contained in an odd number of sets or in none of them. It follows from the Erdős–Szemerédi conjecture, recently proved by Naslund and Sawin, that there is a constant <2 such that every family of subsets of an n-element set that contains no odd-sunflower consists of at most n sets. We construct such families of size at least 1.5021n. We also characterize minimal odd-sunflowers of triples.}, author = {Frankl, Peter and Pach, János and Pálvölgyi, Dömötör}, issn = {1096-0899}, journal = {Journal of Combinatorial Theory, Series A}, number = {8}, publisher = {Elsevier}, title = {{Odd-sunflowers}}, doi = {10.1016/j.jcta.2024.105889}, volume = {206}, year = {2024}, } @article{15248, abstract = {Applying the technique of p-adic integration, we prove the topological mirror symmetry conjecture of Hausel-Thaddeus for the moduli spaces of (strongly) parabolic Higgs bundles for the structure groups SLn and PGLn, building on previous work of Groechenig-Wyss-Ziegler on the non-parabolic case. We also prove the E-polynomial of the smooth moduli space of parabolic GLn-Higgs bundles is independent of the degree of the underlying vector bundles.}, author = {Shen, Shiyu}, issn = {1090-2082}, journal = {Advances in Mathematics}, number = {5}, publisher = {Elsevier}, title = {{Mirror symmetry for parabolic Higgs bundles via p-adic integration}}, doi = {10.1016/j.aim.2024.109616}, volume = {443}, year = {2024}, } @article{15249, abstract = {Observationally mapping the relation between galaxies and the intergalactic medium (IGM) is of key interest for studies of cosmic reionization. Diffuse hydrogen gas has typically been observed in H I Lyman-α (Lyα) absorption in the spectra of bright background quasars. However, it is important to extend these measurements to background galaxies as quasars become increasingly rare at high redshift and rarely probe closely separated sight lines. Here, we use deep integral field spectroscopy in the MUSE eXtremely Deep Field to demonstrate the measurement of the Lyα transmission at z ≈ 4 in absorption to a background galaxy at z = 4.77. The H I transmission is consistent with independent quasar sight lines at similar redshifts. Exploiting the high number of spectroscopic redshifts of faint galaxies (500 between z = 4.0–4.7 within a radius of 8 arcmin) that are tracers of the density field, we show that Lyα transmission is inversely correlated with galaxy density, i.e. transparent regions in the Lyα forest mark underdense regions at z ≈ 4. Due to large-scale clustering, galaxies are surrounded by excess H I absorption over the cosmic mean out to 4 cMpc/h70. We also find that redshifts from the peak of the Lyα line are typically offset from the systemic redshift by +170 km s−1. This work extends results from z ≈ 2–3 to higher redshifts and demonstrates the power of deep integral field spectroscopy to simultaneously measure the ionization structure of the IGM and the large-scale density field in the early Universe.}, author = {Matthee, Jorryt J and Golling, Christopher and Mackenzie, Ruari and Pezzulli, Gabriele and Lilly, Simon and Schaye, Joop and Bacon, Roland and Kusakabe, Haruka and Urrutia, Tanya and Boogaard, Leindert and Brinchmann, Jarle and Maseda, Michael V. and Garel, Thibault and Bouché, Nicolas F. and Wisotzki, Lutz}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {3}, pages = {2794--2806}, publisher = {Oxford University Press}, title = {{Large-scale excess H I absorption around z ≈ 4 galaxies detected in a background galaxy spectrum in the MUSE eXtremely deep field}}, doi = {10.1093/mnras/stae673}, volume = {529}, year = {2024}, } @article{15250, abstract = {Orphan solute carrier (SLC) represents a group of membrane transporters whose exact functions and substrate specificities are not known. Elucidating the function and regulation of orphan SLC transporters is not only crucial for advancing our knowledge of cellular and molecular biology but can potentially lead to the development of new therapeutic strategies. Here, we provide evidence for the biological function of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics revealed that dipeptides containing either lysine or arginine residues accumulate in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport affinities for positively charged dipeptides in the lower mM range, while dipeptides that carry a negative net charge were not transported. This was also true for single amino acids and tripeptides, which MFSD1 failed to transport. Our results identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing dipeptide exporter, which functions as a uniporter.}, author = {Boytsov, Danila and Madej, Gregor M. and Horn, Georg and Blaha, Nadine and Köcher, Thomas and Sitte, Harald H. and Siekhaus, Daria E and Ziegler, Christine and Sandtner, Walter and Roblek, Marko}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {13}, publisher = {National Academy of Sciences}, title = {{Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport}}, doi = {10.1073/pnas.2319686121}, volume = {121}, year = {2024}, } @article{15251, abstract = {Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.}, author = {Ying, Wei and Wang, Yaowei and Wei, Hong and Luo, Yongming and Ma, Qian and Zhu, Heyuan and Janssens, Hilde and Vukašinović, Nemanja and Kvasnica, Miroslav and Winne, Johan M. and Gao, Yongxiang and Tan, Shutang and Friml, Jiří and Liu, Xin and Russinova, Eugenia and Sun, Linfeng}, issn = {1095-9203}, journal = {Science}, number = {6689}, pages = {eadj4591}, publisher = {American Association for the Advancement of Science}, title = {{Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export}}, doi = {10.1126/science.adj4591}, volume = {383}, year = {2024}, } @article{15252, abstract = {A measurable map between measure spaces is shown to have bounded compression if and only if its image via the measure-algebra functor is Lipschitz-continuous w.r.t. the measure-algebra distances. This provides a natural interpretation of maps of bounded compression/deformation by means of the measure-algebra functor and corrobo-rates the assertion that maps of bounded deformation are a natural class of morphisms for the category of complete and separable metric measure spaces.}, author = {Dello Schiavo, Lorenzo}, issn = {1848-8013}, journal = {Mathematical Communications}, number = {1}, pages = {137--142}, publisher = {Udruga Matematicara Osijek}, title = {{A characterization of maps of bounded compression}}, volume = {29}, year = {2024}, } @inproceedings{15253, abstract = {We study the problem of maintaining a differentially private decaying sum under continual observation. We give a unifying framework and an efficient algorithm for this problem for any sufficiently smooth function. Our algorithm is the first differentially private algorithm that does not have a multiplicative error for polynomially decaying weights. Our algorithm improves on all prior works on differentially private decaying sums under continual observation and recovers exactly the additive error for the special case of continual counting from Henzinger et al. (SODA 2023) as a corollary. Our algorithm is a variant of the matrix mechanism whose error depends on the γ2 and γF norm of the underlying matrix. We give a constructive proof for an almost exact upper bound on the γ2 and γF norm and an almost tight lower bound on the γ2 norm for a large class of lower-triangular matrices. This is the first non-trivial lower bound for lower-triangular matrices whose non-zero entries are not all the same. It includes matrices for all continual decaying sums problems, resulting in an upper bound on the additive error of any differentially private decaying sums algorithm under continual observation. We also explore some implications of our result in discrepancy theory and operator algebra. Given the importance of the γ2 norm in computer science and the extensive work in mathematics, we believe our result will have further applications.}, author = {Henzinger, Monika H and Upadhyay, Jalaj and Upadhyay, Sarvagya}, booktitle = {Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Alexandria, VA, United States}, pages = {995--1018}, publisher = {Society for Industrial and Applied Mathematics}, title = {{A unifying framework for differentially private sums under continual observation}}, doi = {10.1137/1.9781611977912.38}, volume = {2024}, year = {2024}, } @article{15257, abstract = {Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.}, author = {Kulich, Ivan and Schmid, Julia and Teplova, Anastasiia and Qi, Linlin and Friml, Jiří}, issn = {2050-084X}, journal = {eLife}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience}, publisher = {eLife Sciences Publications}, title = {{Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism}}, doi = {10.7554/elife.91523}, volume = {12}, year = {2024}, } @article{15258, abstract = {Inclusion at academic events is facing increased scrutiny as the communities these events serve raise their expectations for who can practically attend. Active efforts in recent years to bring more diversity to academic events have brought progress and created momentum. However, we must reflect on these efforts and determine which underrepresented groups are being disadvantaged. Inclusion at academic events is important to ensure diversity of discourse and opinion, to help build networks, and to avoid academic siloing. All of these contribute to the development of a robust and resilient academic field. We have developed these Ten Simple Rules both to amplify the voices that have been speaking out and to celebrate the progress of many Equity, Diversity, and Inclusivity practices that continue to drive the organisation of academic events. The Rules aim to raise awareness as well as provide actionable suggestions and tools to support these initiatives further. This aims to support academic organisations such as the Deep Learning Indaba, Neuromatch Academy, the IBRO-Simons Computational Neuroscience Imbizo, Biodiversity Information Standards (TDWG), Arabs in Neuroscience, FAIRPoints, and OLS (formerly Open Life Science). This article is a call to action for organisers to reevaluate the impact and reach of their inclusive practices.}, author = {Hall, Siobhan Mackenzie and Kochin, Daniel and Carne, Carmel and Herterich, Patricia and Lewers, Kristen Lenay and Abdelhack, Mohamed and Ramasubramanian, Arun and Michael Alphonse, Juno Felecia and Ung, Visotheary and El-Gebali, Sara and Currin, Christopher and Plomp, Esther and Thompson, Rachel and Sharan, Malvika}, issn = {1553-7358}, journal = {PLOS Computational Biology}, number = {3}, publisher = {Public Library of Science}, title = {{Ten simple rules for pushing boundaries of inclusion at academic events}}, doi = {10.1371/journal.pcbi.1011797}, volume = {20}, year = {2024}, } @article{15295, abstract = {Background: Benzodiazepines and antidepressants are effective agents for the treatment of generalized anxiety disorder (GAD), with the HAM-A frequently used as a primary outcome measure. The GAD literature is inconsistent regarding which medications are more effective for somatic versus psychic symptoms of GAD, and treatment guidelines do not advocate for prescribing based on subtype. This meta-analysis aimed to determine whether benzodiazepines and antidepressants have a differential impact on the somatic versus psychic subscales of the HAM-A in GAD. Methods: An electronic search was undertaken for randomized controlled trials of either benzodiazepines or antidepressants for GAD that reported treatment response using the HAM-A subscales. Data were extracted by independent reviewers. A random effects assessment of weighted mean difference with 95% confidence intervals and subgroup difference was applied. All analysis was done on SPSS 26. An assessment of bias, and of quality of evidence was performed. Results: 24 randomized controlled trials met the inclusion criteria: 18 antidepressant trials, 5 benzodiazepine trials and 1 of both. 14 studies were assessed as having between some and high risk of bias, while 10 were assessed as having low risk of bias. Benzodiazepines (WMD of 1.81 [CI 1.03, 2.58]) were significantly more effective than antidepressants (WMD of 0.83 [CI 0.64, 1.02]) for reducing somatic symptoms of GAD (Chi2 = 5.81, p = 0.02), and were also more effective (WMD of 2.46 [CI 1.83, 3.09]) in reducing psychic symptoms than antidepressants (WMD of 1.83 [CI 1.55, 2.10]), although this comparison did not reach statistical significance (Chi2 = 3.31, p = 0.07). Conclusion: The finding that benzodiazepines were significantly more effective than antidepressants for somatic symptoms needs to be weighed up against potential benefits of antidepressants over benzodiazepines. It may be useful for future treatment guidelines for GAD to explicitly consider symptom subtype.}, author = {Beyer, Chad and Currin, Christopher and Williams, Taryn and Stein, Dan J.}, issn = {1532-8384}, journal = {Comprehensive Psychiatry}, publisher = {Elsevier}, title = {{Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder}}, doi = {10.1016/j.comppsych.2024.152479}, volume = {132}, year = {2024}, } @inproceedings{15296, abstract = {In this paper we build a constructive algorithm that returns a rectifiable curve that connects two points in a weakly convex set in a Hilbert space. We have proven that this algorithm converges and obtained an estimate on the curve’s length and compare the length of the curve obtained to known results.}, author = {Lopushanski, Mariana and Ivanov, Grigory}, booktitle = {AIP Conference Proceedings}, issn = {1551-7616}, location = {Virtual}, number = {1}, publisher = {AIP Publishing}, title = {{A constructive algorithm for building rectifiable curves in weakly convex sets}}, doi = {10.1063/5.0195908}, volume = {3030}, year = {2024}, } @article{15301, abstract = {Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.}, author = {Hörmayer, Lukas and Montesinos López, Juan C and Trozzi, N and Spona, Leonhard and Yoshida, Saiko and Marhavá, Petra and Caballero Mancebo, Silvia and Benková, Eva and Heisenberg, Carl-Philipp J and Dagdas, Y and Majda, M and Friml, Jiří}, issn = {1878-1551}, journal = {Developmental Cell}, number = {10}, pages = {1333--1344.e4}, publisher = {Elsevier}, title = {{Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization}}, doi = {10.1016/j.devcel.2024.03.009}, volume = {59}, year = {2024}, } @article{15313, abstract = {Our goal is to investigate fundamental properties of the system of internally cooled convection. The system consists of an upward thermal flux at the lower boundary, a mean temperature lapse-rate and a constant cooling term in the bulk with the bulk cooling in thermal equilibrium with the input heat flux. This simple model represents idealised dry convection in the atmospheric boundary layer, where the cooling mimics the radiative cooling to space notably through longwave radiation. We perform linear stability analysis of the model for different values of the mean stratification to derive the critical forcing above which the fluid is convectively unstable to small perturbations. The dynamic behavior of the fluid system is described and the scaling of various important measured quantities such as the total vertical convective heat flux and the upward mass flux is measured. We introduce a lapse-rate dependent dimensionless Rayleigh-number Ray that determines the behavior of the system, finding that the convective heat-flux and mass-flux scale approximately as Ray0.5 and Ray0.7 respectively. The area-fraction of the domain that is occupied by upward and downward moving fluid and the skewness of the vertical velocity are studied to understand the asymmetry inherent in the system. We conclude with a short discussion on the relevance to atmospheric convection and the scope for further investigations of atmospheric convection using similar simplified approaches.}, author = {Agasthya, Lokahith N and Muller, Caroline J}, issn = {1007-5704}, journal = {Communications in Nonlinear Science and Numerical Simulation}, publisher = {Elsevier}, title = {{Dynamics and scaling of internally cooled convection}}, doi = {10.1016/j.cnsns.2024.108011}, volume = {134}, year = {2024}, } @article{15314, abstract = {Development of electroactive materials exhibiting high performance with superior stability is crucial in the field of supercapacitors and battery research. We report on synthesis of highly stable composite of semi-polycrystalline polyaniline and graphene (SPani-graphene) and its application in supercapacitor electrodes. The electrochemical behavior and device performance of the electrodes were investigated through cyclic voltammetry (CV), galvanostatic charge-discharge GCD) and electrochemical impedance spectroscopy (EIS) in a 3-electrode and a 2-electrode (device) cell configurations, repectively. The cell specific capacitance (Cell Csp) achieved from the 2-electrode symmetric cell configuration was 525.5 F g−1 at 0.1 A g−1 using polymer gel electrolyte (PGE). The PGE in this work is xanthan gum jellied in 1 M aq. Na2SO4. The maximum energy density and power density achieved from the device was 46.7 Wh kg−1 and 16.16 kW kg−1, respectively, at 0.4 A g−1. Furthermore, the device exhibits an excellent retention of cell specific capacitance and coulombic efficiency of 97 % and 94 %, respectively, over 10,000 continuous GCD cycles, indicating an excellent rate capability as well as a promising power management. To investigate the material's electrochemical durability, a detailed EIS study has been carried out using both, 3-electrode, and 2-electrode cell configurations, before and after long cycling test (over 10,000 continuous GCD cycles). Our thorough experimentation delivers satisfactory results and has been explained in detail in the manuscript. Hereby, we propose that the EIS technique can be adopted for investigating materials' electrochemical stability, in addition to long CV and GCD cycles in the field of supercapacitors and battery research.}, author = {Mahato, Neelima and Singh, Saurabh and Sreekanth, T. V.M. and Yoo, Kisoo and Kim, Jonghoon}, issn = {2352-152X}, journal = {Journal of Energy Storage}, publisher = {Elsevier}, title = {{Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material's stability}}, doi = {10.1016/j.est.2024.111464}, volume = {88}, year = {2024}, } @article{15315, abstract = {Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.}, author = {Brückner, David and Broedersz, Chase P.}, issn = {1361-6633}, journal = {Reports on Progress in Physics}, number = {5}, publisher = {IOP Publishing}, title = {{Learning dynamical models of single and collective cell migration: a review}}, doi = {10.1088/1361-6633/ad36d2}, volume = {87}, year = {2024}, } @article{15316, abstract = {Genomic DNA that resides in the nuclei of mammalian neurons can be as old as the organism itself. The life span of nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. In this work, we identified and characterized nuclear RNAs that do not turn over for at least 2 years in a subset of postnatally born cells in the mouse brain. These long-lived RNAs were stably retained in nuclei in a neural cell type–specific manner and were required for the maintenance of heterochromatin. Thus, the life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information and also the extreme stability of RNA for the functional organization of chromatin.}, author = {Zocher, Sara and Mccloskey, Asako and Karasinsky, Anne and Schulte, Roberta and Friedrich, Ulrike and Lesche, Mathias and Rund, Nicole and Gage, Fred H. and Hetzer, Martin W and Toda, Tomohisa}, issn = {1095-9203}, journal = {Science}, number = {6691}, pages = {53--59}, publisher = {AAAS}, title = {{Lifelong persistence of nuclear RNAs in the mouse brain}}, doi = {10.1126/science.adf3481}, volume = {384}, year = {2024}, } @article{15317, abstract = {We consider the open symmetric exclusion (SEP) and inclusion (SIP) processes on a bounded Lipschitz domain Ω, with both fast and slow boundary. For the random walks on Ω dual to SEP/SIP we establish: a functional-CLT-type convergence to the Brownian motion on Ω with either Neumann (slow boundary), Dirichlet (fast boundary), or Robin (at criticality) boundary conditions; the discrete-to-continuum convergence of the corresponding harmonic profiles. As a consequence, we rigorously derive the hydrodynamic and hydrostatic limits for SEP/SIP on Ω, and analyze their stationary nonequilibrium fluctuations. All scaling limit results for SEP/SIP concern finite-dimensional distribution convergence only, as our duality techniques do not require to establish tightness for the fields associated to the particle systems.}, author = {Dello Schiavo, Lorenzo and Portinale, Lorenzo and Sau, Federico}, issn = {1050-5164}, journal = {Annals of Applied Probability}, number = {2}, pages = {1789--1845}, publisher = {Institute of Mathematical Statistics}, title = {{Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains}}, doi = {10.1214/23-AAP2007}, volume = {34}, year = {2024}, }