@article{12239,
  abstract     = {Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.},
  author       = {Johnson, Alexander J and Kaufmann, Walter and Sommer, Christoph M and Costanzo, Tommaso and Dahhan, Dana A. and Bednarek, Sebastian Y. and Friml, Jiří},
  issn         = {1674-2052},
  journal      = {Molecular Plant},
  keywords     = {Plant Science, Molecular Biology},
  number       = {10},
  pages        = {1533--1542},
  publisher    = {Elsevier},
  title        = {{Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution}},
  doi          = {10.1016/j.molp.2022.09.003},
  volume       = {15},
  year         = {2022},
}

@article{12243,
  abstract     = {We consider the eigenvalues of a large dimensional real or complex Ginibre matrix in the region of the complex plane where their real parts reach their maximum value. This maximum follows the Gumbel distribution and that these extreme eigenvalues form a Poisson point process as the dimension asymptotically tends to infinity. In the complex case, these facts have already been established by Bender [Probab. Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips [J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with a sophisticated saddle point analysis. The purpose of this article is to give a very short direct proof in the Ginibre case with an effective error term. Moreover, our estimates on the correlation kernel in this regime serve as a key input for accurately locating [Formula: see text] for any large matrix X with i.i.d. entries in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. },
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J and Xu, Yuanyuan},
  issn         = {1089-7658},
  journal      = {Journal of Mathematical Physics},
  keywords     = {Mathematical Physics, Statistical and Nonlinear Physics},
  number       = {10},
  publisher    = {AIP Publishing},
  title        = {{Directional extremal statistics for Ginibre eigenvalues}},
  doi          = {10.1063/5.0104290},
  volume       = {63},
  year         = {2022},
}

@article{12244,
  abstract     = {Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.},
  author       = {Colombo, Gloria and Cubero, Ryan J and Kanari, Lida and Venturino, Alessandro and Schulz, Rouven and Scolamiero, Martina and Agerberg, Jens and Mathys, Hansruedi and Tsai, Li-Huei and Chachólski, Wojciech and Hess, Kathryn and Siegert, Sandra},
  issn         = {1546-1726},
  journal      = {Nature Neuroscience},
  keywords     = {General Neuroscience},
  number       = {10},
  pages        = {1379--1393},
  publisher    = {Springer Nature},
  title        = {{A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes}},
  doi          = {10.1038/s41593-022-01167-6},
  volume       = {25},
  year         = {2022},
}

@article{12245,
  abstract     = {MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.},
  author       = {Soto, Ximena and Burton, Joshua and Manning, Cerys S. and Minchington, Thomas and Lea, Robert and Lee, Jessica and Kursawe, Jochen and Rattray, Magnus and Papalopulu, Nancy},
  issn         = {1477-9129},
  journal      = {Development},
  keywords     = {Developmental Biology, Molecular Biology},
  number       = {19},
  publisher    = {The Company of Biologists},
  title        = {{Sequential and additive expression of miR-9 precursors control timing of neurogenesis}},
  doi          = {10.1242/dev.200474},
  volume       = {149},
  year         = {2022},
}

@article{12246,
  abstract     = {The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of a classical system of N identical charges only in terms of their one-particle density. We prove here a new estimate on the best constant in this inequality. Numerical evaluation provides the value 1.58, which is a significant improvement to the previously known value 1.64. The best constant has recently been shown to be larger than 1.44. In a second part, we prove that the constant can be reduced to 1.25 when the inequality is restricted to Hartree–Fock states. This is the first proof that the exchange term is always much lower than the full indirect Coulomb energy.},
  author       = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert},
  issn         = {1573-0530},
  journal      = {Letters in Mathematical Physics},
  keywords     = {Mathematical Physics, Statistical and Nonlinear Physics},
  number       = {5},
  publisher    = {Springer Nature},
  title        = {{Improved Lieb–Oxford bound on the indirect and exchange energies}},
  doi          = {10.1007/s11005-022-01584-5},
  volume       = {112},
  year         = {2022},
}

@article{12247,
  abstract     = {Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.},
  author       = {Koch, Eva L. and Ravinet, Mark and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K.},
  issn         = {1558-5646},
  journal      = {Evolution},
  keywords     = {General Agricultural and Biological Sciences, Genetics, Ecology, Evolution, Behavior and Systematics},
  number       = {10},
  pages        = {2332--2346},
  publisher    = {Wiley},
  title        = {{Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution}},
  doi          = {10.1111/evo.14602},
  volume       = {76},
  year         = {2022},
}

@article{12248,
  abstract     = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.},
  author       = {Elkrewi, Marwan N and Khauratovich, Uladzislava and Toups, Melissa A and Bett, Vincent K and Mrnjavac, Andrea and Macon, Ariana and Fraisse, Christelle and Sax, Luca and Huylmans, Ann K and Hontoria, Francisco and Vicoso, Beatriz},
  issn         = {1943-2631},
  journal      = {Genetics},
  keywords     = {Genetics},
  number       = {2},
  publisher    = {Oxford University Press},
  title        = {{ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp}},
  doi          = {10.1093/genetics/iyac123},
  volume       = {222},
  year         = {2022},
}

@article{12249,
  abstract     = {The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. },
  author       = {Cheng, Bingqing},
  issn         = {1089-7690},
  journal      = {The Journal of Chemical Physics},
  keywords     = {Physical and Theoretical Chemistry, General Physics and Astronomy},
  number       = {12},
  publisher    = {AIP Publishing},
  title        = {{Computing chemical potentials of solutions from structure factors}},
  doi          = {10.1063/5.0107059},
  volume       = {157},
  year         = {2022},
}

@article{12251,
  abstract     = {Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions <jats:italic>in vitro</jats:italic> and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.},
  author       = {Weiffert, Tanja and Meisl, Georg and Curk, Samo and Cukalevski, Risto and Šarić, Anđela and Knowles, Tuomas P. J. and Linse, Sara},
  issn         = {1662-453X},
  journal      = {Frontiers in Neuroscience},
  keywords     = {General Neuroscience},
  publisher    = {Frontiers Media},
  title        = {{Influence of denaturants on amyloid β42 aggregation kinetics}},
  doi          = {10.3389/fnins.2022.943355},
  volume       = {16},
  year         = {2022},
}

@article{12252,
  abstract     = {The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 10<jats:sup>11</jats:sup> diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and 9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.},
  author       = {Dormeshkin, Dmitri and Shapira, Michail and Dubovik, Simon and Kavaleuski, Anton and Katsin, Mikalai and Migas, Alexandr and Meleshko, Alexander and Semyonov, Sergei},
  issn         = {1664-3224},
  journal      = {Frontiers in Immunology},
  keywords     = {Immunology, Immunology and Allergy, COVID-19, SARS-CoV-2, synthetic library, RBD, neutralization nanobody, VHH},
  publisher    = {Frontiers Media},
  title        = {{Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library}},
  doi          = {10.3389/fimmu.2022.965446},
  volume       = {13},
  year         = {2022},
}

@article{12253,
  abstract     = {The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.},
  author       = {Stock, Jessica and Kazmar, Tomas and Schlumm, Friederike and Hannezo, Edouard B and Pauli, Andrea},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {37},
  publisher    = {American Association for the Advancement of Science},
  title        = {{A self-generated Toddler gradient guides mesodermal cell migration}},
  doi          = {10.1126/sciadv.add2488},
  volume       = {8},
  year         = {2022},
}

@article{12257,
  abstract     = {Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.},
  author       = {Chatterjee, Krishnendu and Svoboda, Jakub and Zikelic, Dorde and Pavlogiannis, Andreas and Tkadlec, Josef},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Social balance on networks: Local minima and best-edge dynamics}},
  doi          = {10.1103/physreve.106.034321},
  volume       = {106},
  year         = {2022},
}

@article{12259,
  abstract     = {Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. },
  author       = {Choueiri, George H and Suri, Balachandra and Merrin, Jack and Serbyn, Maksym and Hof, Björn and Budanur, Nazmi B},
  issn         = {1089-7682},
  journal      = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
  keywords     = {Applied Mathematics, General Physics and Astronomy, Mathematical Physics, Statistical and Nonlinear Physics},
  number       = {9},
  publisher    = {AIP Publishing},
  title        = {{Crises and chaotic scattering in hydrodynamic pilot-wave experiments}},
  doi          = {10.1063/5.0102904},
  volume       = {32},
  year         = {2022},
}

@article{12261,
  abstract     = {Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.},
  author       = {Angermayr, Andreas and Pang, Tin Yau and Chevereau, Guillaume and Mitosch, Karin and Lercher, Martin J and Bollenbach, Mark Tobias},
  issn         = {1744-4292},
  journal      = {Molecular Systems Biology},
  keywords     = {Applied Mathematics, Computational Theory and Mathematics, General Agricultural and Biological Sciences, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, Information Systems},
  number       = {9},
  publisher    = {Embo Press},
  title        = {{Growth‐mediated negative feedback shapes quantitative antibiotic response}},
  doi          = {10.15252/msb.202110490},
  volume       = {18},
  year         = {2022},
}

@article{12264,
  abstract     = {Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.},
  author       = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H},
  issn         = {1420-9101},
  journal      = {Journal of Evolutionary Biology},
  keywords     = {Ecology, Evolution, Behavior and Systematics},
  number       = {9},
  pages        = {1143--1164},
  publisher    = {Wiley},
  title        = {{What is reproductive isolation?}},
  doi          = {10.1111/jeb.14005},
  volume       = {35},
  year         = {2022},
}

@article{12265,
  author       = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H},
  issn         = {1420-9101},
  journal      = {Journal of Evolutionary Biology},
  keywords     = {Ecology, Evolution, Behavior and Systematics},
  number       = {9},
  pages        = {1200--1205},
  publisher    = {Wiley},
  title        = {{Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’}},
  doi          = {10.1111/jeb.14082},
  volume       = {35},
  year         = {2022},
}

@article{12268,
  abstract     = {The complexity of the microenvironment effects on cell response, show accumulating evidence that glioblastoma (GBM) migration and invasiveness are influenced by the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition (EMT) is a well-recognized driving force of the invasive behavior of cancer. However, the primary mechanisms of EMT initiation and progression remain unclear. We have previously showed that certain substrate stiffness can selectively stimulate human GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies several known EMT mediators to uncover the reason of the regulation and response to these stiffnesses. Our results revealed that changing the rigidity of the mechanical environment tuned the response of both cell lines through change in morphological features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions in an interrelated manner. Specifically, a stiffer microenvironment induced a mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic ROS expression and lower mitochondrial ROS. Finally, we observed that cells more motile showed a more depolarized mitochondrial membrane potential. Unravelling the process that regulates GBM cells’ infiltrative behavior could provide new opportunities for identification of new targets and less invasive approaches for treatment.},
  author       = {Basilico, Bernadette and Palamà, Ilaria Elena and D’Amone, Stefania and Lauro, Clotilde and Rosito, Maria and Grieco, Maddalena and Ratano, Patrizia and Cordella, Federica and Sanchini, Caterina and Di Angelantonio, Silvia and Ragozzino, Davide and Cascione, Mariafrancesca and Gigli, Giuseppe and Cortese, Barbara},
  issn         = {2234-943X},
  journal      = {Frontiers in Oncology},
  keywords     = {Cancer Research, Oncology},
  publisher    = {Frontiers Media},
  title        = {{Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells}},
  doi          = {10.3389/fonc.2022.983507},
  volume       = {12},
  year         = {2022},
}

@article{12269,
  abstract     = {We study the thermalization of a small XX chain coupled to long, gapped XXZ leads at either side by observing the relaxation dynamics of the whole system. Using extensive tensor network simulations, we show that such systems, although not integrable, appear to show either extremely slow thermalization or even lack thereof since the two cannot be distinguished within the accuracy of our numerics. We show that the persistent oscillations observed in the spin current in the middle of the XX chain are related to eigenstates of the entire system located within the gap of the boundary chains. We find from exact diagonalization that some of these states remain strictly localized within the XX chain and do not hybridize with the rest of the system. The frequencies of the persistent oscillations determined by numerical simulations of dynamics match the energy differences between these states exactly. This has important implications for open systems, where the strongly interacting leads are often assumed to thermalize the central system. Our results suggest that, if we employ gapped systems for the leads, this assumption does not hold.},
  author       = {Ljubotina, Marko and Roy, Dibyendu and Prosen, Tomaž},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Absence of thermalization of free systems coupled to gapped interacting reservoirs}},
  doi          = {10.1103/physrevb.106.054314},
  volume       = {106},
  year         = {2022},
}

@article{12272,
  abstract     = {Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant.},
  author       = {Stopp, Julian A and Sixt, Michael K},
  issn         = {1540-8140},
  journal      = {Journal of Cell Biology},
  keywords     = {Cell Biology},
  number       = {8},
  publisher    = {Rockefeller University Press},
  title        = {{Plan your trip before you leave: The neutrophils’ search-and-run journey}},
  doi          = {10.1083/jcb.202206127},
  volume       = {221},
  year         = {2022},
}

@article{12273,
  abstract     = {We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping.},
  author       = {Zhang, Yihan and Vatedka, Shashank and Jaggi, Sidharth and Sarwate, Anand D.},
  issn         = {1557-9654},
  journal      = {IEEE Transactions on Information Theory},
  number       = {8},
  pages        = {4901--4948},
  publisher    = {Institute of Electrical and Electronics Engineers},
  title        = {{Quadratically constrained myopic adversarial channels}},
  doi          = {10.1109/tit.2022.3167554},
  volume       = {68},
  year         = {2022},
}