@article{13216,
  abstract     = {Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude.},
  author       = {Bunting, Rhys and Wodaczek, Felix and Torabi, Tina and Cheng, Bingqing},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
  number       = {27},
  pages        = {14894--14902},
  publisher    = {American Chemical Society},
  title        = {{Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane}},
  doi          = {10.1021/jacs.3c04030},
  volume       = {145},
  year         = {2023},
}

@article{13225,
  abstract     = {Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.},
  author       = {Benedikter, Niels P and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
  issn         = {1432-0673},
  journal      = {Archive for Rational Mechanics and Analysis},
  number       = {4},
  publisher    = {Springer Nature},
  title        = {{Correlation energy of a weakly interacting Fermi gas with large interaction potential}},
  doi          = {10.1007/s00205-023-01893-6},
  volume       = {247},
  year         = {2023},
}

@article{13226,
  abstract     = {We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.},
  author       = {Bossmann, Lea and Petrat, Sören P},
  issn         = {1573-0530},
  journal      = {Letters in Mathematical Physics},
  number       = {4},
  publisher    = {Springer Nature},
  title        = {{Weak Edgeworth expansion for the mean-field Bose gas}},
  doi          = {10.1007/s11005-023-01698-4},
  volume       = {113},
  year         = {2023},
}

@inproceedings{13228,
  abstract     = {A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox.},
  author       = {Henzinger, Thomas A and Karimi, Mahyar and Kueffner, Konstantin and Mallik, Kaushik},
  booktitle    = {FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency},
  isbn         = {9781450372527},
  location     = {Chicago, IL, United States},
  pages        = {604--614},
  publisher    = {Association for Computing Machinery},
  title        = {{Runtime monitoring of dynamic fairness properties}},
  doi          = {10.1145/3593013.3594028},
  year         = {2023},
}

@article{13229,
  abstract     = {Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.},
  author       = {Shamipour, Shayan and Hofmann, Laura and Steccari, Irene and Kardos, Roland and Heisenberg, Carl-Philipp J},
  issn         = {1545-7885},
  journal      = {PLoS Biology},
  number       = {6},
  pages        = {e3002146},
  publisher    = {Public Library of Science},
  title        = {{Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes}},
  doi          = {10.1371/journal.pbio.3002146},
  volume       = {21},
  year         = {2023},
}

@article{13230,
  abstract     = {To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.},
  author       = {Charlton, Julie A. and Mlynarski, Wiktor F and Bai, Yoon H. and Hermundstad, Ann M. and Goris, Robbe L.T.},
  issn         = {1553-7358},
  journal      = {PLoS Computational Biology},
  number       = {6},
  publisher    = {Public Library of Science},
  title        = {{Environmental dynamics shape perceptual decision bias}},
  doi          = {10.1371/journal.pcbi.1011104},
  volume       = {19},
  year         = {2023},
}

@article{13231,
  abstract     = {We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.},
  author       = {Schörner, Maximilian and Bethkenhagen, Mandy and Döppner, Tilo and Kraus, Dominik and Fletcher, Luke B. and Glenzer, Siegfried H. and Redmer, Ronald},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula}},
  doi          = {10.1103/PhysRevE.107.065207},
  volume       = {107},
  year         = {2023},
}

@article{13232,
  abstract     = {The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.},
  author       = {Dormeshkin, Dmitri and Katsin, Mikalai and Stegantseva, Maria and Golenchenko, Sergey and Shapira, Michail and Dubovik, Simon and Lutskovich, Dzmitry and Kavaleuski, Anton and Meleshko, Alexander},
  issn         = {2076-393X},
  journal      = {Vaccines},
  number       = {6},
  publisher    = {MDPI},
  title        = {{Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein}},
  doi          = {10.3390/vaccines11061014},
  volume       = {11},
  year         = {2023},
}

@article{13233,
  abstract     = {We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.},
  author       = {Agafonova, Sofya and Lemeshko, Mikhail and Volosniev, Artem},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Finite-range bias in fitting three-body loss to the zero-range model}},
  doi          = {10.1103/PhysRevA.107.L061304},
  volume       = {107},
  year         = {2023},
}

@article{13234,
  abstract     = {Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure.},
  author       = {Kueffner, Konstantin and Lukina, Anna and Schilling, Christian and Henzinger, Thomas A},
  issn         = {1433-2787},
  journal      = {International Journal on Software Tools for Technology Transfer},
  pages        = {575--592},
  publisher    = {Springer Nature},
  title        = {{Into the unknown: Active monitoring of neural networks (extended version)}},
  doi          = {10.1007/s10009-023-00711-4},
  volume       = {25},
  year         = {2023},
}

@article{13235,
  abstract     = {AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications.},
  author       = {Liu, Yu and Li, Mingquan and Wan, Shanhong and Lim, Khak Ho and Zhang, Yu and Li, Mengyao and Li, Junshan and Ibáñez, Maria and Hong, Min and Cabot, Andreu},
  issn         = {1936-086X},
  journal      = {ACS Nano},
  number       = {12},
  pages        = {11923–11934},
  publisher    = {American Chemical Society},
  title        = {{Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance}},
  doi          = {10.1021/acsnano.3c03541},
  volume       = {17},
  year         = {2023},
}

@inproceedings{13236,
  abstract     = {We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.},
  author       = {Zheng, Da Wei and Henzinger, Monika H},
  booktitle    = {International Conference on Integer Programming and Combinatorial Optimization},
  isbn         = {9783031327254},
  issn         = {1611-3349},
  location     = {Madison, WI, United States},
  pages        = {453--465},
  publisher    = {Springer Nature},
  title        = {{Multiplicative auction algorithm for approximate maximum weight bipartite matching}},
  doi          = {10.1007/978-3-031-32726-1_32},
  volume       = {13904},
  year         = {2023},
}

@article{13237,
  abstract     = {The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.},
  author       = {Michaels, Thomas C.T. and Qian, Daoyuan and Šarić, Anđela and Vendruscolo, Michele and Linse, Sara and Knowles, Tuomas P.J.},
  issn         = {2522-5820},
  journal      = {Nature Reviews Physics},
  pages        = {379–397},
  publisher    = {Springer Nature},
  title        = {{Amyloid formation as a protein phase transition}},
  doi          = {10.1038/s42254-023-00598-9},
  volume       = {5},
  year         = {2023},
}

@article{13251,
  abstract     = {A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.},
  author       = {Wei, Yujing and Volosniev, Artem and Lorenc, Dusan and Zhumekenov, Ayan A. and Bakr, Osman M. and Lemeshko, Mikhail and Alpichshev, Zhanybek},
  issn         = {1948-7185},
  journal      = {The Journal of Physical Chemistry Letters},
  keywords     = {General Materials Science, Physical and Theoretical Chemistry},
  number       = {27},
  pages        = {6309--6314},
  publisher    = {American Chemical Society},
  title        = {{Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites}},
  doi          = {10.1021/acs.jpclett.3c01158},
  volume       = {14},
  year         = {2023},
}

@article{13256,
  abstract     = {The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.},
  author       = {Goswami, Bidyut B and An, Soon Il},
  issn         = {2397-3722},
  journal      = {npj Climate and Atmospheric Science},
  publisher    = {Springer Nature},
  title        = {{An assessment of the ENSO-monsoon teleconnection in a warming climate}},
  doi          = {10.1038/s41612-023-00411-5},
  volume       = {6},
  year         = {2023},
}

@article{13257,
  abstract     = {The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.},
  author       = {Shekhter, A. and Mcdonald, R. D. and Ramshaw, B. J. and Modic, Kimberly A},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Magnetotropic susceptibility}},
  doi          = {10.1103/PhysRevB.108.035111},
  volume       = {108},
  year         = {2023},
}

@article{13258,
  abstract     = {Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.},
  author       = {Kleshnina, Maria and Hilbe, Christian and Simsa, Stepan and Chatterjee, Krishnendu and Nowak, Martin A.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{The effect of environmental information on evolution of cooperation in stochastic games}},
  doi          = {10.1038/s41467-023-39625-9},
  volume       = {14},
  year         = {2023},
}

@article{13259,
  abstract     = {Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.},
  author       = {Ogura, Nao and Sasagawa, Yohei and Ito, Tasuku and Tameshige, Toshiaki and Kawai, Satomi and Sano, Masaki and Doll, Yuki and Iwase, Akira and Kawamura, Ayako and Suzuki, Takamasa and Nikaido, Itoshi and Sugimoto, Keiko and Ikeuchi, Momoko},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {27},
  pages        = {eadg6983},
  publisher    = {American Association for the Advancement of Science},
  title        = {{WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus}},
  doi          = {10.1126/sciadv.adg6983},
  volume       = {9},
  year         = {2023},
}

@article{13260,
  abstract     = {Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.},
  author       = {De Castro Barbosa Rodrigues Barata, Carolina and Snook, Rhonda R. and Ritchie, Michael G. and Kosiol, Carolin},
  issn         = {1759-6653},
  journal      = {Genome biology and evolution},
  number       = {7},
  publisher    = {Oxford University Press},
  title        = {{Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura}},
  doi          = {10.1093/gbe/evad113},
  volume       = {15},
  year         = {2023},
}

@article{13261,
  abstract     = {Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.},
  author       = {Brückner, David and Chen, Hongtao and Barinov, Lev and Zoller, Benjamin and Gregor, Thomas},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6652},
  pages        = {1357--1362},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome}},
  doi          = {10.1126/science.adf5568},
  volume       = {380},
  year         = {2023},
}