@article{17191,
  abstract     = {Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway.},
  author       = {Lembo, Sergio and Sixt, Michael K},
  issn         = {1529-2916},
  journal      = {Nature Immunology},
  pages        = {1131–1132 },
  publisher    = {Springer Nature},
  title        = {{Nuclear squeezing wakes up dendritic cells}},
  doi          = {10.1038/s41590-024-01881-2},
  volume       = {25},
  year         = {2024},
}

@misc{17196,
  abstract     = {This .zip File contains the data for the figures presented in the main text and supplementary material of "A gate tunable transmon qubit in planar Ge" by O.Sagi et al. The measurements were done using Qcodes. The description of the files and the instructions on opening the data can be found in the Readme. An additional Jupyter Notebook is attached that walks through the data analysis.},
  author       = {Sagi, Oliver},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A gate-tunable transmon in planar Ge}},
  doi          = {10.15479/AT:ISTA:17196},
  year         = {2024},
}

@article{18444,
  abstract     = {Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations.},
  author       = {Pokusaeva, Victoria and Satapathy, Roshan K and Symonova, Olga and Jösch, Maximilian A},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies}},
  doi          = {10.1038/s41467-024-53173-w},
  volume       = {15},
  year         = {2024},
}

@article{18445,
  abstract     = {Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus.},
  author       = {Zupančič, Maja and Keimpema, Erik and Tretiakov, Evgenii O. and Eder, Stephanie J. and Lev, Itamar and Englmaier, Lukas and Bhandari, Pradeep and Fietz, Simone A. and Härtig, Wolfgang and Renaux, Estelle and Villunger, Andreas and Hökfelt, Tomas and Zimmer, Manuel and Clotman, Frédéric and Harkany, Tibor},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3}},
  doi          = {10.1038/s41467-024-52762-z},
  volume       = {15},
  year         = {2024},
}

@article{18446,
  abstract     = {How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.},
  author       = {Fabrèges, Dimitri and Corominas-Murtra, Bernat and Moghe, Prachiti and Kickuth, Alison and Ichikawa, Takafumi and Iwatani, Chizuru and Tsukiyama, Tomoyuki and Daniel, Nathalie and Gering, Julie and Stokkermans, Anniek and Wolny, Adrian and Kreshuk, Anna and Duranthon, Véronique and Uhlman, Virginie and Hannezo, Edouard B and Hiiragi, Takashi},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6718},
  publisher    = {AAAS},
  title        = {{Temporal variability and cell mechanics control robustness in mammalian embryogenesis}},
  doi          = {10.1126/science.adh1145},
  volume       = {386},
  year         = {2024},
}

@article{18451,
  abstract     = {Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials.},
  author       = {Zhou, Yu and Shaukat, Ahmed and Seitsonen, Jani and Rigoni, Carlo and Timonen, Jaakko V.I. and Kostiainen, Mauri A.},
  issn         = {2198-3844},
  journal      = {Advanced Science},
  number       = {45},
  publisher    = {Wiley},
  title        = {{Protein cage directed assembly of binary nanoparticle superlattices}},
  doi          = {10.1002/advs.202408416},
  volume       = {11},
  year         = {2024},
}

@article{18465,
  abstract     = {The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.},
  author       = {Janacek, DP and Kolb, M and Schulz, L and Mergner, J and Kuster, B and Glanc, Matous and Friml, Jiří and Ten Tusscher, K and Schwechheimer, C and Hammes, UZ},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {14},
  pages        = {S1534--5807(24)00569--0},
  publisher    = {Elsevier},
  title        = {{Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport}},
  doi          = {10.1016/j.devcel.2024.09.020},
  volume       = {59},
  year         = {2024},
}

@article{18479,
  abstract     = {The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance.},
  author       = {Mcdonough, Yasmine and Ruzicka, Filip and Connallon, Tim},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {44},
  publisher    = {National Academy of Sciences},
  title        = {{Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes}},
  doi          = {10.1073/pnas.2406335121},
  volume       = {121},
  year         = {2024},
}

@article{18480,
  abstract     = {Caloric restriction (CR) can extend the organism life- and health-span by improving glucose homeostasis. How CR affects the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that beta cells upon CR are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive proliferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging hallmarks and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes.},
  author       = {Dos Santos, Cristiane and Cambraia, Amanda and Shrestha, Shristi and Cutler, Melanie and Cottam, Matthew and Perkins, Guy and Lev-Ram, Varda and Roy, Birbickram and Acree, Christopher and Kim, Keun Young and Deerinck, Thomas and Dean, Danielle and Cartailler, Jean Philippe and Macdonald, Patrick E. and Hetzer, Martin W and Ellisman, Mark and Arrojo E Drigo, Rafael},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice}},
  doi          = {10.1038/s41467-024-53127-2},
  volume       = {15},
  year         = {2024},
}

@article{18481,
  abstract     = {A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.},
  author       = {Ho, Richard D.J.G. and Kishi, Kasumi and Majka, Maciej and Kicheva, Anna and Zagórski, Marcin P},
  issn         = {1553-7358},
  journal      = {PLoS Computational Biology},
  publisher    = {Public Library of Science},
  title        = {{Dynamics of morphogen source formation in a growing tissue}},
  doi          = {10.1371/journal.pcbi.1012508},
  volume       = {20},
  year         = {2024},
}

@article{18482,
  abstract     = {This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ 
Rn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied.},
  author       = {Arkhipov, Pavel},
  issn         = {1608-3032},
  journal      = {Automation and Remote Control},
  number       = {6},
  pages        = {522--532},
  publisher    = {Springer Nature},
  title        = {{An algorithm for finding the generalized Chebyshev center of sets defined via their support functions}},
  doi          = {10.1134/S0005117924060031},
  volume       = {85},
  year         = {2024},
}

@article{18483,
  abstract     = {In this paper we prove a perturbative version of a remarkable Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric convex domain with integrable billiard is ellipse. We combine techniques from Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally symmetric one with integrable billiard is ellipse. To combine these results we derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by proving that a notion of rational integrability is equivalent to the C0-integrability condition used in their paper.},
  author       = {Kaloshin, Vadim and Koudjinan, Edmond and Zhang, Ke},
  issn         = {1420-8970},
  journal      = {Geometric and Functional Analysis},
  pages        = {1973--2007},
  publisher    = {Springer Nature},
  title        = {{Birkhoff conjecture for nearly centrally symmetric domains}},
  doi          = {10.1007/s00039-024-00695-6},
  volume       = {34},
  year         = {2024},
}

@article{18488,
  abstract     = {The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum.},
  author       = {Ljubotina, Marko and Petrova, Elena and Schuch, Norbert and Serbyn, Maksym},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{Tangent space generators of matrix product states and exact floquet quantum scars}},
  doi          = {10.1103/prxquantum.5.040311},
  volume       = {5},
  year         = {2024},
}

@article{18490,
  abstract     = {For large classes of even-dimensional Riemannian manifolds (Formula presented.), we construct and analyze conformally invariant random fields. These centered Gaussian fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized by their covariance kernels k which exhibit a precise logarithmic divergence: (Formula presented.). They share a fundamental quasi-invariance property under conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula presented.), we define the Liouville Quantum Gravity measure, a random measure on (Formula presented.), heuristically given as (Formula presented.) and rigorously obtained as almost sure weak limit of the right-hand side with (Formula presented.) replaced by suitable regular approximations (Formula presented.). In terms on the Liouville Quantum Gravity measure, we define the Liouville Brownian motion on (Formula presented.) and the random GJMS operators. Finally, we present an approach to a conformal field theory in arbitrary even dimension with an ansatz based on Branson's (Formula presented.) -curvature: we give a rigorous meaning to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding conformal anomaly. The set of admissible manifolds is conformally invariant. It includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively curved Einstein manifolds of even dimension, and large classes of compact hyperbolic manifolds of even dimension. However, not every compact even-dimensional Riemannian manifold is admissible. Our results concerning the logarithmic divergence of the kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher order Green kernels on arbitrary closed manifolds. },
  author       = {Dello Schiavo, Lorenzo and Herry, Ronan and Kopfer, Eva and Sturm, Karl Theodor},
  issn         = {1469-7750},
  journal      = {Journal of the London Mathematical Society},
  number       = {5},
  publisher    = {London Mathematical Society},
  title        = {{Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension}},
  doi          = {10.1112/jlms.70003},
  volume       = {110},
  year         = {2024},
}

@article{18491,
  abstract     = {Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.},
  author       = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {41},
  publisher    = {AAAS},
  title        = {{Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails}},
  doi          = {10.1126/sciadv.adp2102},
  volume       = {10},
  year         = {2024},
}

@article{18494,
  abstract     = {We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates.},
  author       = {Eilers, Anna Christina and Mackenzie, Ruari and Pizzati, Elia and Matthee, Jorryt J and Hennawi, Joseph F. and Zhang, Haowen and Bordoloi, Rongmon and Kashino, Daichi and Lilly, Simon J. and Naidu, Rohan P. and Simcoe, Robert A. and Yue, Minghao and Frenk, Carlos S. and Helly, John C. and Schaller, Matthieu and Schaye, Joop},
  issn         = {1538-4357},
  journal      = {Astrophysical Journal},
  number       = {2},
  publisher    = {IOP Publishing},
  title        = {{EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6}},
  doi          = {10.3847/1538-4357/ad778b},
  volume       = {974},
  year         = {2024},
}

@misc{18498,
  abstract     = {Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715},
  author       = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M},
  publisher    = {Zenodo},
  title        = {{Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails}},
  doi          = {10.5281/ZENODO.12159343},
  year         = {2024},
}

@inproceedings{18503,
  abstract     = {In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time O(m log3 n) which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In this paper, we give the first deterministic algorithm which runs in near-linear time for weighted graphs.
Previously, the breakthrough results of Kawarabayashi and Thorup [KT19] gave a near-linear time algorithm for simple graphs (which was improved to have running time O(m log2 n log log n) in [HRW20].) The main technique here is a clustering procedure that perfectly preserves minimum cuts. Recently, Li [Li21] gave an m1+o(1) deterministic minimum-cut algorithm for weighted graphs; this form of running time has been termed “almost-linear”. Li uses almost-linear time deterministic expander decompositions which do not perfectly preserve minimum cuts, but he can use these clusterings to, in a sense, “derandomize” the methods of Karger.
In terms of techniques, we provide a structural theorem that says there exists a sparse clustering that preserves minimum cuts in a weighted graph with o(1) error. In addition, we construct it deterministically in near linear time. This was done exactly for simple graphs in [KT19, HRW20] and with polylogarithmic error for weighted graphs in [Li21]. Extending the techniques in [KT19, HRW20] to weighted graphs presents significant challenges, and moreover, the algorithm can only polylogarithmically approximately preserve minimum cuts. A remaining challenge is to reduce the polylogarithmic-approximate clusterings to 1 + o(1/ log n)-approximate so that they can be applied recursively as in [Li21] over O(log n) many levels. This is an additional challenge that requires building on properties of tree-packings in the presence of a wide range of edge weights to, for example, find sources for local flow computations which identify minimum cuts that cross clusters.},
  author       = {Henzinger, Monika H and Li, Jason and Rao, Satish and Wang, Di},
  booktitle    = {35th Annual ACM-SIAM Symposium on Discrete Algorithms},
  location     = {Alexandria, VA,  United States},
  pages        = {3089--3139},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Deterministic near-linear time minimum cut in weighted graphs}},
  doi          = {10.1137/1.9781611977912.111},
  year         = {2024},
}

@phdthesis{18515,
  abstract     = {Understanding the role of evolutionary processes in shaping genetic variation has been a
primary goal in evolutionary genetics. In this regard, a key question is how genetically
distinct populations evolve in the face of gene flow, thereby generating genetic and
phenotypic divergence and reproductive isolation (RI). This requires quantifying the role
and relative contributions of prezygotic and postzygotic isolating mechanisms on the
reduction of gene exchange between populations, and identifying regions in the genome
that mediate RI, which is often polygenic. Further, this needs distinguishing neutral and
selected regions in the genome, and discerning how selection influences patterns of neutral
divergence.
Population structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is
structured in space and shapes the neutral null model. Availability of large scale spatial
genomic datasets now enables us to detect signatures of population structure in genetic
data and infer population genetic parameters. Such inferences are crucial and have wide
applications in biodiversity, conservation genetics, population management and medical
genetics. However, inferences are based on assumptions that do not always match the
complex reality, thus leading to erroneous conclusions. Moreover, the role and interaction
of heterogeneous population density and dispersal, which are ubiquitous in nature, has
been challenging to study owing to their mathematical complexity. In such scenarios,
feedback between theory, data and simulations can prove to be useful.
In this thesis, I examine the effect of population structure on neutral genetic variation
and barriers to gene exchange in hybridising populations, thereby bridging together the
fields of spatial population genetics and speciation.
Despite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative
definition and has been used and measured differently across different fields. Chapter 2
gives a quantitative definition of RI, in terms of the effect of genetic differences on gene
flow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.
In addition to this, we discuss current measures of RI and their limitations, and propose
the need for new measures that combine organismal and genetic perspectives of RI.
In chapter 3, I examine the combined effect of assortative mating, sexual selection
and viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a
mainland-island model. We obtain novel theoretical predictions for molecular divergence
in terms of effective migration rates, which bears a simple relationship to measurable
fitness components of migrants and various early generation hybrids. We explore the
conditions under which local adaptation can be maintained despite maladaptive gene flow
and quantify the relative contributions of viability and sexual selection to genome-wide
barriers to gene flow.
The next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that
consist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow
flowered A.m. striatum. Previous studies have suggested that flower colour is target of
pollinator mediated selection and is influenced only by few genes. While these regions
show high genetic differentiation between the subspecies, the rest of the genome is seen
to be well mixed. Chapter 4 examines the effects of heterogeneous population density
and leptokurtic dispersal on isolation by distance and the distribution of heterozygosity
by focusing on non-flower colour markers.
Chapter 5 analyses cline shapes and associations among 6 focal flower colour markers to
understand how selection and dispersal maintain this hybrid zone. We see sharp coincident
stepped clines at all loci and positive associations throughout the hybrid zone, contrary to
the expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal
combined with multilocus simulations, we show that stepped clines do not reflect genetic
barriers to gene flow, but are rather a result of long-distance migration. This framework
allows us to get realistic estimates gene flow and selection and shows how traditional cline
analysis may lead to inaccurate conclusions when assumptions of the theory are not met.
Overall, this thesis investigates how different features of population structure leave
detectable signatures in genetic variation, namely in patterns of isolation by distance,
linkage disequilibrium and genetic divergence. It also highlights how effective migration
rates provide useful way of analysing polygenic architectures and shed new light into
hybrid zones. In doing so, I identify scenarios when simple models become insufficient
and suggest possibe directions by combining genetic data with simulations.},
  author       = {Surendranadh, Parvathy},
  issn         = {2663-337X},
  pages        = {219},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effect of population structure on neutral genetic variation and barriers to gene exchange}},
  doi          = {10.15479/at:ista:18515},
  year         = {2024},
}

@inproceedings{18521,
  abstract     = {In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples.},
  author       = {Bonakdarpour, Borzoo and Momtaz, Anik and Nickovic, Dejan and Sarac, Naci E},
  booktitle    = {24th International Conference on Runtime Verification},
  isbn         = {9783031742330},
  issn         = {1611-3349},
  location     = {Istanbul, Turkey},
  pages        = {282--301},
  publisher    = {Springer Nature},
  title        = {{Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy}},
  doi          = {10.1007/978-3-031-74234-7_18},
  volume       = {15191},
  year         = {2024},
}