@inproceedings{11181,
  abstract     = {To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance.},
  author       = {Brown, Trevor A and Sigouin, William and Alistarh, Dan-Adrian},
  booktitle    = {Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming},
  isbn         = {9781450392044},
  location     = {Seoul, Republic of Korea},
  pages        = {385--399},
  publisher    = {Association for Computing Machinery},
  title        = {{PathCAS: An efficient middle ground for concurrent search data structures}},
  doi          = {10.1145/3503221.3508410},
  year         = {2022},
}

@article{11182,
  abstract     = {Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.},
  author       = {Kroll, Janina and Ruiz-Fernandez, Mauricio J.A. and Braun, Malte B. and Merrin, Jack and Renkawitz, Jörg},
  issn         = {2691-1299},
  journal      = {Current Protocols},
  number       = {4},
  publisher    = {Wiley},
  title        = {{Quantifying the probing and selection of microenvironmental pores by motile immune cells}},
  doi          = {10.1002/cpz1.407},
  volume       = {2},
  year         = {2022},
}

@inproceedings{11183,
  abstract     = {Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:
- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.
- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.
- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems.},
  author       = {Nikabadi, Amir and Korhonen, Janne},
  booktitle    = {25th International Conference on Principles of Distributed Systems},
  editor       = {Bramas, Quentin and Gramoli, Vincent and Milani, Alessia},
  isbn         = {9783959772198},
  issn         = {1868-8969},
  location     = {Strasbourg, France},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters}},
  doi          = {10.4230/LIPIcs.OPODIS.2021.15},
  volume       = {217},
  year         = {2022},
}

@inproceedings{11184,
  abstract     = {Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node.
In this work, we consider the more general setting where G is an arbitrary regular graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As a sample application, we show that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties. We believe our results will prove generally useful, as they allow efficient technology transfer between the well-mixed (clique) case, and the under-explored spatial setting.},
  author       = {Alistarh, Dan-Adrian and Gelashvili, Rati and Rybicki, Joel},
  booktitle    = {25th International Conference on Principles of Distributed Systems},
  editor       = {Bramas, Quentin and Gramoli, Vincent and Milani, Alessia},
  isbn         = {9783959772198},
  issn         = {1868-8969},
  location     = {Strasbourg, France},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Fast graphical population protocols}},
  doi          = {10.4230/LIPIcs.OPODIS.2021.14},
  volume       = {217},
  year         = {2022},
}

@inproceedings{11185,
  abstract     = {Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite.},
  author       = {Arroyo Guevara, Alan M and Felsner, Stefan},
  booktitle    = {WALCOM 2022: Algorithms and Computation},
  isbn         = {9783030967307},
  issn         = {1611-3349},
  location     = {Jember, Indonesia},
  pages        = {383--395},
  publisher    = {Springer Nature},
  title        = {{Approximating the bundled crossing number}},
  doi          = {10.1007/978-3-030-96731-4_31},
  volume       = {13174},
  year         = {2022},
}

@article{11186,
  abstract     = {In this note, we study large deviations of the number  𝐍  of intercalates ( 2×2  combinatorial subsquares which are themselves Latin squares) in a random  𝑛×𝑛  Latin square. In particular, for constant  𝛿>0  we prove that  exp(−𝑂(𝑛2log𝑛))⩽Pr(𝐍⩽(1−𝛿)𝑛2/4)⩽exp(−Ω(𝑛2))  and  exp(−𝑂(𝑛4/3(log𝑛)))⩽Pr(𝐍⩾(1+𝛿)𝑛2/4)⩽exp(−Ω(𝑛4/3(log𝑛)2/3)) . As a consequence, we deduce that a typical order- 𝑛  Latin square has  (1+𝑜(1))𝑛2/4  intercalates, matching a lower bound due to Kwan and Sudakov and resolving an old conjecture of McKay and Wanless.},
  author       = {Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab},
  issn         = {1469-2120},
  journal      = {Bulletin of the London Mathematical Society},
  number       = {4},
  pages        = {1420--1438},
  publisher    = {Wiley},
  title        = {{Large deviations in random latin squares}},
  doi          = {10.1112/blms.12638},
  volume       = {54},
  year         = {2022},
}

@article{11187,
  abstract     = {During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.},
  author       = {Knyazev, Sergey and Chhugani, Karishma and Sarwal, Varuni and Ayyala, Ram and Singh, Harman and Karthikeyan, Smruthi and Deshpande, Dhrithi and Baykal, Pelin Icer and Comarova, Zoia and Lu, Angela and Porozov, Yuri and Vasylyeva, Tetyana I. and Wertheim, Joel O. and Tierney, Braden T. and Chiu, Charles Y. and Sun, Ren and Wu, Aiping and Abedalthagafi, Malak S. and Pak, Victoria M. and Nagaraj, Shivashankar H. and Smith, Adam L. and Skums, Pavel and Pasaniuc, Bogdan and Komissarov, Andrey and Mason, Christopher E. and Bortz, Eric and Lemey, Philippe and Kondrashov, Fyodor and Beerenwinkel, Niko and Lam, Tommy Tsan Yuk and Wu, Nicholas C. and Zelikovsky, Alex and Knight, Rob and Crandall, Keith A. and Mangul, Serghei},
  issn         = {1548-7105},
  journal      = {Nature Methods},
  number       = {4},
  pages        = {374--380},
  publisher    = {Springer Nature},
  title        = {{Unlocking capacities of genomics for the COVID-19 response and future pandemics}},
  doi          = {10.1038/s41592-022-01444-z},
  volume       = {19},
  year         = {2022},
}

@phdthesis{11193,
  abstract     = {The infiltration of immune cells into tissues underlies the establishment of tissue-resident
macrophages and responses to infections and tumors. However, the mechanisms immune
cells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.
In this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to
overcome the tissue barrier of the germband in the embryo. One strategy is the strengthening
of the actin cortex through developmentally controlled transcriptional regulation induced by
the Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces
expression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the
activated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical
strength allows hemocytes to overcome the physical resistance of the surrounding tissue and
translocate their nucleus to move forward. This mechanism affects the speed of migration
when hemocytes face a confined environment in vivo.
Another aspect of the invasion process is the initial step of the leading hemocytes entering
the tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel
subpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads
penetration into the germband. Hemocytes that are deficient in BMP signaling activation
show impaired persistence at the tissue entry, while their migration speed remains
unaffected.
This suggests that there might be different mechanisms controlling immune cell migration
within the confined environment in vivo, one of these being the general ability to overcome
the resistance of the surrounding tissue and another affecting the order of hemocytes that
collectively invade the tissue in a stream of individual cells.
Together, my findings provide deeper insights into transcriptional changes in immune
cells that enable efficient tissue invasion and pave the way for future studies investigating the
early colonization of tissues by macrophages in higher organisms. Moreover, they extend the
current view of Drosophila immune cell heterogeneity and point toward a potentially
conserved role for canonical BMP signaling in specifying immune cells that lead the migration
of tissue resident macrophages during embryogenesis.},
  author       = {Wachner, Stephanie},
  issn         = {2663-337X},
  pages        = {170},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells}},
  doi          = {10.15479/at:ista:11193},
  year         = {2022},
}

@phdthesis{11196,
  abstract     = {One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). 
	In addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.
},
  author       = {Kim, Olena},
  issn         = {2663-337X},
  pages        = {132},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses}},
  doi          = {10.15479/at:ista:11196},
  year         = {2022},
}

@misc{11321,
  abstract     = {Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. },
  author       = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}},
  doi          = {10.15479/at:ista:11321},
  year         = {2022},
}

@article{11330,
  abstract     = {In this article we study the noncommutative transport distance introduced by Carlen and Maas and its entropic regularization defined by Becker and Li. We prove a duality formula that can be understood as a quantum version of the dual Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions of a Hamilton–Jacobi–Bellmann equation.},
  author       = {Wirth, Melchior},
  issn         = {15729613},
  journal      = {Journal of Statistical Physics},
  number       = {2},
  publisher    = {Springer Nature},
  title        = {{A dual formula for the noncommutative transport distance}},
  doi          = {10.1007/s10955-022-02911-9},
  volume       = {187},
  year         = {2022},
}

@inproceedings{11331,
  abstract     = {We propose separating the task of reliable transaction dissemination from transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based consensus. We design and evaluate a mempool protocol, Narwhal, specializing in high-throughput reliable dissemination and storage of causal histories of transactions. Narwhal tolerates an asynchronous network and maintains high performance despite failures. Narwhal is designed to easily scale-out using multiple workers at each validator, and we demonstrate that there is no foreseeable limit to the throughput we can achieve.
Composing Narwhal with a partially synchronous consensus protocol (Narwhal-HotStuff) yields significantly better throughput even in the presence of faults or intermittent loss of liveness due to asynchrony. However, loss of liveness can result in higher latency. To achieve overall good performance when faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol, to work with Narwhal. We demonstrate its high performance under a variety of configurations and faults.
As a summary of results, on a WAN, Narwhal-Hotstuff achieves over 130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec latency for Hotstuff. Additional workers increase throughput linearly to 600,000 tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3 seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff suffers from increased latency.},
  author       = {Danezis, George and Kokoris Kogias, Eleftherios and Sonnino, Alberto and Spiegelman, Alexander},
  booktitle    = {Proceedings of the 17th European Conference on Computer Systems},
  isbn         = {9781450391627},
  location     = {Rennes, France},
  pages        = {34--50},
  publisher    = {Association for Computing Machinery},
  title        = {{Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus}},
  doi          = {10.1145/3492321.3519594},
  year         = {2022},
}

@article{11332,
  abstract     = {We show that the fluctuations of the largest eigenvalue of a real symmetric or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws at a rate O(N^{-1/3+\omega }), as N tends to infinity. For Wigner matrices this improves the previous rate O(N^{-2/9+\omega }) obtained by Bourgade (J Eur Math Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515, 2012) to prove edge universality, on a finer spectral parameter scale with improved error estimates. The proof relies on the continuous Green function flow induced by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions from the third and fourth order moments of the matrix entries are obtained using iterative cumulant expansions and recursive comparisons for correlation functions, along with uniform convergence estimates for correlation kernels of the Gaussian invariant ensembles.},
  author       = {Schnelli, Kevin and Xu, Yuanyuan},
  issn         = {1432-0916},
  journal      = {Communications in Mathematical Physics},
  pages        = {839--907},
  publisher    = {Springer Nature},
  title        = {{Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices}},
  doi          = {10.1007/s00220-022-04377-y},
  volume       = {393},
  year         = {2022},
}

@article{11333,
  abstract     = {Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.},
  author       = {Thayyil, Sampreeth and Nishigami, Yukinori and Islam, Muhammad J and Hashim, P. K. and Furuta, Ken'Ya and Oiwa, Kazuhiro and Yu, Jian and Yao, Min and Nakagaki, Toshiyuki and Tamaoki, Nobuyuki},
  issn         = {15213765},
  journal      = {Chemistry - A European Journal},
  number       = {30},
  publisher    = {Wiley},
  title        = {{Dynamic control of microbial movement by photoswitchable ATP antagonists}},
  doi          = {10.1002/chem.202200807},
  volume       = {28},
  year         = {2022},
}

@article{11334,
  abstract     = {Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.},
  author       = {Freitas, Susana and Westram, Anja M and Schwander, Tanja and Arakelyan, Marine and Ilgaz, Çetin and Kumlutas, Yusuf and Harris, David James and Carretero, Miguel A. and Butlin, Roger K.},
  issn         = {1558-5646},
  journal      = {Evolution},
  number       = {5},
  pages        = {899--914},
  publisher    = {Wiley},
  title        = {{Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization}},
  doi          = {10.1111/evo.14462},
  volume       = {76},
  year         = {2022},
}

@article{11336,
  abstract     = {The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.},
  author       = {Amberg, Nicole and Pauler, Florian and Streicher, Carmen and Hippenmeyer, Simon},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {44},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression}},
  doi          = {10.1126/sciadv.abq1263},
  volume       = {8},
  year         = {2022},
}

@article{11337,
  abstract     = {Nonanalytic points in the return probability of a quantum state as a function of time, known as dynamical quantum phase transitions (DQPTs), have received great attention in recent years, but the understanding of their mechanism is still incomplete. In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical precession and entanglement generation, leading to the definition of precession (pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional systems by considering semi-infinite ladders of varying width. For square lattices, we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement gap, while eDQPTs correspond to suppressed local observables and avoided crossings in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder width and other details, challenging the extrapolation to the thermodynamic limit especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that lattices with an odd number of nearest neighbors give rise to phenomenologies beyond the one-dimensional classification.},
  author       = {De Nicola, Stefano and Michailidis, Alexios and Serbyn, Maksym},
  issn         = {2469-9950},
  journal      = {Physical Review B},
  publisher    = {American Physical Society},
  title        = {{Entanglement and precession in two-dimensional dynamical quantum phase transitions}},
  doi          = {10.1103/PhysRevB.105.165149},
  volume       = {105},
  year         = {2022},
}

@article{11339,
  abstract     = {The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.},
  author       = {Glover, Georgina and Voliotis, Margaritis and Łapińska, Urszula and Invergo, Brandon M. and Soanes, Darren and O’Neill, Paul and Moore, Karen and Nikolic, Nela and Petrov, Peter and Milner, David S. and Roy, Sumita and Heesom, Kate and Richards, Thomas A. and Tsaneva-Atanasova, Krasimira and Pagliara, Stefano},
  issn         = {2399-3642},
  journal      = {Communications Biology},
  publisher    = {Springer Nature},
  title        = {{Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells}},
  doi          = {10.1038/s42003-022-03336-6},
  volume       = {5},
  year         = {2022},
}

@article{11340,
  abstract     = {Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.},
  author       = {Palaia, Ivan and Goyal, Abhay and Del Gado, Emanuela and Šamaj, Ladislav and Trizac, Emmanuel},
  issn         = {1520-5207},
  journal      = {Journal of Physical Chemistry B},
  number       = {16},
  pages        = {3143--3149},
  publisher    = {American Chemical Society},
  title        = {{Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring}},
  doi          = {10.1021/acs.jpcb.2c00028},
  volume       = {126},
  year         = {2022},
}

@article{11341,
  abstract     = {Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.},
  author       = {Lukacisin, Martin and Espinosa-Cantú, Adriana and Bollenbach, Mark Tobias},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {113--118},
  publisher    = {Springer Nature},
  title        = {{Intron-mediated induction of phenotypic heterogeneity}},
  doi          = {10.1038/s41586-022-04633-0},
  volume       = {605},
  year         = {2022},
}