@article{13971,
  abstract     = {When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.},
  author       = {Grober, Daniel and Palaia, Ivan and Ucar, Mehmet C and Hannezo, Edouard B and Šarić, Anđela and Palacci, Jérémie A},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {1680--1688},
  publisher    = {Springer Nature},
  title        = {{Unconventional colloidal aggregation in chiral bacterial baths}},
  doi          = {10.1038/s41567-023-02136-x},
  volume       = {19},
  year         = {2023},
}

@article{13972,
  abstract     = {This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article.},
  author       = {Næsborg, Line and Pieber, Bartholomäus and Wenger, Oliver S.},
  issn         = {1867-3899},
  journal      = {ChemCatChem},
  publisher    = {Wiley},
  title        = {{Special Collection: Photocatalytic synthesis}},
  doi          = {10.1002/cctc.202300683},
  year         = {2023},
}

@article{13973,
  abstract     = {We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle.},
  author       = {Lyczak, Julian},
  issn         = {0373-0956},
  journal      = {Annales de l'Institut Fourier},
  number       = {2},
  pages        = {447--478},
  publisher    = {Association des Annales de l'Institut Fourier},
  title        = {{Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces}},
  doi          = {10.5802/aif.3529},
  volume       = {73},
  year         = {2023},
}

@article{13974,
  abstract     = {The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2.},
  author       = {Fulek, Radoslav and Gärtner, Bernd and Kupavskii, Andrey and Valtr, Pavel and Wagner, Uli},
  issn         = {1432-0444},
  journal      = {Discrete and Computational Geometry},
  publisher    = {Springer Nature},
  title        = {{The crossing Tverberg theorem}},
  doi          = {10.1007/s00454-023-00532-x},
  year         = {2023},
}

@article{13975,
  abstract     = {We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An
 is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln  converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure.},
  author       = {Campbell, Andrew J and O’Rourke, Sean},
  issn         = {1572-9230},
  journal      = {Journal of Theoretical Probability},
  publisher    = {Springer Nature},
  title        = {{Spectrum of Lévy–Khintchine random laplacian matrices}},
  doi          = {10.1007/s10959-023-01275-4},
  year         = {2023},
}

@article{13976,
  abstract     = {Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.},
  author       = {Wolfsberger, Walter and Chhugani, Karishma and Shchubelka, Khrystyna and Frolova, Alina and Salyha, Yuriy and Zlenko, Oksana and Arych, Mykhailo and Dziuba, Dmytro and Parkhomenko, Andrii and Smolanka, Volodymyr and Gümüş, Zeynep H. and Sezgin, Efe and Diaz-Lameiro, Alondra and Toth, Viktor R. and Maci, Megi and Bortz, Eric and Kondrashov, Fyodor and Morton, Patricia M. and Łabaj, Paweł P. and Romero, Veronika and Hlávka, Jakub and Mangul, Serghei and Oleksyk, Taras K.},
  issn         = {2047-217X},
  journal      = {GigaScience},
  publisher    = {Oxford Academic},
  title        = {{Scientists without borders: Lessons from Ukraine}},
  doi          = {10.1093/gigascience/giad045},
  volume       = {12},
  year         = {2023},
}

@phdthesis{13984,
  abstract     = {Social insects fight disease using their individual immune systems and the cooperative
sanitary behaviors of colony members. These social defenses are well explored against
externally-infecting pathogens, but little is known about defense strategies against
internally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades
it has become evident that also many ant species harbor viruses. We present one of the first
studies addressing transmission dynamics and collective disease defenses against viruses in
ants on a mechanistic level. I successfully established an experimental ant host – viral
pathogen system as a model for the defense strategies used by social insects against internal
pathogen infections, as outlined in the third chapter. In particular, we studied how garden ants
(Lasius neglectus) defend themselves and their colonies against the generalist insect virus
CrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’
hemolymph because it allowed us to use a defined exposure dose. Here we show that this is a
good model system, as the virus is replicating and thus infecting the host. The ants mount a
clear individual immune response against the viral infection, which is characterized by a
specific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21
and 22 bp long fragments. The onset of this immune response is consistent with the timeline
of viral replication that starts already within two days post injection. The disease manifests in
decreased survival over a course of two to three weeks.
Regarding group living, we find that infected ants show a strong individual immune response,
but that their course of disease is little affected by nestmate presence, as described in chapter
four. Hence, we do not find social immunity in the context of viral infections in ants.
Nestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we
showed that 94 % of the nestmates contract active virus within four days of social contact to
an infected individual. Virus is transmitted in low doses, thus not causing disease
transmission within the colony. While virus can be transmitted during short direct contacts,
we also assume transmission from deceased ants and show that the nestmates’ immune
system gets activated after contracting a low viral dose. We find considerable potential for
indirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one
week and is also picked up by other ants. Apart from that, we want to underline the potential
of ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV
in vitro. However, we found no evidence for effective poison use to sanitize the nest space.
On the other hand, local application of ant poison by oral poison uptake, which is part of the
ants prophylactic behavioral repertoire, probably contributes to keeping the gut of each
individual sanitized. We hypothesize that oral poison uptake might be the reason why we did
not find viable virus in the trophallactic fluid.
The fifth chapter encompasses preliminary data on potential social immunization. However,
our experiments do not confirm an actual survival benefit for the nestmates upon pathogen
challenge under the given experimental settings. Nevertheless, we do not want to rule out the
possibility for nestmate immunization, but rather emphasize that considering different
experimental timelines and viral doses would provide a multitude of options for follow-up
experiments.
In conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,
might play a role in preventing viral disease transmission. Compared to colony defense
against external pathogens, internal pathogen infections require a stronger component of
individual physiological immunity than behavioral social immunity, yet could still lead to
collective protection.},
  author       = {Franschitz, Anna},
  isbn         = {978-3-99078-034-3},
  issn         = {2663 - 337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Individual and social immunity against viral infections in ants}},
  doi          = {10.15479/at:ista:13984},
  year         = {2023},
}

@article{13988,
  abstract     = {Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains.},
  author       = {Neiheiser, Ray and Inacio, Gustavo and Rech, Luciana and Montez, Carlos and Matos, Miguel and Rodrigues, Luis},
  issn         = {2169-3536},
  journal      = {IEEE Access},
  keywords     = {General Engineering, General Materials Science, General Computer Science, Electrical and Electronic Engineering},
  pages        = {8651--8662},
  publisher    = {Institute of Electrical and Electronics Engineers},
  title        = {{Practical limitations of Ethereum’s layer-2}},
  doi          = {10.1109/access.2023.3237897},
  volume       = {11},
  year         = {2023},
}

@article{14032,
  abstract     = {Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.},
  author       = {Mukhopadhyay, Soham and Senior, Jorden L and Saez Mollejo, Jaime and Puglia, Denise and Zemlicka, Martin and Fink, Johannes M and Higginbotham, Andrew P},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  keywords     = {General Physics and Astronomy},
  pages        = {1630--1635},
  publisher    = {Springer Nature},
  title        = {{Superconductivity from a melted insulator in Josephson junction arrays}},
  doi          = {10.1038/s41567-023-02161-w},
  volume       = {19},
  year         = {2023},
}

@article{14036,
  abstract     = {Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.},
  author       = {Napoli, Federico and Becker, Lea Marie and Schanda, Paul},
  issn         = {1879-033X},
  journal      = {Current Opinion in Structural Biology},
  number       = {10},
  publisher    = {Elsevier},
  title        = {{Protein dynamics detected by magic-angle spinning relaxation dispersion NMR}},
  doi          = {10.1016/j.sbi.2023.102660},
  volume       = {82},
  year         = {2023},
}

@article{14037,
  abstract     = {Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.},
  author       = {Vardi, Ofek and Maroudas-Sklare, Naama and Kolodny, Yuval and Volosniev, Artem and Saragovi, Amijai and Galili, Nir and Ferrera, Stav and Ghazaryan, Areg and Yuran, Nir and Affek, Hagit P. and Luz, Boaz and Goldsmith, Yonaton and Keren, Nir and Yochelis, Shira and Halevy, Itay and Lemeshko, Mikhail and Paltiel, Yossi},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {32},
  publisher    = {National Academy of Sciences},
  title        = {{Nuclear spin effects in biological processes}},
  doi          = {10.1073/pnas.2300828120},
  volume       = {120},
  year         = {2023},
}

@article{14039,
  abstract     = {Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.},
  author       = {Leonard, Thomas A. and Loose, Martin and Martens, Sascha},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {15},
  pages        = {1315--1332},
  publisher    = {Elsevier},
  title        = {{The membrane surface as a platform that organizes cellular and biochemical processes}},
  doi          = {10.1016/j.devcel.2023.06.001},
  volume       = {58},
  year         = {2023},
}

@article{14040,
  abstract     = {Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.},
  author       = {Zhao, Ziyu and Vercellino, Irene and Knoppová, Jana and Sobotka, Roman and Murray, James W. and Nixon, Peter J. and Sazanov, Leonid A and Komenda, Josef},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis}},
  doi          = {10.1038/s41467-023-40388-6},
  volume       = {14},
  year         = {2023},
}

@article{14041,
  abstract     = {Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.},
  author       = {Méhes, Elod and Mones, Enys and Varga, Máté and Zsigmond, Áron and Biri-Kovács, Beáta and Nyitray, László and Barone, Vanessa and Krens, Gabriel and Heisenberg, Carl-Philipp J and Vicsek, Tamás},
  issn         = {2399-3642},
  journal      = {Communications Biology},
  publisher    = {Springer Nature},
  title        = {{3D cell segregation geometry and dynamics are governed by tissue surface tension regulation}},
  doi          = {10.1038/s42003-023-05181-7},
  volume       = {6},
  year         = {2023},
}

@article{14042,
  abstract     = {Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions.},
  author       = {Bulíček, Miroslav and Málek, Josef and Maringová, Erika},
  issn         = {1422-6952},
  journal      = {Journal of Mathematical Fluid Mechanics},
  number       = {3},
  publisher    = {Springer Nature},
  title        = {{On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary}},
  doi          = {10.1007/s00021-023-00803-w},
  volume       = {25},
  year         = {2023},
}

@article{14043,
  abstract     = {Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart.},
  author       = {Henzinger, Monika H and Jin, Billy and Peng, Richard and Williamson, David P.},
  issn         = {1432-0541},
  journal      = {Algorithmica},
  pages        = {2680--3716},
  publisher    = {Springer Nature},
  title        = {{A combinatorial cut-toggling algorithm for solving Laplacian linear systems}},
  doi          = {10.1007/s00453-023-01154-8},
  volume       = {85},
  year         = {2023},
}

@phdthesis{14058,
  abstract     = {Females and males across species are subject to divergent selective pressures arising
from di↵erent reproductive interests and ecological niches. This often translates into a
intricate array of sex-specific natural and sexual selection on traits that have a shared
genetic basis between both sexes, causing a genetic sexual conflict. The resolution of
this conflict mostly relies on the evolution of sex-specific expression of the shared genes,
leading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought
to evolve via modifications of the genetic networks ultimately linked to sex-determining
transcription factors. Although much empirical and theoretical evidence supports this
standard picture of the molecular basis of sexual conflict resolution, there still are a
few open questions regarding the complex array of selective forces driving phenotypic
di↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.
First, how do patterns of phenotypic sexual dimorphism vary within populations,
as a response to the temporal and spatial changes in sex-specific selective forces? To
tackle this question, I analyze the patterns of sex-specific phenotypic variation along
three life stages and across populations spanning the whole geographical range of Rumex
hastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.
Second, how do gene expression patterns lead to phenotypic dimorphism, and what
are the molecular mechanisms underlying the observed transcriptomic variation? I
address this question by examining the sex- and tissue-specific expression variation in
newly-generated datasets of sex-specific expression in heads and gonads of Drosophila
melanogaster. I additionally used two complementary approaches for the study of the
genetic basis of sex di↵erences in gene expression in the second and third Chapters of
the thesis.
Third, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual
dimorphism? I develop models of sex-specific stabilizing selection, mutation and drift
to formalize common intuition regarding the patterns of covariation between intersex
correlation and sexual dimorphism in the fourth Chapter of the thesis.
Alltogether, the work described in this PhD thesis provides useful insights into the
links between genetic, transcriptomic and phenotypic layers of sex-specific variation,
and contributes to our general understanding of the dynamics of sexual dimorphism
evolution.},
  author       = {Puixeu Sala, Gemma},
  isbn         = {978-3-99078-035-0},
  issn         = {2663-337X},
  pages        = {230},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation}},
  doi          = {10.15479/at:ista:14058},
  year         = {2023},
}

@inproceedings{14076,
  abstract     = {Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism.},
  author       = {Chalupa, Marek and Henzinger, Thomas A},
  booktitle    = {23nd International Conference on Runtime Verification},
  isbn         = {978-3-031-44266-7},
  location     = {Thessaloniki, Greek},
  pages        = {168--190},
  publisher    = {Springer Nature},
  title        = {{Monitoring hyperproperties with prefix transducers}},
  doi          = {10.1007/978-3-031-44267-4_9},
  volume       = {14245},
  year         = {2023},
}

@article{14077,
  abstract     = {The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed
so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues
and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila
melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate
crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,
testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that
have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation
of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression
and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis
variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary
expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance
as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled
experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.},
  author       = {Puixeu Sala, Gemma and Macon, Ariana and Vicoso, Beatriz},
  issn         = {2160-1836},
  journal      = {G3: Genes, Genomes, Genetics},
  keywords     = {Genetics (clinical), Genetics, Molecular Biology},
  number       = {8},
  publisher    = {Oxford University Press},
  title        = {{Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}},
  doi          = {10.1093/g3journal/jkad121},
  volume       = {13},
  year         = {2023},
}

@article{14080,
  abstract     = {Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors.},
  author       = {Hirashima, Tsuyoshi and Hino, Naoya and Aoki, Kazuhiro and Matsuda, Michiyuki},
  issn         = {1879-0410},
  journal      = {Current Opinion in Cell Biology},
  number       = {10},
  publisher    = {Elsevier},
  title        = {{Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation}},
  doi          = {10.1016/j.ceb.2023.102217},
  volume       = {84},
  year         = {2023},
}