@phdthesis{14510,
  abstract     = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and
development by controlling plasma membrane protein composition and cargo uptake. CME
relies on the precise recruitment control of protein regulators for vesicle maturation and
release. During the early stages of endocytosis, an area of flat membrane is remodelled by
proteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated
vesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,
and cargo proceeds for recycling or degradation through early endosomes / Trans Golgi
network. Protein machineries that mediate membrane bending and vesicle release in plants
are unknown. However, studies show, that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced
live microscopy approaches we investigate the TPLATE complex, a plant-specific
endocytosis protein complex. We found that TPLATE is peripherally associated with
clathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of
plant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a
role in vesicle release, shows the recruitment of the protein already at the early stages of
endocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to
induce membrane deformation and tubulation, suggesting its role also in membrane bending
during early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle
scission machinery; however, their precise role in plant CME has not been yet elucidated.
Here, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution
imaging of endocytic events in vivo and protein characterisation. Although DRP2s and
SH3P2 arrive together during late CME and physically interact, genetic analysis using
∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest
that SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our
research, these observations provide new important insights into the mechanism of plant
CME and show that, despite plants posses many homologues of mammalian and yeast CME
components, they do not necessarily act in the same manner. },
  author       = {Gnyliukh, Nataliia},
  isbn         = {978-3-99078-037-4},
  issn         = {2663-337X},
  keywords     = {Clathrin-Mediated Endocytosis, vesicle scission, Dynamin-Related Protein 2, SH3P2, TPLATE complex, Total internal reflection fluorescence microscopy, Arabidopsis thaliana},
  pages        = {180},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanism of clathrin-coated vesicle  formation during endocytosis in plants}},
  doi          = {10.15479/at:ista:14510},
  year         = {2023},
}

@unpublished{14591,
  abstract     = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.},
  author       = {Gnyliukh, Nataliia and Johnson, Alexander J and Nagel, Marie-Kristin and Monzer, Aline and Hlavata, Annamaria and Isono, Erika and Loose, Martin and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants}},
  doi          = {10.1101/2023.10.09.561523},
  year         = {2023},
}

@phdthesis{12470,
  abstract     = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of 
connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is 
pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of 
nm-small synapses.
To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across 
Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular
space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse 
identification.
I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue 
architecture, neuronal in- and output-fields, down to synapse morphology.
Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy 
fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 
pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal 
connectivity with light microscopy.},
  author       = {Michalska, Julia M},
  isbn         = {978-3-99078-026-8},
  issn         = {2663-337X},
  pages        = {201},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}},
  doi          = {10.15479/at:ista:12470},
  year         = {2023},
}

@article{12521,
  abstract     = {Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.},
  author       = {Mrnjavac, Andrea and Khudiakova, Kseniia and Barton, Nicholas H and Vicoso, Beatriz},
  issn         = {2056-3744},
  journal      = {Evolution Letters},
  keywords     = {Genetics, Ecology, Evolution, Behavior and Systematics},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution}},
  doi          = {10.1093/evlett/qrac004},
  volume       = {7},
  year         = {2023},
}

@phdthesis{14622,
  abstract     = {This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms
(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum
computation due to their moderate hardware requirements and resilience to noise. Our
primary focus lies on two particular types of VQAs: the Quantum Approximate Optimization
Algorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum
Eigensolver (VQE), utilized for finding ground states of quantum many-body systems.
In the first part of the thesis, we examine the issue of effective parameter initialization for
the QAOA. The work demonstrates that random initialization of the QAOA often leads to
convergence in local minima with sub-optimal performance. To mitigate this issue, we propose
an initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).
We show that TQA initialization leads to the same performance as the best of an exponentially
scaling number of random initializations.
The second study introduces Transition States (TS), stationary points with a single direction
of descent, as a tool for systematically exploring the QAOA optimization landscape. This
leads us to propose a novel greedy parameter initialization strategy that guarantees for the
energy to decrease with increasing number of circuit layers.
In the third section, we extend the QAOA to qudit systems, which are higher-dimensional
generalizations of qubits. This chapter provides theoretical insights and practical strategies for
leveraging the increased computational power of qudits in the context of quantum optimization
algorithms and suggests a quantum circuit for implementing the algorithm on an ion trap
quantum computer.
Finally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with
vanishing gradients that obstruct efficient parameter optimization. This novel approach relies
on defining a notion of weak barren plateaus based on the entropies of local reduced density
matrices and showcases how these can be efficiently quantified using shadow tomography.
To illustrate the approach we employ the strategy in the VQE and show that it allows to
successfully avoid barren plateaus in the initialization and throughout the optimization.
Taken together, this thesis greatly enhances our understanding of parameter initialization and
optimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,
and presents a method to address the challenge of barren plateaus using the VQE. These
insights are instrumental in advancing the field of near-term quantum computation.},
  author       = {Sack, Stefan},
  issn         = {2663-337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems}},
  doi          = {10.15479/at:ista:14622},
  year         = {2023},
}

@article{13125,
  abstract     = {The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. },
  author       = {Sack, Stefan and Medina Ramos, Raimel A and Kueng, Richard and Serbyn, Maksym},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement}},
  doi          = {10.1103/physreva.107.062404},
  volume       = {107},
  year         = {2023},
}

@article{13117,
  abstract     = {The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.},
  author       = {Redchenko, Elena and Poshakinskiy, Alexander V. and Sett, Riya and Zemlicka, Martin and Poddubny, Alexander N. and Fink, Johannes M},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Tunable directional photon scattering from a pair of superconducting qubits}},
  doi          = {10.1038/s41467-023-38761-6},
  volume       = {14},
  year         = {2023},
}

@inproceedings{14692,
  abstract     = {The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions.
In this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach.
The main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.},
  author       = {Auerbach, Benedikt and Hoffmann, Charlotte and Pascual Perez, Guillermo},
  booktitle    = {21st International Conference on Theory of Cryptography},
  isbn         = {9783031486203},
  issn         = {1611-3349},
  pages        = {301--330},
  publisher    = {Springer Nature},
  title        = {{Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing}},
  doi          = {10.1007/978-3-031-48621-0_11},
  volume       = {14371},
  year         = {2023},
}

@inproceedings{13310,
  abstract     = {Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation.},
  author       = {Henzinger, Thomas A and Karimi, Mahyar and Kueffner, Konstantin and Mallik, Kaushik},
  booktitle    = {Computer Aided Verification},
  isbn         = {9783031377020},
  issn         = {1611-3349},
  location     = {Paris, France},
  pages        = {358–382},
  publisher    = {Springer Nature},
  title        = {{Monitoring algorithmic fairness}},
  doi          = {10.1007/978-3-031-37703-7_17},
  volume       = {13965},
  year         = {2023},
}

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

@inproceedings{14691,
  abstract     = {Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].
The recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.
In this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.
We prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.
Our lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper.},
  author       = {Auerbach, Benedikt and Cueto Noval, Miguel and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z},
  booktitle    = {21st International Conference on Theory of Cryptography},
  isbn         = {9783031486203},
  issn         = {1611-3349},
  location     = {Taipei, Taiwan},
  pages        = {271--300},
  publisher    = {Springer Nature},
  title        = {{On the cost of post-compromise security in concurrent Continuous Group-Key Agreement}},
  doi          = {10.1007/978-3-031-48621-0_10},
  volume       = {14371},
  year         = {2023},
}

@inproceedings{14454,
  abstract     = {As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples.},
  author       = {Henzinger, Thomas A and Kueffner, Konstantin and Mallik, Kaushik},
  booktitle    = {23rd International Conference on Runtime Verification},
  isbn         = {9783031442667},
  issn         = {1611-3349},
  location     = {Thessaloniki, Greece},
  pages        = {291--311},
  publisher    = {Springer Nature},
  title        = {{Monitoring algorithmic fairness under partial observations}},
  doi          = {10.1007/978-3-031-44267-4_15},
  volume       = {14245},
  year         = {2023},
}

@article{10818,
  abstract     = {Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses.},
  author       = {Basilico, Bernadette and Ferrucci, Laura and Ratano, Patrizia and Golia, Maria T. and Grimaldi, Alfonso and Rosito, Maria and Ferretti, Valentina and Reverte, Ingrid and Sanchini, Caterina and Marrone, Maria C. and Giubettini, Maria and De Turris, Valeria and Salerno, Debora and Garofalo, Stefano and St‐Pierre, Marie‐Kim and Carrier, Micael and Renzi, Massimiliano and Pagani, Francesca and Modi, Brijesh and Raspa, Marcello and Scavizzi, Ferdinando and Gross, Cornelius T. and Marinelli, Silvia and Tremblay, Marie‐Ève and Caprioli, Daniele and Maggi, Laura and Limatola, Cristina and Di Angelantonio, Silvia and Ragozzino, Davide},
  issn         = {1098-1136},
  journal      = {Glia},
  keywords     = {Cellular and Molecular Neuroscience, Neurology},
  number       = {1},
  pages        = {173--195},
  publisher    = {Wiley},
  title        = {{Microglia control glutamatergic synapses in the adult mouse hippocampus}},
  doi          = {10.1002/glia.24101},
  volume       = {70},
  year         = {2022},
}

@inproceedings{10820,
  abstract     = {Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.},
  author       = {Liu, Jianxin and Marensi, Elena and Wu, Xuesong},
  booktitle    = {IUTAM Laminar-Turbulent Transition},
  isbn         = {9783030679019},
  issn         = {1875-3493},
  location     = {London, United Kingdom},
  pages        = {587--598},
  publisher    = {Springer Nature},
  title        = {{Effects of streaky structures on the instability of supersonic boundary layers}},
  doi          = {10.1007/978-3-030-67902-6_51},
  volume       = {38},
  year         = {2022},
}

@article{10825,
  abstract     = {In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.},
  author       = {Yanagida, Ayaka and Corujo-Simon, Elena and Revell, Christopher K. and Sahu, Preeti and Stirparo, Giuliano G. and Aspalter, Irene M. and Winkel, Alex K. and Peters, Ruby and De Belly, Henry and Cassani, Davide A.D. and Achouri, Sarra and Blumenfeld, Raphael and Franze, Kristian and Hannezo, Edouard B and Paluch, Ewa K. and Nichols, Jennifer and Chalut, Kevin J.},
  issn         = {1097-4172},
  journal      = {Cell},
  number       = {5},
  pages        = {777--793.e20},
  publisher    = {Cell Press},
  title        = {{Cell surface fluctuations regulate early embryonic lineage sorting}},
  doi          = {10.1016/j.cell.2022.01.022},
  volume       = {185},
  year         = {2022},
}

@article{10826,
  abstract     = {Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.},
  author       = {Valperga, Giulio and De Bono, Mario},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans}},
  doi          = {10.7554/eLife.68040},
  volume       = {11},
  year         = {2022},
}

@inproceedings{10828,
  abstract     = {Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown.},
  author       = {Heiss, Teresa and Tymochko, Sarah and Story, Brittany and Garin, Adélie and Bui, Hoa and Bleile, Bea and Robins, Vanessa},
  booktitle    = {2021 IEEE International Conference on Big Data},
  isbn         = {9781665439022},
  location     = {Orlando, FL, United States; Virtuell},
  pages        = {3824--3834},
  publisher    = {IEEE},
  title        = {{The impact of changes in resolution on the persistent homology of images}},
  doi          = {10.1109/BigData52589.2021.9671483},
  year         = {2022},
}

@article{10829,
  abstract     = {A novel multivariable system, combining a transistor with fiber optic-based surface plasmon resonance spectroscopy with the gate electrode simultaneously acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows for discrimination of mass and charge contributions for binding assays on the same sensor surface. Furthermore, we optimize the sensor geometry by investigating the influence of the fiber area to transistor channel area ratio and distance. We show that larger fiber optic tip diameters are favorable for electronic and optical signals and demonstrate the reversibility of plasmon resonance wavelength shifts after electric field application. As a proof of principle, a layer-by-layer assembly of polyelectrolytes is performed to benchmark the system against multivariable sensing platforms with planar surface plasmon resonance configurations. Furthermore, the biosensing performance is assessed using a thrombin binding assay with surface-immobilized aptamers as receptors, allowing for the detection of medically relevant thrombin concentrations.},
  author       = {Hasler, Roger and Reiner-Rozman, Ciril and Fossati, Stefan and Aspermair, Patrik and Dostalek, Jakub and Lee, Seungho and Ibáñez, Maria and Bintinger, Johannes and Knoll, Wolfgang},
  issn         = {2379-3694},
  journal      = {ACS Sensors},
  number       = {2},
  pages        = {504--512},
  publisher    = {American Chemical Society},
  title        = {{Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device}},
  doi          = {10.1021/acssensors.1c02313},
  volume       = {7},
  year         = {2022},
}

@misc{10833,
  abstract     = {Detailed information about the data set see "dataset description.txt" file.},
  author       = {Hasler, Roger and Reiner-Rozman, Ciril and Fossati, Stefan and Aspermair, Patrik and Dostalek, Jakub and Lee, Seungho and Ibáñez, Maria and Bintinger, Johannes and Knoll, Wolfgang},
  publisher    = {Zenodo},
  title        = {{Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device}},
  doi          = {10.5281/ZENODO.5500360},
  year         = {2022},
}

@article{10841,
  abstract     = {In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.},
  author       = {Dahhan, DA and Reynolds, GD and Cárdenas, JJ and Eeckhout, D and Johnson, Alexander J and Yperman, K and Kaufmann, Walter and Vang, N and Yan, X and Hwang, I and Heese, A and De Jaeger, G and Friml, Jiří and Van Damme, D and Pan, J and Bednarek, SY},
  issn         = {1532-298x},
  journal      = {Plant Cell},
  number       = {6},
  pages        = {2150--2173},
  publisher    = {Oxford University Press},
  title        = {{Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components}},
  doi          = {10.1093/plcell/koac071},
  volume       = {34},
  year         = {2022},
}