@article{14834,
  abstract     = {Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.},
  author       = {Radler, Philipp and Loose, Martin},
  issn         = {0171-9335},
  journal      = {European Journal of Cell Biology},
  keywords     = {Cell Biology, General Medicine, Histology, Pathology and Forensic Medicine},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches}},
  doi          = {10.1016/j.ejcb.2023.151380},
  volume       = {103},
  year         = {2024},
}

@article{15257,
  abstract     = {Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.},
  author       = {Kulich, Ivan and Schmid, Julia and Teplova, Anastasiia and Qi, Linlin and Friml, Jiří},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism}},
  doi          = {10.7554/elife.91523},
  volume       = {12},
  year         = {2024},
}

@article{15033,
  abstract     = {The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.},
  author       = {Adamowski, Maciek and Matijevic, Ivana and Friml, Jiří},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery}},
  doi          = {10.7554/elife.68993},
  volume       = {13},
  year         = {2024},
}

@article{12172,
  abstract     = {In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case.},
  author       = {Khatoon, Bushra and Kamil, Shoaib and Babu, Hitesh and Siraj Alam, M.},
  issn         = {2214-7853},
  journal      = {Materials Today: Proceedings},
  keywords     = {General Medicine},
  number       = {Part 1},
  pages        = {40--47},
  publisher    = {Elsevier},
  title        = {{Experimental analysis of Cascade CSTRs with step and pulse inputs}},
  doi          = {10.1016/j.matpr.2022.11.037},
  volume       = {78},
  year         = {2023},
}

@article{14776,
  abstract     = {Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.},
  author       = {Teplova, Anastasiia and Pigidanov, Artemii A. and Serebryakova, Marina V. and Golyshev, Sergei A. and Galiullina, Raisa A. and Chichkova, Nina V. and Vartapetian, Andrey B.},
  issn         = {1422-0067},
  journal      = {International Journal of Molecular Sciences},
  keywords     = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry, Computer Science Applications, Spectroscopy, Molecular Biology, General Medicine, Catalysis},
  number       = {22},
  publisher    = {MDPI},
  title        = {{Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3}},
  doi          = {10.3390/ijms242216527},
  volume       = {24},
  year         = {2023},
}

@article{14783,
  abstract     = {Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.},
  author       = {Cheung, Giselle T and Chever, Oana and Rollenhagen, Astrid and Quenech’du, Nicole and Ezan, Pascal and Lübke, Joachim H. R. and Rouach, Nathalie},
  issn         = {2073-4409},
  journal      = {Cells},
  keywords     = {General Medicine},
  number       = {8},
  publisher    = {MDPI},
  title        = {{Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses}},
  doi          = {10.3390/cells12081133},
  volume       = {12},
  year         = {2023},
}

@inproceedings{14830,
  abstract     = {We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks.},
  author       = {Zikelic, Dorde and Lechner, Mathias and Henzinger, Thomas A and Chatterjee, Krishnendu},
  booktitle    = {Proceedings of the 37th AAAI Conference on Artificial Intelligence},
  issn         = {2374-3468},
  keywords     = {General Medicine},
  location     = {Washington, DC, United States},
  number       = {10},
  pages        = {11926--11935},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{Learning control policies for stochastic systems with reach-avoid guarantees}},
  doi          = {10.1609/aaai.v37i10.26407},
  volume       = {37},
  year         = {2023},
}

@article{14835,
  abstract     = {Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht.},
  author       = {Becker, Lea Marie and Berbon, Mélanie and Vallet, Alicia and Grelard, Axelle and Morvan, Estelle and Bardiaux, Benjamin and Lichtenecker, Roman and Ernst, Matthias and Loquet, Antoine and Schanda, Paul},
  issn         = {1521-3757},
  journal      = {Angewandte Chemie},
  keywords     = {General Medicine},
  number       = {19},
  publisher    = {Wiley},
  title        = {{Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten}},
  doi          = {10.1002/ange.202219314},
  volume       = {135},
  year         = {2023},
}

@article{14854,
  abstract     = {We study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type.},
  author       = {Mitrouskas, David Johannes and Seiringer, Robert},
  issn         = {2578-5885},
  journal      = {Pure and Applied Analysis},
  keywords     = {General Medicine},
  number       = {4},
  pages        = {973--1008},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{Ubiquity of bound states for the strongly coupled polaron}},
  doi          = {10.2140/paa.2023.5.973},
  volume       = {5},
  year         = {2023},
}

@article{14274,
  abstract     = {Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.},
  author       = {Alanko, Jonna H and Ucar, Mehmet C and Canigova, Nikola and Stopp, Julian A and Schwarz, Jan and Merrin, Jack and Hannezo, Edouard B and Sixt, Michael K},
  issn         = {2470-9468},
  journal      = {Science Immunology},
  keywords     = {General Medicine, Immunology},
  number       = {87},
  publisher    = {American Association for the Advancement of Science},
  title        = {{CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration}},
  doi          = {10.1126/sciimmunol.adc9584},
  volume       = {8},
  year         = {2023},
}

@article{11713,
  abstract     = {Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).
Results: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.},
  author       = {Nikolic, Nela and Sauert, Martina and Albanese, Tanino G. and Moll, Isabella},
  issn         = {1756-0500},
  journal      = {BMC Research Notes},
  keywords     = {General Biochemistry, Genetics and Molecular Biology, General Medicine},
  publisher    = {Springer Nature},
  title        = {{Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli}},
  doi          = {10.1186/s13104-022-06061-9},
  volume       = {15},
  year         = {2022},
}

@article{12157,
  abstract     = {Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.},
  author       = {Hayward, Laura and Sella, Guy},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Polygenic adaptation after a sudden change in environment}},
  doi          = {10.7554/elife.66697},
  volume       = {11},
  year         = {2022},
}

@article{12235,
  abstract     = {Background: About 800 women die every day worldwide from pregnancy-related complications, including excessive blood loss, infections and high-blood pressure (World Health Organization, 2019). To improve screening for high-risk pregnancies, we set out to identify patterns of maternal hematological changes associated with future pregnancy complications.

Methods: Using mixed effects models, we established changes in 14 complete blood count (CBC) parameters for 1710 healthy pregnancies and compared them to measurements from 98 pregnancy-induced hypertension, 106 gestational diabetes and 339 postpartum hemorrhage cases.

Results: Results show interindividual variations, but good individual repeatability in CBC values during physiological pregnancies, allowing the identification of specific alterations in women with obstetric complications. For example, in women with uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16, −0.09) significantly per gestation week (p value <.001). Interestingly, this decrease is three times more pronounced in women who will develop pregnancy-induced hypertension, with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm that obstetric complications and white CBC predict the likelihood of giving birth earlier during pregnancy.

Conclusion: We provide a comprehensive description of the associations between haematological changes through pregnancy and three major obstetric complications to support strategies for prevention, early-diagnosis and maternal care.},
  author       = {Patxot, Marion and Stojanov, Miloš and Ojavee, Sven Erik and Gobert, Rosanna Pescini and Kutalik, Zoltán and Gavillet, Mathilde and Baud, David and Robinson, Matthew Richard},
  issn         = {1600-0609},
  journal      = {European Journal of Haematology},
  keywords     = {Hematology, General Medicine},
  number       = {5},
  pages        = {566--575},
  publisher    = {Wiley},
  title        = {{Haematological changes from conception to childbirth: An indicator of major pregnancy complications}},
  doi          = {10.1111/ejh.13844},
  volume       = {109},
  year         = {2022},
}

@article{13993,
  abstract     = {Photoionization is a process taking place on attosecond time scales. How its properties evolve from isolated particles to the condensed phase is an open question of both fundamental and practical relevance. Here, we review recent work that has advanced the study of photoionization dynamics from atoms to molecules, clusters and the liquid phase. The first measurements of molecular photoionization delays have revealed the attosecond dynamics of electron emission from a molecular shape resonance and their sensitivity to the molecular potential. Using electron-ion coincidence spectroscopy these measurements have been extended from isolated molecules to clusters. A continuous increase of the delays with the water-cluster size has been observed up to a size of 4-5 molecules, followed by a saturation towards larger clusters. Comparison with calculations has revealed a correlation of the time delay with the spatial extension of the created electron hole. Using cylindrical liquid-microjet techniques, these measurements have also been extended to liquid water, revealing a delay relative to isolated water molecules that was very similar to the largest water clusters studied. Detailed modeling based on Monte-Carlo simulations confirmed that these delays are dominated by the contributions of the first two solvation shells, which agrees with the results of the cluster measurements. These combined results open the perspective of experimentally characterizing the delocalization of electronic wave functions in complex systems and studying their evolution on attosecond time scales.},
  author       = {Gong, Xiaochun and Jordan, Inga and Huppert, Martin and Heck, Saijoscha and Baykusheva, Denitsa Rangelova and Jelovina, Denis and Schild, Axel and Wörner, Hans Jakob},
  issn         = {2673-2424},
  journal      = {Chimia},
  keywords     = {General Medicine, General Chemistry},
  number       = {6},
  pages        = {520--528},
  publisher    = {Swiss Chemical Society},
  title        = {{Attosecond photoionization dynamics: from molecules over clusters to the liquid phase}},
  doi          = {10.2533/chimia.2022.520},
  volume       = {76},
  year         = {2022},
}

@article{12276,
  abstract     = {Ongoing development of quantum simulators allows for a progressively finer degree of control of quantum many-body systems. This motivates the development of efficient approaches to facilitate the control of such systems and enable the preparation of nontrivial quantum states. Here we formulate an approach to control quantum systems based on matrix product states (MPSs). We compare counterdiabatic and leakage minimization approaches to the so-called local steering problem that consists in finding the best value of the control parameters for generating a unitary evolution of the specific MPS in a given direction. In order to benchmark the different approaches, we apply them to the generalization of the PXP model known to exhibit coherent quantum dynamics due to quantum many-body scars. We find that the leakage-based approach generally outperforms the counterdiabatic framework and use it to construct a Floquet model with quantum scars. We perform the first steps towards global trajectory optimization and demonstrate entanglement steering capabilities in the generalized PXP model. Finally, we apply our leakage minimization approach to construct quantum scars in the periodically driven nonintegrable Ising model.},
  author       = {Ljubotina, Marko and Roos, Barbara and Abanin, Dmitry A. and Serbyn, Maksym},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  keywords     = {General Medicine},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Optimal steering of matrix product states and quantum many-body scars}},
  doi          = {10.1103/prxquantum.3.030343},
  volume       = {3},
  year         = {2022},
}

@article{12288,
  abstract     = {To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo.},
  author       = {Sumser, Anton L and Jösch, Maximilian A and Jonas, Peter M and Ben Simon, Yoav},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling}},
  doi          = {10.7554/elife.79848},
  volume       = {11},
  year         = {2022},
}

@article{12510,
  abstract     = {We introduce a new statistical verification algorithm that formally quantifies the behavioral robustness of any time-continuous process formulated as a continuous-depth model. Our algorithm solves a set of global optimization (Go) problems over a given time horizon to construct a tight enclosure (Tube) of the set of all process executions starting from a ball of initial states. We call our algorithm GoTube. Through its construction, GoTube ensures that the bounding tube is conservative up to a desired probability and up to a desired tightness.
 GoTube is implemented in JAX and optimized to scale to complex continuous-depth neural network models. Compared to advanced reachability analysis tools for time-continuous neural networks, GoTube does not accumulate overapproximation errors between time steps and avoids the infamous wrapping effect inherent in symbolic techniques. We show that GoTube substantially outperforms state-of-the-art verification tools in terms of the size of the initial ball, speed, time-horizon, task completion, and scalability on a large set of experiments.
 GoTube is stable and sets the state-of-the-art in terms of its ability to scale to time horizons well beyond what has been previously possible.},
  author       = {Gruenbacher, Sophie A. and Lechner, Mathias and Hasani, Ramin and Rus, Daniela and Henzinger, Thomas A and Smolka, Scott A. and Grosu, Radu},
  isbn         = {978577358350},
  issn         = {2374-3468},
  journal      = {Proceedings of the AAAI Conference on Artificial Intelligence},
  keywords     = {General Medicine},
  number       = {6},
  pages        = {6755--6764},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{GoTube: Scalable statistical verification of continuous-depth models}},
  doi          = {10.1609/aaai.v36i6.20631},
  volume       = {36},
  year         = {2022},
}

@article{11448,
  abstract     = {Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.},
  author       = {Gonzalez Somermeyer, Louisa and Fleiss, Aubin and Mishin, Alexander S and Bozhanova, Nina G and Igolkina, Anna A and Meiler, Jens and Alaball Pujol, Maria-Elisenda and Putintseva, Ekaterina V and Sarkisyan, Karen S and Kondrashov, Fyodor},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Heterogeneity of the GFP fitness landscape and data-driven protein design}},
  doi          = {10.7554/elife.75842},
  volume       = {11},
  year         = {2022},
}

@article{12511,
  abstract     = {We consider the problem of formally verifying almost-sure (a.s.) asymptotic stability in discrete-time nonlinear stochastic control systems. While verifying stability in deterministic control systems is extensively studied in the literature, verifying stability in stochastic control systems is an open problem. The few existing works on this topic either consider only specialized forms of stochasticity or make restrictive assumptions on the system, rendering them inapplicable to learning algorithms with neural network policies. 
 In this work, we present an approach for general nonlinear stochastic control problems with two novel aspects: (a) instead of classical stochastic extensions of Lyapunov functions, we use ranking supermartingales (RSMs) to certify a.s. asymptotic stability, and (b) we present a method for learning neural network RSMs. 
 We prove that our approach guarantees a.s. asymptotic stability of the system and
 provides the first method to obtain bounds on the stabilization time, which stochastic Lyapunov functions do not.
 Finally, we validate our approach experimentally on a set of nonlinear stochastic reinforcement learning environments with neural network policies.},
  author       = {Lechner, Mathias and Zikelic, Dorde and Chatterjee, Krishnendu and Henzinger, Thomas A},
  isbn         = {9781577358350},
  issn         = {2374-3468},
  journal      = {Proceedings of the AAAI Conference on Artificial Intelligence},
  keywords     = {General Medicine},
  number       = {7},
  pages        = {7326--7336},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{Stability verification in stochastic control systems via neural network supermartingales}},
  doi          = {10.1609/aaai.v36i7.20695},
  volume       = {36},
  year         = {2022},
}

@article{11471,
  abstract     = {Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. },
  author       = {Sack, Stefan and Medina Ramos, Raimel A and Michailidis, Alexios and Kueng, Richard and Serbyn, Maksym},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  keywords     = {General Medicine},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Avoiding barren plateaus using classical shadows}},
  doi          = {10.1103/prxquantum.3.020365},
  volume       = {3},
  year         = {2022},
}