@article{10705, abstract = {Although rigidity and jamming transitions have been widely studied in physics and material science, their importance in a number of biological processes, including embryo development, tissue homeostasis, wound healing, and disease progression, has only begun to be recognized in the past few years. The hypothesis that biological systems can undergo rigidity/jamming transitions is attractive, as it would allow these systems to change their material properties rapidly and strongly. However, whether such transitions indeed occur in biological systems, how they are being regulated, and what their physiological relevance might be, is still being debated. Here, we review theoretical and experimental advances from the past few years, focusing on the regulation and role of potential tissue rigidity transitions in different biological processes.}, author = {Hannezo, Edouard B and Heisenberg, Carl-Philipp J}, issn = {1879-3088}, journal = {Trends in Cell Biology}, number = {5}, pages = {P433--444}, publisher = {Cell Press}, title = {{Rigidity transitions in development and disease}}, doi = {10.1016/j.tcb.2021.12.006}, volume = {32}, year = {2022}, } @article{10706, abstract = {This is a collection of problems composed by some participants of the workshop “Differential Geometry, Billiards, and Geometric Optics” that took place at CIRM on October 4–8, 2021.}, author = {Bialy, Misha and Fiorebe, Corentin and Glutsyuk, Alexey and Levi, Mark and Plakhov, Alexander and Tabachnikov, Serge}, issn = {2199-6806}, journal = {Arnold Mathematical Journal}, location = {Hybrid}, pages = {411--422}, publisher = {Springer Nature}, title = {{Open problems on billiards and geometric optics}}, doi = {10.1007/s40598-022-00198-y}, volume = {8}, year = {2022}, } @article{10712, abstract = {Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in a mouse model. We identified an increased migratory potential in MFSD1-/- tumor cells which was mediated by increased focal adhesion turn-over, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, down-regulation of MFSD1 expression was observed during early steps of tumorigenesis and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.}, author = {Roblek, Marko and Bicher, Julia and van Gogh, Merel and György, Attila and Seeböck, Rita and Szulc, Bozena and Damme, Markus and Olczak, Mariusz and Borsig, Lubor and Siekhaus, Daria E}, issn = {2234-943X}, journal = {Frontiers in Oncology}, publisher = {Frontiers}, title = {{The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis}}, doi = {10.3389/fonc.2022.777634}, volume = {12}, year = {2022}, } @article{10713, abstract = {Cells migrate through crowded microenvironments within tissues during normal development, immune response, and cancer metastasis. Although migration through pores and tracks in the extracellular matrix (ECM) has been well studied, little is known about cellular traversal into confining cell-dense tissues. We find that embryonic tissue invasion by Drosophila macrophages requires division of an epithelial ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM attachment formed by integrin-mediated focal adhesions next to mesodermal cells, allowing macrophages to move their nuclei ahead and invade between two immediately adjacent tissues. Invasion efficiency depends on division frequency, but reduction of adhesion strength allows macrophage entry independently of division. This work demonstrates that tissue dynamics can regulate cellular infiltration.}, author = {Akhmanova, Maria and Emtenani, Shamsi and Krueger, Daniel and György, Attila and Pereira Guarda, Mariana and Vlasov, Mikhail and Vlasov, Fedor and Akopian, Andrei and Ratheesh, Aparna and De Renzis, Stefano and Siekhaus, Daria E}, issn = {0036-8075}, journal = {Science}, number = {6591}, pages = {394--396}, publisher = {American Association for the Advancement of Science}, title = {{Cell division in tissues enables macrophage infiltration}}, doi = {10.1126/science.abj0425}, volume = {376}, year = {2022}, } @article{10714, abstract = {Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.}, author = {Martin, Elliot T. and Blatt, Patrick and Ngyuen, Elaine and Lahr, Roni and Selvam, Sangeetha and Yoon, Hyun Ah M. and Pocchiari, Tyler and Emtenani, Shamsi and Siekhaus, Daria E and Berman, Andrea and Fuchs, Gabriele and Rangan, Prashanth}, issn = {1878-1551}, journal = {Developmental Cell}, number = {7}, pages = {883--900.e10}, publisher = {Elsevier}, title = {{A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis}}, doi = {10.1016/j.devcel.2022.03.005}, volume = {57}, year = {2022}, } @article{10717, abstract = {Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots.}, author = {Wang, R and Himschoot, E and Grenzi, M and Chen, J and Safi, A and Krebs, M and Schumacher, K and Nowack, MK and Moeder, W and Yoshioka, K and Van Damme, D and De Smet, I and Geelen, D and Beeckman, T and Friml, Jiří and Costa, A and Vanneste, S}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {8}, publisher = {Oxford Academic}, title = {{Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots}}, doi = {10.1093/jxb/erac019}, volume = {73}, year = {2022}, } @article{10719, abstract = {Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development.}, author = {Yu, Z and Zhang, F and Friml, Jiří and Ding, Z}, issn = {1744-7909}, journal = {Journal of Integrative Plant Biology}, number = {2}, pages = {371--392}, publisher = {Wiley}, title = {{Auxin signaling: Research advances over the past 30 years}}, doi = {10.1111/jipb.13225}, volume = {64}, year = {2022}, } @phdthesis{10727, abstract = {Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization). In the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression. In the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners. First, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care. In the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.}, author = {Metzler, Sina}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Pathogen-mediated sexual selection and immunization in ant colonies}}, doi = {10.15479/AT:ISTA:10727}, year = {2022}, } @article{10731, abstract = {Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening.}, author = {Svoboda, Jakub and Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.}, issn = {2045-2322}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, title = {{Infection dynamics of COVID-19 virus under lockdown and reopening}}, doi = {10.1038/s41598-022-05333-5}, volume = {12}, year = {2022}, } @article{10732, abstract = {We compute the deterministic approximation of products of Sobolev functions of large Wigner matrices W and provide an optimal error bound on their fluctuation with very high probability. This generalizes Voiculescu's seminal theorem from polynomials to general Sobolev functions, as well as from tracial quantities to individual matrix elements. Applying the result to eitW for large t, we obtain a precise decay rate for the overlaps of several deterministic matrices with temporally well separated Heisenberg time evolutions; thus we demonstrate the thermalisation effect of the unitary group generated by Wigner matrices.}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1096-0783}, journal = {Journal of Functional Analysis}, number = {8}, publisher = {Elsevier}, title = {{Thermalisation for Wigner matrices}}, doi = {10.1016/j.jfa.2022.109394}, volume = {282}, year = {2022}, } @article{10733, abstract = {When a cylindrical object penetrates granular matter near a vertical boundary, it experiences two effects: its center of mass moves horizontally away from the wall, and it rotates around its symmetry axis. Here we show experimentally that, if two identical intruders instead of one are released side-by-side near the wall, both effects are also detected. However, unexpected phenomena appear due to a cooperative dynamics between the intruders. The net horizontal distance traveled by the common center of mass of the twin intruders is much larger than that traveled by one intruder released at the same initial distance from the wall, and the rotation is also larger. The experimental results are well described by the Discrete Element Method (DEM), which reveals that, as the number of intruders horizontally released side-by-side increases, the total energy dissipation per intruder decreases. Finally, DEM simulations demonstrate that the horizontal repulsion is substantially enhanced if groups of intruders are released forming a column near the wall.}, author = {Espinosa, M. and Diaz Melian, Vicente L and Serrano-Muñoz, A. and Altshuler, E.}, issn = {1434-7636}, journal = {Granular Matter}, keywords = {granular matter, boundary effects, intruder penetration, sedimentation}, number = {1}, publisher = {Springer Nature}, title = {{Intruders cooperatively interact with a wall into granular matter}}, doi = {10.1007/s10035-021-01200-8}, volume = {24}, year = {2022}, } @article{10735, abstract = {Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies.}, author = {Nauman, Muhammad and Hussain, Tayyaba and Choi, Joonyoung and Lee, Nara and Choi, Young Jai and Kang, Woun and Jo, Younjung}, issn = {1361-648X}, journal = {Journal of physics: Condensed matter}, number = {13}, publisher = {IOP Publishing}, title = {{Low-field magnetic anisotropy of Sr2IrO4}}, doi = {10.1088/1361-648X/ac484d}, volume = {34}, year = {2022}, } @article{10736, abstract = {Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought.}, author = {Lagator, Mato and Sarikas, Srdjan and Steinrueck, Magdalena and Toledo-Aparicio, David and Bollback, Jonathan P and Guet, Calin C and Tkačik, Gašper}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Predicting bacterial promoter function and evolution from random sequences}}, doi = {10.7554/eLife.64543}, volume = {11}, year = {2022}, } @article{10737, abstract = {We consider two models for the sequence labeling (tagging) problem. The first one is a Pattern-Based Conditional Random Field (PB), in which the energy of a string (chain labeling) x=x1⁢…⁢xn∈Dn is a sum of terms over intervals [i,j] where each term is non-zero only if the substring xi⁢…⁢xj equals a prespecified word w∈Λ. The second model is a Weighted Context-Free Grammar (WCFG) frequently used for natural language processing. PB and WCFG encode local and non-local interactions respectively, and thus can be viewed as complementary. We propose a Grammatical Pattern-Based CRF model (GPB) that combines the two in a natural way. We argue that it has certain advantages over existing approaches such as the Hybrid model of Benedí and Sanchez that combines N-grams and WCFGs. The focus of this paper is to analyze the complexity of inference tasks in a GPB such as computing MAP. We present a polynomial-time algorithm for general GPBs and a faster version for a special case that we call Interaction Grammars.}, author = {Takhanov, Rustem and Kolmogorov, Vladimir}, issn = {1571-4128}, journal = {Intelligent Data Analysis}, number = {1}, pages = {257--272}, publisher = {IOS Press}, title = {{Combining pattern-based CRFs and weighted context-free grammars}}, doi = {10.3233/IDA-205623}, volume = {26}, year = {2022}, } @inproceedings{10752, abstract = {The digitalization of almost all aspects of our everyday lives has led to unprecedented amounts of data being freely available on the Internet. In particular social media platforms provide rich sources of user-generated data, though typically in unstructured form, and with high diversity, such as written in many different languages. Automatically identifying meaningful information in such big data resources and extracting it efficiently is one of the ongoing challenges of our time. A common step for this is sentiment analysis, which forms the foundation for tasks such as opinion mining or trend prediction. Unfortunately, publicly available tools for this task are almost exclusively available for English-language texts. Consequently, a large fraction of the Internet users, who do not communicate in English, are ignored in automatized studies, a phenomenon called rare-language discrimination.In this work we propose a technique to overcome this problem by a truly multi-lingual model, which can be trained automatically without linguistic knowledge or even the ability to read the many target languages. The main step is to combine self-annotation, specifically the use of emoticons as a proxy for labels, with multi-lingual sentence representations.To evaluate our method we curated several large datasets from data obtained via the free Twitter streaming API. The results show that our proposed multi-lingual training is able to achieve sentiment predictions at the same quality level for rare languages as for frequent ones, and in particular clearly better than what mono-lingual training achieves on the same data. }, author = {Lampert, Jasmin and Lampert, Christoph}, booktitle = {2021 IEEE International Conference on Big Data}, isbn = {9781665439022}, location = {Orlando, FL, United States}, pages = {5185--5192}, publisher = {IEEE}, title = {{Overcoming rare-language discrimination in multi-lingual sentiment analysis}}, doi = {10.1109/bigdata52589.2021.9672003}, year = {2022}, } @article{10753, abstract = {This is a comment on "Meta-learning synaptic plasticity and memory addressing for continual familiarity detection." Neuron. 2022 Feb 2;110(3):544-557.e8.}, author = {Confavreux, Basile J and Vogels, Tim P}, issn = {1097-4199}, journal = {Neuron}, number = {3}, pages = {361--362}, publisher = {Elsevier}, title = {{A familiar thought: Machines that replace us?}}, doi = {10.1016/j.neuron.2022.01.014}, volume = {110}, year = {2022}, } @article{10754, abstract = {Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.}, author = {Chang, Yan and Funk, Marah and Roy, Souvik and Stephenson, Elizabeth R and Choi, Sangyong and Kojouharov, Hristo V. and Chen, Benito and Pan, Zui}, issn = {14220067}, journal = {International Journal of Molecular Sciences}, number = {3}, publisher = {MDPI}, title = {{Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer}}, doi = {10.3390/ijms23031763}, volume = {23}, year = {2022}, } @article{10755, abstract = {We provide a definition of the effective mass for the classical polaron described by the Landau–Pekar (LP) equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by LP (1948 J. Exp. Theor. Phys. 18 419–423).}, author = {Feliciangeli, Dario and Rademacher, Simone Anna Elvira and Seiringer, Robert}, issn = {1751-8121}, journal = {Journal of Physics A: Mathematical and Theoretical}, number = {1}, publisher = {IOP Publishing}, title = {{The effective mass problem for the Landau-Pekar equations}}, doi = {10.1088/1751-8121/ac3947}, volume = {55}, year = {2022}, } @phdthesis{10759, abstract = {In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data.}, author = {Rzadkowski, Wojciech}, issn = {2663-337X}, pages = {120}, publisher = {Institute of Science and Technology Austria}, title = {{Analytic and machine learning approaches to composite quantum impurities}}, doi = {10.15479/at:ista:10759}, year = {2022}, } @article{10763, abstract = {AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance.}, author = {Herguedas, Beatriz and Kohegyi, Bianka K. and Dohrke, Jan Niklas and Watson, Jake and Zhang, Danyang and Ho, Hinze and Shaikh, Saher A. and Lape, Remigijus and Krieger, James M. and Greger, Ingo H.}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor}}, doi = {10.1038/s41467-022-28404-7}, volume = {13}, year = {2022}, }