@article{15331, abstract = {This is a test entry.}, author = {Ernst, Doris}, journal = {Try Out}, number = {2}, publisher = {Publish Here}, title = {{Test Entry}}, volume = {1}, year = {2026}, } @article{15333, author = {Ernst, Doris}, journal = {PokeWiki}, title = {{Nachtara}}, year = {2026}, } @article{15287, author = {Ernst, Doris}, journal = {asdfew}, title = {{awera}}, year = {2025}, } @book{15310, author = {Ernst, Doris}, keywords = {Frustrating}, publisher = {Springer Nature}, title = {{Vacation}}, year = {2025}, } @unpublished{15315, author = {Ernst, Doris}, booktitle = {PokeWiki}, keywords = {Pokemon, Elektro}, title = {{Pikachu}}, year = {2025}, } @article{15316, author = {Ernst, Doris}, journal = {PokeWiki}, keywords = {Pokemon, Nintendo}, title = {{Raichu}}, year = {2025}, } @article{15307, author = {Ernst, Doris}, journal = {Trollhausen}, keywords = {Norway, Troll, Fjell}, publisher = {Trollingten}, title = {{Troll}}, year = {2025}, } @misc{14705, abstract = {Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.}, author = {Elkrewi, Marwan N}, keywords = {sex chromosome evolution, genome assembly, dosage compensation}, publisher = {Institute of Science and Technology Austria}, title = {{Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation"}}, doi = {10.15479/AT:ISTA:14705}, year = {2024}, } @phdthesis{14711, abstract = {In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies. For species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges as well as in highly fragmented populations. In this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters. Chapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate. In chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist. The focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts. Chapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence. Overall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.}, author = {Olusanya, Oluwafunmilola O}, issn = {2663 - 337X}, pages = {183}, publisher = {Institute of Science and Technology Austria}, title = {{Local adaptation, genetic load and extinction in metapopulations}}, doi = {10.15479/at:ista:14711}, year = {2024}, } @inproceedings{14769, abstract = {For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.}, author = {Henzinger, Monika H and Saulpic, David and Sidl, Leonhard}, booktitle = {2024 Proceedings of the Symposium on Algorithm Engineering and Experiments}, location = {Alexandria, VA, United States}, pages = {220--233}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Experimental evaluation of fully dynamic k-means via coresets}}, doi = {10.1137/1.9781611977929.17}, year = {2024}, } @article{14794, abstract = {Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects. For complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3}, author = {Hansen, Andi H and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, number = {1}, publisher = {Elsevier}, title = {{Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers}}, doi = {10.1016/j.xpro.2023.102795}, volume = {5}, year = {2024}, } @article{14795, abstract = {Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells.}, author = {Arslan, Feyza N and Hannezo, Edouard B and Merrin, Jack and Loose, Martin and Heisenberg, Carl-Philipp J}, issn = {1879-0445}, journal = {Current Biology}, number = {1}, pages = {171--182.e8}, publisher = {Elsevier}, title = {{Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts}}, doi = {10.1016/j.cub.2023.11.067}, volume = {34}, year = {2024}, } @article{14797, abstract = {We study a random matching problem on closed compact 2 -dimensional Riemannian manifolds (with respect to the squared Riemannian distance), with samples of random points whose common law is absolutely continuous with respect to the volume measure with strictly positive and bounded density. We show that given two sequences of numbers n and m=m(n) of points, asymptotically equivalent as n goes to infinity, the optimal transport plan between the two empirical measures μn and νm is quantitatively well-approximated by (Id,exp(∇hn))#μn where hn solves a linear elliptic PDE obtained by a regularized first-order linearization of the Monge-Ampère equation. This is obtained in the case of samples of correlated random points for which a stretched exponential decay of the α -mixing coefficient holds and for a class of discrete-time Markov chains having a unique absolutely continuous invariant measure with respect to the volume measure.}, author = {Clozeau, Nicolas and Mattesini, Francesco}, issn = {1432-2064}, journal = {Probability Theory and Related Fields}, keywords = {Troll, Norway, Fjell}, publisher = {Springer Nature}, title = {{Annealed quantitative estimates for the quadratic 2D-discrete random matching problem}}, doi = {10.1007/s00440-023-01254-0}, year = {2024}, } @article{14802, abstract = {Frequency-stable lasers form the back bone of precision measurements in science and technology. Such lasers typically attain their stability through frequency locking to reference cavities. State-of-the-art locking performances to date had been achieved using frequency modulation based methods, complemented with active drift cancellation systems. We demonstrate an all passive, modulation-free laser-cavity locking technique (squash locking) that utilizes changes in spatial beam ellipticity for error signal generation, and a coherent polarization post-selection for noise resilience. By comparing two identically built proof-of-principle systems, we show a frequency locking instability of 5×10−7 relative to the cavity linewidth at 10 s averaging. The results surpass the demonstrated performances of methods engineered over the last five decades, potentially enabling an advancement in the precision control of lasers, while creating avenues for bridging the performance gaps between industrial grade lasers with scientific ones due to the afforded simplicity and scalability.}, author = {Diorico, Fritz R and Zhutov, Artem and Hosten, Onur}, issn = {2334-2536}, journal = {Optica}, keywords = {Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials}, number = {1}, pages = {26--31}, publisher = {Optica Publishing Group}, title = {{Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth}}, doi = {10.1364/optica.507451}, volume = {11}, year = {2024}, } @phdthesis{14821, author = {Chiossi, Heloisa}, issn = {2663 - 337X}, pages = {89}, publisher = {Institute of Science and Technology Austria}, title = {{Adaptive hierarchical representations in the hippocampus}}, doi = {10.15479/at:ista:14821}, year = {2024}, } @article{14826, abstract = {The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.}, author = {Kuhn, Andre and Roosjen, Mark and Mutte, Sumanth and Dubey, Shiv Mani and Carrillo Carrasco, Vanessa Polet and Boeren, Sjef and Monzer, Aline and Koehorst, Jasper and Kohchi, Takayuki and Nishihama, Ryuichi and Fendrych, Matyas and Sprakel, Joris and Friml, Jiří and Weijers, Dolf}, issn = {1097-4172}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {1}, pages = {130--148.e17}, publisher = {Elsevier}, title = {{RAF-like protein kinases mediate a deeply conserved, rapid auxin response}}, doi = {10.1016/j.cell.2023.11.021}, volume = {187}, year = {2024}, } @article{14828, abstract = {Production of hydrogen at large scale requires development of non-noble, inexpensive, and high-performing catalysts for constructing water-splitting devices. Herein, we report the synthesis of Zn-doped NiO heterostructure (ZnNiO) catalysts at room temperature via a coprecipitation method followed by drying (at 80 °C, 6 h) and calcination at an elevated temperature of 400 °C for 5 h under three distinct conditions, namely, air, N2, and vacuum. The vacuum-synthesized catalyst demonstrates a low overpotential of 88 mV at −10 mA cm–2 and a small Tafel slope of 73 mV dec–1 suggesting relatively higher charge transfer kinetics for hydrogen evolution reactions (HER) compared with the specimens synthesized under N2 or O2 atmosphere. It also demonstrates an oxygen evolution (OER) overpotential of 260 mV at 10 mA cm–2 with a low Tafel slope of 63 mV dec–1. In a full-cell water-splitting device, the vacuum-synthesized ZnNiO heterostructure demonstrates a cell voltage of 1.94 V at 50 mA cm–2 and shows remarkable stability over 24 h at a high current density of 100 mA cm–2. It is also demonstrated in this study that Zn-doping, surface, and interface engineering in transition-metal oxides play a crucial role in efficient electrocatalytic water splitting. Also, the results obtained from density functional theory (DFT + U = 0–8 eV), where U is the on-site Coulomb repulsion parameter also known as Hubbard U, based electronic structure calculations confirm that Zn doping constructively modifies the electronic structure, in both the valence band and the conduction band, and found to be suitable in tailoring the carrier’s effective masses of electrons and holes. The decrease in electron’s effective masses together with large differences between the effective masses of electrons and holes is noticed, which is found to be mainly responsible for achieving the best water-splitting performance from a 9% Zn-doped NiO sample prepared under vacuum.}, author = {Kiran, Gundegowda Kalligowdanadoddi and Singh, Saurabh and Mahato, Neelima and Sreekanth, Thupakula Venkata Madhukar and Dillip, Gowra Raghupathy and Yoo, Kisoo and Kim, Jonghoon}, issn = {2574-0962}, journal = {ACS Applied Energy Materials}, keywords = {Electrical and Electronic Engineering, Materials Chemistry, Electrochemistry, Energy Engineering and Power Technology, Chemical Engineering (miscellaneous)}, number = {1}, pages = {214--229}, publisher = {American Chemical Society}, title = {{Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity}}, doi = {10.1021/acsaem.3c02519}, volume = {7}, year = {2024}, } @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{14841, abstract = {De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy.}, author = {Clatot, Jerome and Currin, Christopher and Liang, Qiansheng and Pipatpolkai, Tanadet and Massey, Shavonne L. and Helbig, Ingo and Delemotte, Lucie and Vogels, Tim P and Covarrubias, Manuel and Goldberg, Ethan M.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {3}, publisher = {Proceedings of the National Academy of Sciences}, title = {{A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction}}, doi = {10.1073/pnas.2307776121}, volume = {121}, year = {2024}, } @article{14843, abstract = {The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.}, author = {Chen, JingJing and Kaufmann, Walter and Chen, Chong and Arai, Itaru and Kim, Olena and Shigemoto, Ryuichi and Jonas, Peter M}, issn = {1097-4199}, journal = {Neuron}, publisher = {Elsevier}, title = {{Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse}}, doi = {10.1016/j.neuron.2023.12.002}, year = {2024}, }