@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 Steinrück, 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         = {1422-0067},
  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},
}

@article{10758,
  abstract     = {5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.},
  author       = {Dubini, Romeo C. A. and Korytiaková, Eva and Schinkel, Thea and Heinrichs, Pia and Carell, Thomas and Rovo, Petra},
  issn         = {2694-2445},
  journal      = {ACS Physical Chemistry Au},
  number       = {3},
  pages        = {237--246},
  publisher    = {American Chemical Society},
  title        = {{1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives}},
  doi          = {10.1021/acsphyschemau.1c00050},
  volume       = {2},
  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         = {2041-1723},
  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},
}

@article{10764,
  abstract     = {Presynaptic glutamate replenishment is fundamental to brain function. In high activity regimes, such as epileptic episodes, this process is thought to rely on the glutamate-glutamine cycle between neurons and astrocytes. However the presence of an astroglial glutamine supply, as well as its functional relevance in vivo in the healthy brain remain controversial, partly due to a lack of tools that can directly examine glutamine transfer. Here, we generated a fluorescent probe that tracks glutamine in live cells, which provides direct visual evidence of an activity-dependent glutamine supply from astroglial networks to presynaptic structures under physiological conditions. This mobilization is mediated by connexin43, an astroglial protein with both gap-junction and hemichannel functions, and is essential for synaptic transmission and object recognition memory. Our findings uncover an indispensable recruitment of astroglial glutamine in physiological synaptic activity and memory via an unconventional pathway, thus providing an astrocyte basis for cognitive processes.},
  author       = {Cheung, Giselle T and Bataveljic, Danijela and Visser, Josien and Kumar, Naresh and Moulard, Julien and Dallérac, Glenn and Mozheiko, Daria and Rollenhagen, Astrid and Ezan, Pascal and Mongin, Cédric and Chever, Oana and Bemelmans, Alexis Pierre and Lübke, Joachim and Leray, Isabelle and Rouach, Nathalie},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Physiological synaptic activity and recognition memory require astroglial glutamine}},
  doi          = {10.1038/s41467-022-28331-7},
  volume       = {13},
  year         = {2022},
}

@article{10768,
  abstract     = {Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development.},
  author       = {Hajny, Jakub and Tan, Shutang and Friml, Jiří},
  issn         = {1369-5266},
  journal      = {Current Opinion in Plant Biology},
  number       = {2},
  publisher    = {Elsevier},
  title        = {{Auxin canalization: From speculative models toward molecular players}},
  doi          = {10.1016/j.pbi.2022.102174},
  volume       = {65},
  year         = {2022},
}

@article{10769,
  abstract     = {studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía de entrelazamiento en un intervalo, construimos la función c entrópica que es finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo alcance proveniente de la superficie de Fermi. Motivados por trabajos previos de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una medida de correlación entre diferentes regiones. Usando una expansión de distancia grande desarrollada por Cardy, argumentamos que la información mutua detecta las correlaciones inducidas por la superficie de Fermi todavía al orden dominante en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones de Renyi para distinguir estados con diferente carga. Encontramos que estados en diferentes sectores de superselección dan origen a un comportamiento super-extensivo en la entropía relativa.},
  author       = {Daguerre, L. and Torroba, G. and Medina Ramos, Raimel A and Solís, M.},
  issn         = {1850-1168},
  journal      = {Anales de la Asociacion Fisica Argentina},
  number       = {4},
  pages        = {93--98},
  publisher    = {Asociación Física Argentina},
  title        = {{Non relativistic quantum field theory: Dynamics and irreversibility}},
  doi          = {10.31527/analesafa.2021.32.4.93},
  volume       = {32},
  year         = {2022},
}

@article{10771,
  abstract     = {A critical overview of the theory of the chirality-induced spin selectivity (CISS) effect, that is, phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes, is provided. Based on discussions in a recently held workshop, and further work published since, the status of CISS effects—in electron transmission, electron transport, and chemical reactions—is reviewed. For each, a detailed discussion of the state-of-the-art in theoretical understanding is provided and remaining challenges and research opportunities are identified.},
  author       = {Evers, Ferdinand and Aharony, Amnon and Bar-Gill, Nir and Entin-Wohlman, Ora and Hedegård, Per and Hod, Oded and Jelinek, Pavel and Kamieniarz, Grzegorz and Lemeshko, Mikhail and Michaeli, Karen and Mujica, Vladimiro and Naaman, Ron and Paltiel, Yossi and Refaely-Abramson, Sivan and Tal, Oren and Thijssen, Jos and Thoss, Michael and Van Ruitenbeek, Jan M. and Venkataraman, Latha and Waldeck, David H. and Yan, Binghai and Kronik, Leeor},
  issn         = {1521-4095},
  journal      = {Advanced Materials},
  number       = {13},
  publisher    = {Wiley},
  title        = {{Theory of chirality induced spin selectivity: Progress and challenges}},
  doi          = {10.1002/adma.202106629},
  volume       = {34},
  year         = {2022},
}

@article{10772,
  abstract     = {We introduce tropical corals, balanced trees in a half-space, and show that they correspond to holomorphic polygons capturing the product rule in Lagrangian Floer theory for the elliptic curve. We then prove a correspondence theorem equating counts of tropical corals to punctured log Gromov–Witten invariants of the Tate curve. This implies that the homogeneous coordinate ring of the mirror to the Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming a prediction of homological mirror symmetry.},
  author       = {Arguez, Nuroemuer Huelya},
  issn         = {1469-7750},
  journal      = {Journal of the London Mathematical Society},
  number       = {1},
  pages        = {343--411},
  publisher    = {London Mathematical Society},
  title        = {{Mirror symmetry for the Tate curve via tropical and log corals}},
  doi          = {10.1112/jlms.12515},
  volume       = {105},
  year         = {2022},
}

@article{10773,
  abstract     = {The Voronoi tessellation in Rd is defined by locally minimizing the power distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined by locally maximizing the negative power distance to other such points. We prove that the average of the two piecewise quadratic functions is piecewise linear, and that all three functions have the same critical points and values. Discretizing the two piecewise quadratic functions, we get the alpha shapes as sublevel sets of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel sets of the discrete function on the Voronoi tessellation. For the same non-critical value, the corresponding shapes are disjoint, separated by a narrow channel that contains no critical points but the entire level set of the piecewise linear function.},
  author       = {Biswas, Ranita and Cultrera Di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza},
  issn         = {1432-0444},
  journal      = {Discrete and Computational Geometry},
  pages        = {811--842},
  publisher    = {Springer Nature},
  title        = {{Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics}},
  doi          = {10.1007/s00454-022-00371-2},
  volume       = {67},
  year         = {2022},
}

@inproceedings{10774,
  abstract     = {We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.},
  author       = {Bartocci, Ezio and Ferrere, Thomas and Henzinger, Thomas A and Nickovic, Dejan and Da Costa, Ana Oliveira},
  booktitle    = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
  isbn         = {9783030945824},
  issn         = {1611-3349},
  location     = {Philadelphia, PA, United States},
  pages        = {1--19},
  publisher    = {Springer Nature},
  title        = {{Flavors of sequential information flow}},
  doi          = {10.1007/978-3-030-94583-1_1},
  volume       = {13182},
  year         = {2022},
}

@article{10775,
  abstract     = {List-decodability of Reed–Solomon codes has received a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance.},
  author       = {Ferber, Asaf and Kwan, Matthew Alan and Sauermann, Lisa},
  issn         = {1557-9654},
  journal      = {IEEE Transactions on Information Theory},
  number       = {6},
  pages        = {3823--3828},
  publisher    = {IEEE},
  title        = {{List-decodability with large radius for Reed-Solomon codes}},
  doi          = {10.1109/TIT.2022.3148779},
  volume       = {68},
  year         = {2022},
}

@article{10776,
  abstract     = {Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p0 is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n≥2, there are always at least three distinct barycentric cuts through the point p0∈K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.},
  author       = {Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
  issn         = {1432-0444},
  journal      = {Discrete and Computational Geometry},
  pages        = {1133--1154},
  publisher    = {Springer Nature},
  title        = {{Barycentric cuts through a convex body}},
  doi          = {10.1007/s00454-021-00364-7},
  volume       = {68},
  year         = {2022},
}

@article{10787,
  abstract     = {A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.
This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.},
  author       = {Barton, Nicholas H and Olusanya, Oluwafunmilola O},
  issn         = {1471-2970},
  journal      = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  keywords     = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology},
  number       = {1848},
  publisher    = {The Royal Society},
  title        = {{The response of a metapopulation to a changing environment}},
  doi          = {10.1098/rstb.2021.0009},
  volume       = {377},
  year         = {2022},
}

@article{10791,
  abstract     = {The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general.},
  author       = {Hansen, Andi H and Pauler, Florian and Riedl, Michael and Streicher, Carmen and Heger, Anna-Magdalena and Laukoter, Susanne and Sommer, Christoph M and Nicolas, Armel and Hof, Björn and Tsai, Li Huei and Rülicke, Thomas and Hippenmeyer, Simon},
  issn         = {2753-149X},
  journal      = {Oxford Open Neuroscience},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Tissue-wide effects override cell-intrinsic gene function in radial neuron migration}},
  doi          = {10.1093/oons/kvac009},
  volume       = {1},
  year         = {2022},
}