@article{17148,
  abstract     = {During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.},
  author       = {Krammer, Teresa and Stuart, Hannah T. and Gromberg, Elena and Ishihara, Keisuke and Cislo, Dillon and Melchionda, Manuela and Becerril Perez, Fernando and Wang, Jingkui and Costantini, Elena and Rus, Stefanie and Arbanas, Laura and Hörmann, Alexandra and Neumüller, Ralph A. and Elvassore, Nicola and Siggia, Eric and Briscoe, James and Kicheva, Anna and Tanaka, Elly M.},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {15},
  pages        = {1940--1953.e10},
  publisher    = {Elsevier},
  title        = {{Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition}},
  doi          = {10.1016/j.devcel.2024.04.021},
  volume       = {59},
  year         = {2024},
}

@article{18601,
  abstract     = {Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.
For complete details on the use and execution of this protocol, please refer to Lehr et al.1},
  author       = {Rus, Stefanie and Merrin, Jack and Kulig, Monika Aleksandra and Minchington, Thomas and Kicheva, Anna},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Elsevier},
  title        = {{Protocol for fabricating elastomeric stencils for patterned stem cell differentiation}},
  doi          = {10.1016/j.xpro.2024.103187},
  volume       = {5},
  year         = {2024},
}

@article{17890,
  abstract     = {Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.},
  author       = {Elkrewi, Marwan N and Vicoso, Beatriz},
  issn         = {1553-7404},
  journal      = {PLoS Genetics},
  number       = {8},
  publisher    = {Public Library of Science},
  title        = {{Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome}},
  doi          = {10.1371/journal.pgen.1011376},
  volume       = {20},
  year         = {2024},
}

@phdthesis{18129,
  abstract     = {State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate
for qubits due to their long coherence, tunability, control, and readout. However, their natural
coupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.
Long-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a
coherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of
high-impedance resonators to compensate for this has gained significant attention in the past
decade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not
exceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The
large kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude
enhancement. However, fully exploiting the potential of disordered or granular superconductors
is challenging as their impedances close to the superconductor-to-insulator transition are
difficult to control reproducibly. We report on the realization of a wireless ohmmeter which
allows in situ resistance measurements during film deposition and, therefore, indirect control
of the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators
with characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due
to the large sheet kinetic inductance of up to 3 nH □−1
. By integrating an 8 kW resonator
with a germanium double QD, we demonstrate a strong charge-photon coupling with the
highest rate reported, 566 MHz. The demonstrated method and grAl properties make these
resonators suitable for boosting the spin-photon coupling strength, a crucial requirement for
fast, high-fidelity, long-distance two-qubit gates.
},
  author       = {Janik, Marian},
  issn         = {2663-337X},
  pages        = {164},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors}},
  doi          = {10.15479/at:ista:18129},
  year         = {2024},
}

@unpublished{18144,
  abstract     = {High kinetic inductance superconductors are gaining increasing interest for
the realisation of qubits, amplifiers and detectors. Moreover, thanks to their
high impedance, quantum buses made of such materials enable large zero-point
fluctuations of the voltage, boosting the coupling rates to spin and charge
qubits. However, fully exploiting the potential of disordered or granular
superconductors is challenging, as their inductance and, therefore, impedance
at high values are difficult to control. Here we have integrated a granular
aluminium resonator, having a characteristic impedance exceeding the resistance
quantum, with a germanium double quantum dot and demonstrate strong
charge-photon coupling with a rate of $g_\text{c}/2\pi= (566 \pm 2)$ MHz. This
was achieved due to the realisation of a wireless ohmmeter, which allows
\emph{in situ} measurements during film deposition and, therefore, control of
the kinetic inductance of granular aluminium films. Reproducible fabrication of
circuits with impedances (inductances) exceeding 13 k$\Omega$ (1 nH per square)
is now possible. This broadly applicable method opens the path for novel qubits
and high-fidelity, long-distance two-qubit gates.},
  author       = {Janik, Marian and Roux, Kevin Etienne Robert and Borja Espinosa, Carla N and Sagi, Oliver and Baghdadi, Abdulhamid and Adletzberger, Thomas and Calcaterra, Stefano and Botifoll, Marc and Manjón, Alba Garzón and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Pop, Ioan M. and Katsaros, Georgios},
  booktitle    = {arXiv},
  title        = {{Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors}},
  doi          = {10.48550/arXiv.2407.03079},
  year         = {2024},
}

@article{14796,
  abstract     = {Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.},
  author       = {Stankowski, Sean and Zagrodzka, Zuzanna B. and Garlovsky, Martin D. and Pal, Arka and Shipilina, Daria and Garcia Castillo, Diego Fernando and Lifchitz, Hila and Le Moan, Alan and Leder, Erica and Reeve, James and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6678},
  pages        = {114--119},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The genetic basis of a recent transition to live-bearing in marine snails}},
  doi          = {10.1126/science.adi2982},
  volume       = {383},
  year         = {2024},
}

@article{17183,
  abstract     = {The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology.},
  author       = {Sett, Riya and Hassani, Farid and Phan, Duc T and Barzanjeh, Shabir and Vukics, Andras and Fink, Johannes M},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Emergent macroscopic bistability induced by a single superconducting qubit}},
  doi          = {10.1103/prxquantum.5.010327},
  volume       = {5},
  year         = {2024},
}

@phdthesis{17881,
  abstract     = {This work can be broadly classified into the study of critical phenomena in a one dimensional
array of Josephson junctions. While we study quantum criticality when the array is in thermal
equilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the
array at a critical non-zero bias. This work furthers our knowledge in understanding quantum
critical behaviour at finite temperatures in a one dimensional Josephson array, while also
establishing relaxation behaviour dual to that observed in a single Josephson junction.
Chapter 1 briefly introduces the model to understand superconductor-insulator phase transition
in a one dimensional Josephson array and points out the state of the field from where we
started our zero-bias experiments. In this context it discusses the phase-charge duality observed
in a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the
ground for our non-equilibrium study of the array.
Chapter 2 shows the experimental setup and the chip layout of the device we measured.
In chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads
to a regime of superconductivity at high temperature, arising from the melted zero-temperature
insulator. Our results quantitatively explain the low-temperature onset of superconductivity in
nominally insulating regimes, and the transition to the strongly insulating phase. We further
present, to our knowledge, the first understanding of the onset of anomalous-metallic resistance
saturation [30]. This work demonstrates a non-trivial interplay between thermal effects and
quantum criticality. A practical consequence is that, counterintuitively, the coherence of
high-impedance quantum circuits is expected to be stabilized by thermal fluctuations.
In chapter 4, we show relaxation oscillations in a current-biased one dimensional array of
Josephson junctions. These oscillations are well described by a circuit model, dual to the
ordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in
current plateaux. The relaxation step is found to obey a characteristic self-consistent relation,
suggesting that it is governed by overheating effects.
Chapter 5 describes the various checks and analysis we performed to support our conclusions
made in chapters 3 and 4.
Finally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic
simulations we performed to fabricate our devices.},
  author       = {Mukhopadhyay, Soham},
  isbn         = {978-3-99078-043-5},
  issn         = {2663-337X},
  pages        = {82},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Thermal effects in one dimensional Josephson chains}},
  doi          = {10.15479/at:ista:17881},
  year         = {2024},
}

@unpublished{18057,
  abstract     = {We report relaxation oscillations in a one-dimensional array of Josephson
junctions. The oscillations are circuit-dual to those ordinarily observed in
single junctions. The dual circuit quantitatively accounts for temporal
dynamics of the array, including the dependence on biasing conditions.
Injection locking the oscillations results in well-developed current plateaux.
A thermal model explains the relaxation step of the oscillations.},
  author       = {Mukhopadhyay, Soham and Lancheros Naranjo, Diego A and Senior, Jorden L and Higginbotham, Andrew P},
  booktitle    = {arXiv},
  title        = {{Dual relaxation oscillations in a Josephson junction array}},
  doi          = {10.48550/arXiv.2408.07829},
  year         = {2024},
}

@misc{18978,
  abstract     = {Data analysis files for the manuscript "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit".

This contains the raw data and the data analysis files for generating the figures in the manuscript.

 Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.
 Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file
 Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.
Figure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  },
  author       = {Sett, Riya and Hassani, Farid and Phan, Duc T and Barzanjeh, Shabir and Vukics, Andras and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Data Analysis files for "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit"}},
  doi          = {10.5281/ZENODO.10518320},
  year         = {2024},
}

@article{15009,
  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, is 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 A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, 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       = {Bett, Vincent K and Macon, Ariana and Vicoso, Beatriz and Elkrewi, Marwan N},
  issn         = {1759-6653},
  journal      = {Genome Biology and Evolution},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation}},
  doi          = {10.1093/gbe/evae006},
  volume       = {16},
  year         = {2024},
}

@article{11479,
  abstract     = {Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.},
  author       = {De Jode, Aurélien and Le Moan, Alan and Johannesson, Kerstin and Faria, Rui and Stankowski, Sean and Westram, Anja M and Butlin, Roger K. and Rafajlović, Marina and Fraisse, Christelle},
  issn         = {1752-4571},
  journal      = {Evolutionary Applications},
  number       = {2},
  pages        = {542--559},
  publisher    = {Wiley},
  title        = {{Ten years of demographic modelling of divergence and speciation in the sea}},
  doi          = {10.1111/eva.13428},
  volume       = {16},
  year         = {2023},
}

@article{11706,
  abstract     = {We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. },
  author       = {Liebenau, Anita and Mattos, Letícia and Mendonca Dos Santos, Walner and Skokan, Jozef},
  issn         = {1098-2418},
  journal      = {Random Structures and Algorithms},
  number       = {4},
  pages        = {1035--1055},
  publisher    = {Wiley},
  title        = {{Asymmetric Ramsey properties of random graphs involving cliques and cycles}},
  doi          = {10.1002/rsa.21106},
  volume       = {62},
  year         = {2023},
}

@article{11741,
  abstract     = {Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {1432-2064},
  journal      = {Probability Theory and Related Fields},
  pages        = {1183–1218},
  publisher    = {Springer Nature},
  title        = {{Quenched universality for deformed Wigner matrices}},
  doi          = {10.1007/s00440-022-01156-7},
  volume       = {185},
  year         = {2023},
}

@article{11999,
  abstract     = {A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.},
  author       = {Arroyo Guevara, Alan M and Klute, Fabian and Parada, Irene and Vogtenhuber, Birgit and Seidel, Raimund and Wiedera, Tilo},
  issn         = {1432-0444},
  journal      = {Discrete and Computational Geometry},
  pages        = {745–770},
  publisher    = {Springer Nature},
  title        = {{Inserting one edge into a simple drawing is hard}},
  doi          = {10.1007/s00454-022-00394-9},
  volume       = {69},
  year         = {2023},
}

@article{12086,
  abstract     = {We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.},
  author       = {Edelsbrunner, Herbert and Osang, Georg F},
  issn         = {1432-0541},
  journal      = {Algorithmica},
  pages        = {277--295},
  publisher    = {Springer Nature},
  title        = {{A simple algorithm for higher-order Delaunay mosaics and alpha shapes}},
  doi          = {10.1007/s00453-022-01027-6},
  volume       = {85},
  year         = {2023},
}

@article{12087,
  abstract     = {Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.},
  author       = {Wirth, Melchior and Zhang, Haonan},
  issn         = {1424-0637},
  journal      = {Annales Henri Poincare},
  pages        = {717--750},
  publisher    = {Springer Nature},
  title        = {{Curvature-dimension conditions for symmetric quantum Markov semigroups}},
  doi          = {10.1007/s00023-022-01220-x},
  volume       = {24},
  year         = {2023},
}

@article{12104,
  abstract     = {We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.},
  author       = {Dello Schiavo, Lorenzo and Wirth, Melchior},
  issn         = {1424-3202},
  journal      = {Journal of Evolution Equations},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{Ergodic decompositions of Dirichlet forms under order isomorphisms}},
  doi          = {10.1007/s00028-022-00859-7},
  volume       = {23},
  year         = {2023},
}

@article{12106,
  abstract     = {Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.},
  author       = {Yeung, Jake and Florescu, Maria and Zeller, Peter and De Barbanson, Buys Anton and Wellenstein, Max D. and Van Oudenaarden, Alexander},
  issn         = {1546-1696},
  journal      = {Nature Biotechnology},
  pages        = {813–823},
  publisher    = {Springer Nature},
  title        = {{scChIX-seq infers dynamic relationships between histone modifications in single cells}},
  doi          = {10.1038/s41587-022-01560-3},
  volume       = {41},
  year         = {2023},
}

@article{12113,
  abstract     = {The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.},
  author       = {Zhang, Li and Liu, Xingyu and Wu, Ting and Xu, Shengduo and Suo, Guoquan and Ye, Xiaohui and Hou, Xiaojiang and Yang, Yanling and Liu, Qingfeng and Wang, Hongqiang},
  issn         = {0169-4332},
  journal      = {Applied Surface Science},
  keywords     = {Surfaces, Coatings and Films, Condensed Matter Physics, Surfaces and Interfaces, General Physics and Astronomy, General Chemistry},
  publisher    = {Elsevier},
  title        = {{Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient}},
  doi          = {10.1016/j.apsusc.2022.156101},
  volume       = {613},
  year         = {2023},
}