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Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests
No full textPlant–plant interactions are key to understanding ecosystem services and shaping restoration strategies, as they can produce either negative or positive effects, determining species establishment and growth. Recognizing these interactions during early-life stages provides valuable insights for restoration in human-disturbed areas. One promising approach is nucleation planting, which establishes small clusters of native species in strategically selected sites, being particularly useful in sites with large herbivores. In southern Patagonia, livestock production has historically been the main economic activity, severely impacting extensive areas of Nothofagus antarctica forest through grazing and intentional burning to increase forage. In this context, nucleation planting with Berberis microphylla, a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate this, we conducted an experiment testing the response of trees to varying shrub number, while also assessing intraspecific effects in both species. We measured survival, biomass, and functional traits. Results showed that the combination of four shrubs surrounding a single tree maintained tree survival at levels comparable to trees growing alone, while seedlings exhibited conspecific negative plant number dependence. Additionally, B. microphylla increased its below- to above-ground biomass ratio under higher plant number, indicating resource reallocation and niche differentiation through spatial separation of root systems
Impedance-engineered Josephson parametric amplifier with single-step lithography
No full textWe present an experimental demonstration of an impedance-engineered Josephson parametric amplifier (IEJPA) fabricated in a single-step lithography process. Impedance-engineering is implemented using a lumped-element series LC circuit. We use a simpler lithography process where the entire device—impedance transformer and Josephson parametric amplifier (JPA)—is patterned in a single electron beam lithography step, followed by a double-angle Dolan-bridge technique for Al–AlOx–Al deposition. We observe amplification with 18 dB gain over a wide 400 MHz bandwidth centered around 5.3 GHz with added noise approaching the quantum limit, and a saturation power of −114 dBm. To accurately explain our experimental results, we extend existing theories for IEJPAs to incorporate the full sine nonlinearity of both the JPA and the transformer. Our work provides a route to simpler realization of broadband JPAs and a theoretical foundation for a regime of JPA operation that has been less explored in literature
Common valuations of division polynomials
No full textIn this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields
Generalized minimum 0-extension problem and discrete convexity
No full textGiven a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs
Methods in Molecular Biology
No full textMosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution
Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance
No full textTernary liquid-like thermoelectric materials have garnered significant attention due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands out for its exceptionally low sound velocity and thermal conductivity. However, the inherent poor electrical conductivity and suboptimal thermoelectric properties of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization with intrinsic doping. For the first time, this work successfully synthesizes single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and composition using a robust and reliable colloidal method. This approach represents a significant improvement over previous reports on this material. Reducing the crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects, increasing the density of states near the Fermi surface. It also introduces additional grain boundaries, which lower the lattice thermal conductivity and simplify structural design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6 nanocrystals before consolidation further enhances the thermoelectric performance. Sn acts as a donor dopant, increasing the electronic concentration while at the same time improving their mobility by reducing interface barriers, thus significantly improving the material transport properties. Additionally, the presence of Sn leads to the formation of point defects, dislocations, and secondary phases, which increase phonon scattering and further reduce the thermal conductivity. Through this synergistic optimization, the figure of merit shows a significant increase across a wide temperature range. Overall, a strategy is presented for the controlled preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal transport, and the practical application of this material to thermoelectric single-leg modules
Subchromatic numbers of powers of graphs with excluded minors
No full textA k-subcolouring of a graph G is a function f : V (G) → {0,...,k − 1} such that the set of
vertices coloured i induce a disjoint union of cliques. The subchromatic number, χsub(G),
is the minimum k such that G admits a k-subcolouring. Nešetril, ˇ Ossona de Mendez,
Pilipczuk, and Zhu (2020), recently raised the problem of finding tight upper bounds for
χsub(G2) when G is planar. We show that χsub(G2) ≤ 43 when G is planar, improving
their bound of 135. We give even better bounds when the planar graph G has larger girth.
Moreover, we show that χsub(G3) ≤ 95, improving the previous bound of 364. For these
we adapt some recent techniques of Almulhim and Kierstead (2022), while also extending
the decompositions of triangulated planar graphs of Van den Heuvel, Ossona de Mendez,
Quiroz, Rabinovich and Siebertz (2017), to planar graphs of arbitrary girth. Note that these
decompositions are the precursors of the graph product structure theorem of planar graphs.
We give improved bounds for χsub(Gp) for all p ≥ 2, whenever G has bounded treewidth,
bounded simple treewidth, bounded genus, or excludes a clique or biclique as a minor.
For this we introduce a family of parameters which form a gradation between the strong
and the weak colouring numbers. We give upper bounds for these parameters for graphs
coming from such classes.
Finally, we give a 2-approximation algorithm for the subchromatic number of graphs
having a layering in which each layer has bounded cliquewidth and this layering is
computable in polynomial time (like the class of all dth powers of planar graphs, for fixed
d). This algorithm works even if the power p and the graph G is unknown
Analytical strength-duration curve for the spiking response of the LIF neuron to an alpha-function-shaped excitatory current pulse
No full textWhether or not the neuron emits a spike in response to stimulation by an excitatory current pulse is determined by a strength-duration curve (SDC) for the pulse parameters. The SDC is a dependence of the minimal pulse amplitude required to elicit the spiking response on either the pulse duration or its decay time. Excitatory neurons affect the others through pulses of excitatory postsynaptic current. A simple yet plausible approximation for the time course of such a pulse is the alpha function, with linear rise at the start and exponential decay at the end. However, an exact analytical SDC for this case is hitherto not known, even for the leaky integrate-and-fire (LIF) neuron, the simplest spiking neuron model used in practice. We have obtained general SDC equations for the LIF neuron. Using the Lambert W function — a widely-implemented special function, we have found the exact analytical SDC for the spiking response of the LIF neuron stimulated by an excitatory current pulse in the form of the alpha function. To compare results in a unified way, we have also derived the analytical SDCs for (i) rectangular pulse, (ii) ascending ramp pulse, and (iii) instantly rising and exponentially decaying pulse. In the limit of no leakage, we show that the SDC is reduced to the classical hyperbola for all considered cases
Light-microscopy based connectomic reconstruction of mammalian brain tissue
No full textThe information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner
Data for "Pulsatile basal gene expression as a fitness determinant in bacteria"
No full textActive regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of non-functional “promoter leakiness”, merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the non-canonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g. control of costly-to-induce multi-drug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multi-drug resistance is crucial for effective public health measures