Spontaneous symmetry breaking in plasmon lattice lasers.

Spontaneous symmetry breaking (SSB) is key for our understanding of phase transitions and the spontaneous emergence of order. In this work, we report that, for a two-dimensional (2D) periodic metasurface with gain, SSB occurs in the lasing transition. We study diffractive hexagonal plasmon nanoparticle lattices, where the K-points in momentum space provide two modes that are degenerate in frequency and identically distributed in space. Using femtosecond pulses to energize the gain medium, we simultaneously capture single-shot real-space and Fourier-space images of laser emission. By combining Fourier and real space, we resolve the two order parameters for which symmetry breaking simultaneously occurs: spatial parity and U(1) (rotational) symmetry breaking, evident respectively as random relative mode amplitude and phase. The methodology reported in this work is generally applicable to 2D plasmonic and dielectric metasurfaces and opens numerous opportunities for the study of SSB and the emergence of spatial coherence in metaphotonics.

Power-law intermittency in the gradient-induced self-propulsion of colloidal swimmers.

Active colloidal microswimmers serve as archetypical active fluid systems, and as models for biological swimmers. Here, by studying in detail their velocity traces, we find robust power-law intermittency with system-dependent exponential cut off. We model the intermittent motion by an interplay of the field gradient-dependent active force, which depends on a fluid gradient and is reduced when the swimmer moves, and the locally fluctuating hydrodynamic drag, that is set by the wetting properties of the substrate. The model closely describes the velocity distributions of two disparate swimmer systems: AC field activated and catalytic swimmers. The generality is highlighted by the collapse of all data in a single master curve, suggesting the applicability to further systems, both synthetic and biological.

Optoelectronic Properties of Nitrogen-Doped Hexagonal Graphene Quantum Dots: A First-Principles Study.

Graphene quantum dots have been widely studied owing to their unique optical, electrical, and optoelectrical properties for various applications in solar devices. Here, we investigate the optoelectronic properties of hexagonal and nitrogen-doped graphene quantum dots using the first-principles method. We find that doping nitrogen atoms to hexagonal graphene quantum dots results in a significant red shift toward the visible light range as compared to that of the pristine graphene quantum dots, and the doped nitrogen atoms also induce a clear signature of anisotropy of the frontier orbitals induced by the electron correlation between the doped nitrogen atoms and their adjacent carbon atoms. Moreover, time-dependent density functional theory calculations with the M06-2X functional and 6-311++G(d,p) basis set reproduce well the experimental absorption spectra reported recently. These results provide us with a novel approach for more systematic investigations on next-generation solar devices with assembled quantum dots to improve their light selectivity as well as efficiency.

New Theoretical Model to Describe Carrier Multiplication in Semiconductors: Explanation of Disparate Efficiency in MoTe2 versus PbS and PbSe.

We present a theoretical model to compute the efficiency of the generation of two or more electron-hole pairs in a semiconductor by the absorption of one photon via the process of carrier multiplication (CM). The photogeneration quantum yield of electron-hole pairs is calculated from the number of possible CM decay pathways of the electron and the hole. We apply our model to investigate the underlying cause of the high efficiency of CM in bulk 2H-MoTe2, as compared to bulk PbS and PbSe. Electronic band structures were calculated with density functional theory, from which the number of possible CM decay pathways was calculated for all initial electron and hole states that can be produced at a given photon energy. The variation of the number of CM pathways with photon energy reflects the dependence of experimental CM quantum yields on the photon energy and material composition. We quantitatively reproduce experimental CM quantum yields for MoTe2, PbS, and PbSe from the calculated number of CM pathways and one adjustable fit parameter. This parameter is related to the ratio of Coulomb coupling matrix elements and the cooling rate of the electrons and holes. Large variations of this fit parameter result in small changes in the modeled quantum yield for MoTe2, which confirms that its high CM efficiency can be mainly attributed to its extraordinary large number of CM pathways. The methodology of this work can be applied to analyze or predict the CM efficiency of other materials.

Pickering stabilization mechanism revealed through direct imaging of particles with tuneable contact angle in a phase-separated binary solvent.

Pickering emulsions have attracted increasing attention from multiple fields, including food, cosmetics, healthcare, pharmaceutical, and agriculture. Their stability relies on the presence of colloidal particles instead of surfactant at the droplet interface, providing steric stabilization. Here, we demonstrate the microscopic attachment and detachment of particles with tunable contact angle at the interface underlying the Pickering emulsion stability. We vary the interfacial tension continuously by varying the temperature offset of a phase-separated binary liquid from its critical point, and employ confocal microscopy to directly observe the particles at the interface to determine their coverage and contact angle as a function of the varying interfacial tension. When the interfacial tension decreases upon approaching the binary liquid's critical point, the contact angle and detachment energy (ΔE) drop, and the particles move out of the interface. Microscopic imaging suggests necking and capillary interactions lead to clustering of the particles, before they eventually desorb from the interface. Macroscopic measurements show that concomitantly, coalescence takes place, and the emulsion loses its stability. These results reveal the interplay of interfacial energies, contact angle and surface coverage that underlies the Pickering emulsion stability, opening up ways to manipulate and design the stability through the microscopic behavior of the adsorbed particles.

Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation.

Oocyte maturation is accompanied by changes in abundances of thousands of mRNAs, many degraded and many preferentially stabilized. mRNA stability can be regulated by diverse features including GC content, codon bias, and motifs within the 3'-untranslated region (UTR) interacting with RNA binding proteins (RBPs) and miRNAs. Many studies have identified factors participating in mRNA splicing, bulk mRNA storage, and translational recruitment in mammalian oocytes, but the roles of potentially hundreds of expressed factors, how they regulate cohorts of thousands of mRNAs, and to what extent their functions are conserved across species has not been determined. We performed an extensive in silico cross-species analysis of features associated with mRNAs of different stability classes during oocyte maturation (stable, moderately degraded, and highly degraded) for five mammalian species. Using publicly available RNA sequencing data for germinal vesicle (GV) and MII oocyte transcriptomes, we determined that 3'-UTR length and synonymous codon usage are positively associated with stability, while greater GC content is negatively associated with stability. By applying machine learning and feature selection strategies, we identified RBPs and miRNAs that are predictive of mRNA stability, including some across multiple species and others more species-restricted. The results provide new insight into the mechanisms regulating maternal mRNA stabilization or degradation.NEW & NOTEWORTHY Conservation across species of mRNA features regulating maternal mRNA stability during mammalian oocyte maturation was analyzed. 3'-Untranslated region length and synonymous codon usage are positively associated with stability, while GC content is negatively associated. Just three RNA binding protein motifs were predicted to regulate mRNA stability across all five species examined, but associated pathways and functions are shared, indicating oocytes of different species arrive at comparable physiological destinations via different routes.

Formation of mineral-associated organic matter in temperate soils is primarily controlled by mineral type and modified by land use and management intensity.

Formation of mineral-associated organic matter (MAOM) supports the accumulation and stabilization of carbon (C) in soil, and thus, is a key factor in the global C cycle. Little is known about the interplay of mineral type, land use and management intensity in MAOM formation, especially on subdecadal time scales. We exposed mineral containers with goethite or illite, the most abundant iron oxide and phyllosilicate clay in temperate soils, for 5 years in topsoils of 150 forest and 150 grassland sites in three regions across Germany. Results show that irrespective of land use and management intensity, more C accumulated on goethite than illite (on average 0.23 ± 0.10 and 0.06 ± 0.03 mg m-2 mineral surface respectively). Carbon accumulation across regions was consistently higher in coniferous forests than in deciduous forests and grasslands. Structural equation models further showed that thinning and harvesting reduced MAOM formation in forests. Formation of MAOM in grasslands was not affected by grazing. Fertilization had opposite effects on MAOM formation, with the positive effect being mediated by enhanced plant productivity and the negative effect by reduced plant species richness. This highlights the caveat of applying fertilizers as a strategy to increase soil C stocks in temperate grasslands. Overall, we demonstrate that the rate and amount of MAOM formation in soil is primarily driven by mineral type, and can be modulated by land use and management intensity even on subdecadal time scales. Our results suggest that temperate soils dominated by oxides have a higher capacity to accumulate and store C than those dominated by phyllosilicate clays, even under circumneutral pH conditions. Therefore, adopting land use and management practices that increase C inputs into oxide-rich soils that are under their capacity to store C may offer great potential to enhance near-term soil C sequestration.

Genome-wide methylation patterns from canine nanopore assemblies.

Recent advances in long-read sequencing have enabled the creation of reference-quality genome assemblies for multiple individuals within a species. In particular, 8 long-read genome assemblies have recently been published for the canine model (dogs and wolves). These assemblies were created using a range of sequencing and computational approaches, with only limited comparisons described among subsets of the assemblies. Here we present 3 high-quality de novo reference assemblies based upon Oxford Nanopore long-read sequencing: 2 Bernese Mountain Dogs (BD & OD) and a Cairn terrier (CA611). These breeds are of particular interest due to the enrichment of unresolved genetic disorders. Leveraging advancement in software technologies, we utilized published data of Labrador Retriever (Yella) to generate a new assembly, resulting in a ∼280-fold increase in continuity (N50 size of 91 kbp vs 25.75 Mbp). In conjunction with these 4 new assemblies, we uniformly assessed 8 existing assemblies for generalized quality metrics, sequence divergence, and a detailed BUSCO assessment. We identified a set of ∼400 conserved genes during the BUSCO analysis missing in all assemblies. Genome-wide methylation profiles were generated from the nanopore sequencing, resulting in broad concordance with existing whole-genome and reduced-representation bisulfite sequencing, while highlighting superior overage of mobile elements. These analyses demonstrate the ability of Nanopore sequencing to resolve the sequence and epigenetic profile of canine genomes.

Ovarian stimulation with excessive FSH doses causes cumulus cell and oocyte dysfunction in small ovarian reserve heifers.

Excessive FSH doses during ovarian stimulation in the small ovarian reserve heifer (SORH) cause premature cumulus expansion and follicular hyperstimulation dysgenesis (FHD) in nearly all ovulatory-size follicles with predicted disruptions in cell-signaling pathways in cumulus cells and oocytes (before ovulatory hCG stimulation). These observations support the hypothesis that excessive FSH dysregulates cumulus cell function and oocyte maturation. To test this hypothesis, we determined whether excessive FSH-induced differentially expressed genes (DEGs) in cumulus cells identified in our previously published transcriptome analysis were altered independent of extreme phenotypic differences observed amongst ovulatory-size follicles, and assessed predicted roles of these DEGs in cumulus and oocyte biology. We also determined if excessive FSH alters cumulus cell morphology, and oocyte nuclear maturation before (premature) or after an ovulatory hCG stimulus or during IVM. Excessive FSH doses increased expression of 17 cumulus DEGs with known roles in cumulus cell and oocyte functions (responsiveness to gonadotrophins, survival, expansion, and oocyte maturation). Excessive FSH also induced premature cumulus expansion and oocyte maturation but inhibited cumulus expansion and oocyte maturation post-hCG and diminished the ability of oocytes with prematurely expanded cumulus cells to undergo IVF or nuclear maturation during IVM. Ovarian stimulation with excessive FSH is concluded to disrupt cumulus cell and oocyte functions by inducing premature cumulus expansion and dysregulating oocyte maturation without an ovulatory hCG stimulus yielding poor-quality cumulus-oocyte complexes that may be incorrectly judged morphologically as suitable for IVF during ART.

Stacking-Order-Dependent Excitonic Properties Reveal Interlayer Interactions in Bulk ReS2.

Rhenium disulfide, a member of the transition metal dichalcogenide family of semiconducting materials, is unique among 2D van der Waals materials due to its anisotropy and, albeit weak, interlayer interactions, confining excitons within single atomic layers and leading to monolayer-like excitonic properties even in bulk crystals. While recent work has established the existence of two stacking modes in bulk, AA and AB, the influence of the different interlayer coupling on the excitonic properties has been poorly explored. Here, we use polarization-dependent optical measurements to elucidate the nature of excitons in AA and AB-stacked rhenium disulfide to obtain insight into the effect of interlayer interactions. We combine polarization-dependent Raman with low-temperature photoluminescence and reflection spectroscopy to show that, while the similar polarization dependence of both stacking orders indicates similar excitonic alignments within the crystal planes, differences in peak width, position, and degree of anisotropy reveal a different degree of interlayer coupling. DFT calculations confirm the very similar band structure of the two stacking orders while revealing a change of the spin-split states at the top of the valence band to possibly underlie their different exciton binding energies. These results suggest that the excitonic properties are largely determined by in-plane interactions, however, strongly modified by the interlayer coupling. These modifications are stronger than those in other 2D semiconductors, making ReS2 an excellent platform for investigating stacking as a tuning parameter for 2D materials. Furthermore, the optical anisotropy makes this material an interesting candidate for polarization-sensitive applications such as photodetectors and polarimetry.

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.

BACKGROUND: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Controlled Assembly of CdSe Nanoplatelet Thin Films and Nanowires.

We assemble semiconductor CdSe nanoplatelets (NPs) at the air/liquid interface into 2D monolayers several micrometers wide, distinctly displaying nematic order. We show that this configuration is the most favorable energetically and that the edge-to-edge distance between neighboring NPs can be tuned by ligand exchange without disrupting film topology and nanoparticle orientation. We explore the rich assembly phase space by using depletion interactions to direct the formation of 1D nanowires from stacks of NPs. The improved control and understanding of the assembly of semiconductor NPs offers opportunities for the development of cheaper optoelectronic devices that rely on 1D or 2D charge delocalization throughout the assembled monolayers and nanowires.

Self-Oscillation and Synchronization Transitions in Elastoactive Structures.

The interplay between activity and elasticity often found in active and living systems triggers a plethora of autonomous behaviors ranging from self-assembly and collective motion to actuation. Among these, spontaneous self-oscillations of mechanical structures is perhaps the simplest and most widespread type of nonequilibrium phenomenon. Yet, we lack experimental model systems to investigate the various dynamical phenomena that may appear. Here, we introduce a centimeter-sized model system for one-dimensional elastoactive structures. We show that such structures exhibit flagellar motion when pinned at one end, self-snapping when pinned at two ends, and synchronization when coupled together with a sufficiently stiff link. We further demonstrate that these transitions can be described quantitatively by simple models of coupled pendula with follower forces. Beyond the canonical case considered here, we anticipate our work to open avenues for the understanding and design of the self-organization and response of active biological and synthetic solids, e.g., in higher dimensions and for more intricate geometries.

High-resolution 3D forest structure explains ecomorphological trait variation in assemblages of saproxylic beetles.

Climate, topography and the 3D structure of forests are major drivers affecting local species communities. However, little is known about how the specific functional traits of saproxylic (wood-living) beetles, involved in the recycling of wood, might be affected by those environmental characteristics.Here, we combine ecological and morphological traits available for saproxylic beetles and airborne laser scanning (ALS) data in Bayesian trait-based joint species distribution models to study how traits drive the distributions of more than 230 species in temperate forests of Europe.We found that elevation (as a proxy for temperature and precipitation) and the proportion of conifers played important roles in species occurrences while variables related to habitat heterogeneity and forest complexity were less relevant. Furthermore, we showed that local communities were shaped by environmental variation primarily through their ecological traits whereas morphological traits were involved only marginally. As predicted, ecological traits influenced species' responses to forest structure, and to other environmental variation, with canopy niche, wood decay niche and host preference as the most important ecological traits. Conversely, no links between morphological traits and environmental characteristics were observed. Both models, however, revealed strong phylogenetic signal in species' response to environmental characteristics.These findings imply that alterations of climate and tree species composition have the potential to alter saproxylic beetle communities in temperate forests. Additionally, ecological traits help explain species' responses to environmental characteristics and thus should prove useful in predicting their responses to future change. It remains challenging, however, to link simple morphological traits to species' complex ecological niches. Read the free Plain Language Summary for this article on the Journal blog.

Phases of surface-confined trivalent colloidal particles.

Patchy colloids promise the design and modelling of complex materials, but the realization of equilibrium patchy particle structures remains challenging. Here, we assemble pseudo-trivalent particles and elucidate their phase behaviour when confined to a plane. We observe the honeycomb phase, as well as more complex amorphous network and triangular phases. Structural analysis performed on the three condensed phases reveals their shared structural motifs. Using a combined experimental and simulation approach, we elucidate the energetics of these phases and construct the phase diagram of this system, using order parameters to determine the phase coexistence lines. Our results reveal the rich phase behaviour that a relatively simple patchy particle system can display, and open the door to a larger joined simulation and experimental exploration of the full patchy-particle phase space.

Insect decline in forests depends on species' traits and may be mitigated by management.

Insects are declining, but the underlying drivers and differences in responses between species are still largely unclear. Despite the importance of forests, insect trends therein have received little attention. Using 10 years of standardized data (120,996 individuals; 1,805 species) from 140 sites in Germany, we show that declines occurred in most sites and species across trophic groups. In particular, declines (quantified as the correlation between year and the respective community response) were more consistent in sites with many non-native trees or a large amount of timber harvested before the onset of sampling. Correlations at the species level depended on species' life-history. Larger species, more abundant species, and species of higher trophic level declined most, while herbivores increased. This suggests potential shifts in food webs possibly affecting ecosystem functioning. A targeted management, including promoting more natural tree species composition and partially reduced harvesting, can contribute to mitigating declines.

Visualizing defect dynamics by assembling the colloidal graphene lattice.

Graphene has been under intense scientific interest because of its remarkable optical, mechanical and electronic properties. Its honeycomb structure makes it an archetypical two-dimensional material exhibiting a photonic and phononic band gap with topologically protected states. Here, we assemble colloidal graphene, the analogue of atomic graphene using pseudo-trivalent patchy particles, allowing particle-scale insight into crystal growth and defect dynamics. We directly observe the formation and healing of common defects, like grain boundaries and vacancies using confocal microscopy. We identify a pentagonal defect motif that is kinetically favoured in the early stages of growth, and acts as seed for more extended defects in the later stages. We determine the conformational energy of the crystal from the bond saturation and bond angle distortions, and follow its evolution through the energy landscape upon defect rearrangement and healing. These direct observations reveal that the origins of the most common defects lie in the early stages of graphene assembly, where pentagons are kinetically favoured over the equilibrium hexagons of the honeycomb lattice, subsequently stabilized during further growth. Our results open the door to the assembly of complex 2D colloidal materials and investigation of their dynamical, mechanical and optical properties.

The HAInich: A multidisciplinary vision data-set for a better understanding of the forest ecosystem.

We present a multidisciplinary forest ecosystem 3D perception dataset. The dataset was collected in the Hainich-Dün region in central Germany, which includes two dedicated areas, which are part of the Biodiversity Exploratories - a long term research platform for comparative and experimental biodiversity and ecosystem research. The dataset combines several disciplines, including computer science and robotics, biology, bio-geochemistry, and forestry science. We present results for common 3D perception tasks, including classification, depth estimation, localization, and path planning. We combine the full suite of modern perception sensors, including high-resolution fisheye cameras, 3D dense LiDAR, differential GPS, and an inertial measurement unit, with ecological metadata of the area, including stand age, diameter, exact 3D position, and species. The dataset consists of three hand held measurement series taken from sensors mounted on a UAV during each of three seasons: winter, spring, and early summer. This enables new research opportunities and paves the way for testing forest environment 3D perception tasks and mission set automation for robotics.

Identification of a Hypomorphic FANCG Variant in Bernese Mountain Dogs.

Bernese mountain dogs (BMDs), have an overall cancer incidence of 50%, half of which is comprised of an otherwise rare tumor, histiocytic sarcoma (HS). While recent studies have identified driver mutations in the MAPK pathway, identification of key predisposing genes has been elusive. Studies have identified several loci to be associated with predisposition to HS in BMDs, including near the MTAP/CDKN2A region, but no causative coding variant has been identified. Here we report the presence of a coding polymorphism in the gene encoding FANCG, near the MTAP/CDKN2A locus. This variant is in a conserved region of the protein and appears to be specific to BMDs. Canine fibroblasts derived from dogs homozygous for this variant are hypersensitive to cisplatin. We show this canine FANCG variant and a previously defined hypomorphic FANCG allele in humans impart similar defects in DNA repair. However, our data also indicate that this variant is neither necessary nor sufficient for the development of HS. Furthermore, BMDs homozygous for this FANCG allele display none of the characteristic phenotypes associated with Fanconi anemia (FA) such as anemia, short stature, infertility, or an earlier age of onset for HS. This is similar to findings in FA deficient mice, which do not develop overt FA without secondary genetic mutations that exacerbate the FA deficit. In sum, our data suggest that dogs with deficits in the FA pathway are, like mice, innately resistant to the development of FA.