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Abstract The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

Abstract Seasonal storage of solar thermal energy through supercooled phase change materials (PCM) offers a promising solution for decarbonizing space and water heating in winter. Despite the high energy density and adaptability, natural PCMs often lack the necessary supercooling for stable, long-term storage. Leveraging erythritol, a sustainable mid-temperature PCM with high latent heat, we introduce a straightforward method to stabilize its supercooling by incorporating carrageenan (CG), a bio-derived food thickener. By improving the solid-liquid interfacial energy with the addition of CG the latent heat of erythritol can be effectively locked at a very low temperature. We show that the composite PCM can sustain an ultrastable supercooled state below −30 °C, which guarantees no accidental loss of the latent heat in severe cold regions on Earth. We further demonstrate that the common ultrasonication method can be used as the key to unlocking the latent heat stored in the CG-thickened erythritol, showing its great potential to serve as a high-performance, eco-friendly PCM for long-term seasonal solar energy storage.

Abstract We present an interpretable implementation of the autoencoding algorithm, used as an anomaly detector, built with a forest of deep decision trees on FPGA, field programmable gate arrays. Scenarios at the Large Hadron Collider at CERN are considered, for which the autoencoder is trained using known physical processes of the Standard Model. The design is then deployed in real-time trigger systems for anomaly detection of unknown physical processes, such as the detection of rare exotic decays of the Higgs boson. The inference is made with a latency value of 30 ns at percent-level resource usage using the Xilinx Virtex UltraScale+ VU9P FPGA. Our method offers anomaly detection at low latency values for edge AI users with resource constraints.

Abstract Reservoir computing is a concept involving mapping signals onto a high-dimensional phase space of a dynamical system called “reservoir” for subsequent recognition by an artificial neural network. We implement this concept in a nanodevice consisting of a sandwich of a semiconductor phonon waveguide and a patterned ferromagnetic layer. A pulsed write-laser encodes input signals into propagating phonon wavepackets, interacting with ferromagnetic magnons. The second laser reads the output signal reflecting a phase-sensitive mix of phonon and magnon modes, whose content is highly sensitive to the write- and read-laser positions. The reservoir efficiently separates the visual shapes drawn by the write-laser beam on the nanodevice surface in an area with a size comparable to a single pixel of a modern digital camera. Our finding suggests the phonon-magnon interaction as a promising hardware basis for realizing on-chip reservoir computing in future neuromorphic architectures.

Abstract Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.

Using shallow geothermal energy systems to recycle the heat accumulating in the subsurface due to climate change and urbanization is a feasible, sustainable, and opportunistic alternative to conventional space heating in the face of climate change

Abstract The deep pelagic ocean is increasingly subjected to human-induced environmental change. While pelagic animals provide important ecosystem functions including climate regulation, species-specific responses to stressors remain poorly documented. Here, we investigate the effects of simulated ocean warming and sediment plumes on the cosmopolitan deep-sea jellyfish Periphylla periphylla, combining insights gained from physiology, gene expression and changes in associated microbiota. Metabolic demand was elevated following a 4 °C rise in temperature, promoting genes related to innate immunity but suppressing aerobic respiration. Suspended sediment plumes provoked the most acute and energetically costly response through the production of excess mucus (at ≥17 mg L−1), while inducing genes related to aerobic respiration and wound repair (at ≥167 mg L−1). Microbial symbionts appeared to be unaffected by both stressors, with mucus production maintaining microbial community composition. If these responses are representative for other gelatinous fauna, an abundant component of pelagic ecosystems, the effects of planned exploitation of seafloor resources may impair deep pelagic biodiversity and ecosystem functioning.

Abstract Coherent many-body states are highly promising for robust quantum information processing. While far-reaching theoretical predictions have been made for various implementations, direct experimental evidence of their appealing properties can be challenging. Here, we demonstrate optical manipulation of the nuclear spin ensemble in the lead halide perovskite semiconductor FAPbBr3 (FA = formamidinium), targeting a long-postulated collective dark state that is insensitive to optical pumping after its build-up. Via optical orientation of localized hole spins we drive the nuclear many-body system into this entangled state, requiring a weak magnetic field of only a few milli-Tesla strength at cryogenic temperatures. During its fast establishment, the nuclear polarization along the optical axis remains small, while the transverse nuclear spin fluctuations are strongly reduced, corresponding to spin squeezing as evidenced by a strong violation of the generalized nuclear squeezing-inequality with ξ s

Abstract Bacterial σI factors of the σ70-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σI paralogues in some cellulolytic bacteria have been shown to be responsible for the regulation of the cellulosome, a multienzyme complex that mediates efficient cellulose degradation. Here, we report two structures at 3.0 Å and 3.3 Å of two transcription open complexes formed by two σI factors, SigI1 and SigI6, respectively, from the thermophilic, cellulolytic bacterium, Clostridium thermocellum. These structures reveal a unique, hitherto-unknown recognition mode of bacterial transcriptional promoters, both with respect to domain organization and binding to promoter DNA. The key characteristics that determine the specificities of the σI paralogues were further revealed by comparison of the two structures. Consequently, the σI factors represent a distinct set of the σ70-family σ factors, thus highlighting the diversity of bacterial transcription.

Abstract Altered vasoactivity is a major characteristic of cardiovascular and oncological diseases, and many therapies are therefore targeted to the vasculature. Therapeutics which are selective for the diseased vasculature are ideal, but whole-body selectivity of a therapeutic is challenging to assess in practice. Vessel myography is used to determine the functional mechanisms and evaluate pharmacological responses of vascularly-targeted therapeutics. However, myography can only be performed on ex vivo sections of individual arteries. We have developed methods for implementation of spherical-view photoacoustic tomography for non-invasive and in vivo myography. Using photoacoustic tomography, we demonstrate the measurement of acute vascular reactivity in the systemic vasculature and the placenta of female pregnant mice in response to two vasodilators. Photoacoustic tomography simultaneously captures the significant acute vasodilation of major arteries and detects selective vasoactivity of the maternal-fetal vasculature. Photoacoustic tomography has the potential to provide invaluable preclinical information on vascular response that cannot be obtained by other established methods.

Abstract The AAA+ ATPase p97/VCP together with different sets of substrate-delivery adapters and accessory cofactor proteins unfolds ubiquitinated substrates to facilitate degradation by the proteasome. The UBXD1 cofactor is connected to p97-associated multisystem proteinopathy but its biochemical function and structural organization on p97 has remained largely elusive. Using a combination of crosslinking mass spectrometry and biochemical assays, we identify an extended UBX (eUBX) module in UBXD1 related to a lariat in another cofactor, ASPL. Of note, the UBXD1-eUBX intramolecularly associates with the PUB domain in UBXD1 close to the substrate exit pore of p97. The UBXD1 PUB domain can also bind the proteasomal shuttling factor HR23b via its UBL domain. We further show that the eUBX domain has ubiquitin binding activity and that UBXD1 associates with an active p97-adapter complex during substrate unfolding. Our findings suggest that the UBXD1-eUBX module receives unfolded ubiquitinated substrates after they exit the p97 channel and before hand-over to the proteasome. The interplay of full-length UBXD1 and HR23b and their function in the context of an active p97:UBXD1 unfolding complex remains to be studied in future work.

Halide perovskites have a variety of attractive feature such as high quantum yield, and tunable optical properties, combined with easy fabrication. Here, Kirstein et al demonstrate spin-mode locking in CsPb(Cl0.56Br0.44)3 lead halide perovskite nanocrystals embedded in a fluorophosphate glass matrix, and a hole spin lifetime extending into the microsecond range.

The leaf epidermis is sealed by a lipid-rich cuticle to prevent water loss and interspersed with stomatal pores to allow gas exchange. Here the authors provide evidence that two barley proteins, HvYDA1 and HvBRX-Solo, regulate both processes linking epidermal patterning with cuticular properties in a cereal crop.

Iron homeostasis is known to influence plant immune signaling. Here the authors characterize SRF3, a receptor kinase that acts as a negative regulator of callose synthesis, that is required for root responses to iron deficiency and pathogen signals.

The Landé factors govern all the spin-related basic phenomena and are the key parameters which guide spintronics applications. Here, Kirstein et al. demonstrate a universal dependence of the Landé factors on the bandgap energy of several perovskite materials.

Here, Koster et al., model human papillomavirus and Chlamydia coinfection dynamics in patient-derived ectocervical organoids, and characterize the effects of multiple infections in the cellular microenvironment, potentially contributing to neoplasia.

While metal organic frameworks offer highly tunable materials for photocatalytic applications, catalytic site accessibility is a crucial parameter. Here, authors demonstrate selective ligand removal to introduce new active sites and mesopores and to enhance photocatalytic H2 evolution.

Abdominal surgery can often lead to complications including the formation of peritoneal adhesions and the molecular mechanisms underlying this process are still unknown. Here, the authors suggest that bacterial contamination drives adhesion formation through mesothelial EGFR signalling.

The authors describe a vesicular transporter, VST-1, that is required in glutamatergic chemosensory neurons for chemotactic avoidance behavior in C. elegans. VST-1 antagonizes VGLUT-dependent packaging of glutamate into synaptic vesicles and determines the strength of synaptic glutamate signaling.