Proceedings of the National Academy of Sciences of the United States of America

Increasing the speed of scientific progress is urgently needed to address the many challenges associated with the biosphere in the Anthropocene. Consequently, the critical question becomes: How can science most rapidly progress to address large, complex global problems? We suggest that the lag in the development of a more predictive science of the biosphere is not only because the biosphere is so much more complex, or because we do not have enough data, or are not doing enough experiments, but, in large part, because of unresolved tension between the three dominant scientific cultures that pervade the research community...

Over the past few years, machine learning models have significantly increased in size and complexity, especially in the area of generative AI such as large language models. These models require massive amounts of data and compute capacity to train, to the extent that concerns over the training data (such as protected or private content) cannot be practically addressed by retraining the model "from scratch" with the questionable data removed or altered. Furthermore, despite significant efforts and controls dedicated to ensuring that training corpora are properly curated and composed, the sheer volume required makes it infeasible to manually inspect each datum comprising a training corpus...

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone...

Zebra finches, a species of songbirds, learn to sing by creating an auditory template through the memorization of model songs (sensory learning phase) and subsequently translating these perceptual memories into motor skills (sensorimotor learning phase). It has been traditionally believed that babbling in juvenile birds initiates the sensorimotor phase while the sensory phase of song learning precedes the onset of babbling. However, our findings challenge this notion by demonstrating that testosterone-induced premature babbling actually triggers the onset of the sensory learning phase instead...

Hippocampal somatostatin-expressing ( Sst ) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single-cell transcriptome analyses have provided a comprehensive Sst -IN subpopulations census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst -INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst- INs that largely tiled the morpho-functional parameter space of the Sst -INs superfamily...

Near-field radiative heat transfer has recently attracted increasing interests for its applications in energy technologies, such as thermophotovoltaics. Existing works, however, are restricted to time-independent systems. Here, we explore near-field radiative heat transfer between two bodies under time modulation by developing a rigorous fluctuational electrodynamics formalism. We demonstrate that time modulation can result in the enhancement, suppression, elimination, or reversal of radiative heat flow between the two bodies, and can be used to create a radiative thermal diode with an infinite contrast ratio, as well as a near-field radiative heat engine that pumps heat from the cold to the hot bodies...

The central aim of quantum networks is to facilitate user connectivity via quantum channels, but there is an open need for benchmarking metrics to compare diverse quantum networks. Here, we propose a general framework for quantifying the performance of a quantum network by estimating the value created by connecting users through quantum channels. In this framework, we define the quantum network utility metric [Formula: see text] to capture the social and economic value of quantum networks. The proposed framework accommodates a variety of applications from secure communications to distributed sensing...

Quantum amplification enables the enhancement of weak signals and is of great importance for precision measurements, such as biomedical science and tests of fundamental symmetries. Here, we observe a previously unexplored magnetic amplification using dark noble-gas nuclear spins in the absence of pump light. Such dark spins exhibit remarkable coherence lasting up to 6 min and the resilience against the perturbations caused by overlapping alkali-metal gas. We demonstrate that the observed phenomenon, referred to as "dark spin amplification," significantly magnifies magnetic field signals by at least three orders of magnitude...

Distributed nonconvex optimization underpins key functionalities of numerous distributed systems, ranging from power systems, smart buildings, cooperative robots, vehicle networks to sensor networks. Recently, it has also merged as a promising solution to handle the enormous growth in data and model sizes in deep learning. A fundamental problem in distributed nonconvex optimization is avoiding convergence to saddle points, which significantly degrade optimization accuracy. We find that the process of quantization, which is necessary for all digital communications, can be exploited to enable saddle-point avoidance...

Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth...

Anti-microbial resistance (AMR) is one of the greatest threats to global health. The continual battle between the emergence of AMR and the development of drugs will be extremely difficult to stop as long as traditional anti-biotic approaches are taken. In order to overcome this impasse, we here focused on the type III secretion system (T3SS), which is highly conserved in many Gram-negative pathogenic bacteria. The T3SS is known to be indispensable in establishing disease processes but not essential for pathogen survival...

This article builds on recent work of the first three authors where a notion of congruence modules in higher codimension is introduced. The main results are a criterion for detecting regularity of local rings in terms of congruence modules, and a more refined version of a result tracking the change of congruence modules under deformation. Number theoretic applications include the construction of canonical lines in certain Galois cohomology groups arising from adjoint motives of Hilbert modular forms.

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Time-resolved X-ray photoelectron spectroscopy (TR-XPS) is used in a simulation study to monitor the excited state intramolecular proton transfer between oxygen and nitrogen atoms in 2-(iminomethyl)phenol. Real-time monitoring of the chemical bond breaking and forming processes is obtained through the time evolution of excited-state chemical shifts. By employing individual atomic probes of the proton donor and acceptor atoms, we predict distinct signals with opposite chemical shifts of the donor and acceptor groups during proton transfer...

Functional neuroimaging studies indicate that the human brain can represent concepts and their relational structure in memory using coding schemes typical of spatial navigation. However, whether we can read out the internal representational geometries of conceptual spaces solely from human behavior remains unclear. Here, we report that the relational structure between concepts in memory might be reflected in spontaneous eye movements during verbal fluency tasks: When we asked participants to randomly generate numbers, their eye movements correlated with distances along the left-to-right one-dimensional geometry of the number space (mental number line), while they scaled with distance along the ring-like two-dimensional geometry of the color space (color wheel) when they randomly generated color names...

The MYC-Associated Zinc Finger Protein (MAZ) plays important roles in chromatin organization and gene transcription regulation. Dysregulated expression of MAZ causes diseases, such as glioblastoma, breast cancer, prostate cancer, and liposarcoma. Previously, it has been reported that MAZ controls the proinflammatory response in colitis and colon cancer via STAT3 signaling, suggesting that MAZ is involved in regulating immunity-related pathways. However, the molecular mechanism underlying this regulation remains elusive...

A fundamental question associated with chirality is how mixtures containing equal amounts of interconverting enantiomers can spontaneously convert to systems enriched in only one of them. Enantiomers typically have similar chemical properties, but can exhibit distinct reactivity under specific conditions, and these differences can be used to bias the system's composition in favor of one enantiomer. Transport properties are also expected to differ for enantiomers in chiral solvents, but the role of such differences in chiral symmetry breaking has not been clarified yet...

The development of seizures in epilepsy syndromes associated with malformations of cortical development (MCDs) has traditionally been attributed to intrinsic cortical alterations resulting from abnormal network excitability. However, recent analyses at single-cell resolution of human brain samples from MCD patients have indicated the possible involvement of adaptive immunity in the pathogenesis of these disorders. By exploiting the MethylAzoxyMethanol (MAM)/pilocarpine (MP) rat model of drug-resistant epilepsy associated with MCD, we show here that the occurrence of status epilepticus and subsequent spontaneous recurrent seizures in the malformed, but not in the normal brain, are associated with the outbreak of a destructive autoimmune response with encephalitis-like features, involving components of both cell-mediated and humoral immune responses...

Auxin regulates plant growth and development through downstream signaling pathways, including the best-known SCFTIR1/AFB -Aux/IAA-ARF pathway and several other less characterized "noncanonical" pathways. Recently, one SCFTIR1/AFB -independent noncanonical pathway, mediated by Transmembrane Kinase 1 (TMK1), was discovered through the analyses of its functions in Arabidopsis apical hook development. Asymmetric accumulation of auxin on the concave side of the apical hook triggers DAR1-catalyzed release of the C-terminal of TMK1, which migrates into the nucleus, where it phosphorylates and stabilizes IAA32/34 to inhibit cell elongation, which is essential for full apical hook formation...

Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. Escherichia coli adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain...