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At least 991 records · Page 55

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. Furthermore, the transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.

60 APPLIED LIFE SCIENCES↗

Tuning crystallization pathways through sequence engineering of biomimetic polymers

Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede the appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct versus two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent. When a short hydrophobic region is added to a sequence that directly forms crystalline particles, crystallization instead follows a two-step pathway that begins with the creation of disordered clusters of 10–20 molecules and is characterized by highly non-linear crystallization kinetics in which clusters transform into ordered structures that then enter the growth phase. The results shed new light on non-classical crystallization mechanisms and have implications for the design of self-assembling polymer systems.

36 MATERIALS SCIENCE↗

Anisotropic attosecond charge carrier dynamics and layer decoupling in quasi-2D layered SnS 2

Strong quantum confinement effects lead to striking new physics in two-dimensional materials such as graphene or transition metal dichalcogenides. While spectroscopic fingerprints of such quantum confinement have been demonstrated widely, the consequences for carrier dynamics are at present less clear, particularly on ultrafast timescales. This is important for tailoring, probing, and understanding spin and electron dynamics in layered and two-dimensional materials even in cases where the desired bandgap engineering has been achieved. Here in this paper we show by means of core–hole clock spectroscopy that SnS 2 exhibits spindependent attosecond charge delocalization times (τ deloc ) for carriers confined within a layer, τ deloc < 400 as, whereas interlayer charge delocalization is dynamically quenched in excess of a factor of 10, τ deloc > 2.7 fs. These layer decoupling dynamics are a direct consequence of strongly anisotropic screening established within attoseconds, and demonstrate that important two-dimensional characteristics are also present in bulk crystals of van der Waalslayered materials, at least on ultrafast timescales.

36 MATERIALS SCIENCE↗

Strong and fragile topological Dirac semimetals with higher-order Fermi arcs

Abstract Dirac and Weyl semimetals both exhibit arc-like surface states. However, whereas the surface Fermi arcs in Weyl semimetals are topological consequences of the Weyl points themselves, the surface Fermi arcs in Dirac semimetals are not directly related to the bulk Dirac points, raising the question of whether there exists a topological bulk-boundary correspondence for Dirac semimetals. In this work, we discover that strong and fragile topological Dirac semimetals exhibit one-dimensional (1D) higher-order hinge Fermi arcs (HOFAs) as universal, direct consequences of their bulk 3D Dirac points. To predict HOFAs coexisting with topological surface states in solid-state Dirac semimetals, we introduce and layer a spinful model of an s – d -hybridized quadrupole insulator (QI). We develop a rigorous nested Jackiw–Rebbi formulation of QIs and HOFA states. Employing ab initio calculations, we demonstrate HOFAs in both the room- ( α ) and intermediate-temperature ( α ″ ) phases of Cd 3 As 2 , KMgBi, and rutile-structure ( $$ \beta ^{\prime} $$ β ′ -) PtO 2 .

Science & Technology - Other Topics↗

Room-temperature polariton quantum fluids in halide perovskites

Abstract Quantum fluids exhibit quantum mechanical effects at the macroscopic level, which contrast strongly with classical fluids. Gain-dissipative solid-state exciton-polaritons systems are promising emulation platforms for complex quantum fluid studies at elevated temperatures. Recently, halide perovskite polariton systems have emerged as materials with distinctive advantages over other room-temperature systems for future studies of topological physics, non-Abelian gauge fields, and spin-orbit interactions. However, the demonstration of nonlinear quantum hydrodynamics, such as superfluidity and Čerenkov flow, which is a consequence of the renormalized elementary excitation spectrum, remains elusive in halide perovskites. Here, using homogenous halide perovskites single crystals, we report, in both one- and two-dimensional cases, the complete set of quantum fluid phase transitions from normal classical fluids to scatterless polariton superfluids and supersonic fluids—all at room temperature, clear consequences of the Landau criterion. Specifically, the supersonic Čerenkov wave pattern was observed at room temperature. The experimental results are also in quantitative agreement with theoretical predictions from the dissipative Gross-Pitaevskii equation. Our results set the stage for exploring the rich non-equilibrium quantum fluid many-body physics at room temperature and also pave the way for important polaritonic device applications.

42 ENGINEERING↗

Future precipitation increase constrained by climatological pattern of cloud effect

The fractional increase in global mean precipitation (?P ¯/P ¯) is a first-order measure of the hydrological cycle intensification under anthropogenic warming. However, ?P ¯/P ¯ varies by a factor of more than three among model projections, hindering credible assessments of the associated climate impacts. The uncertainty in ?P ¯/P ¯ stems from uncertainty in both hydrological sensitivity (global mean precipitation increase per unit warming) and climate sensitivity (global mean temperature increase per forcing). Here, by investigating hydrological and climate sensitivities in a unified surface-energy-balance perspective, we find that both sensitivities are significantly correlated with surface shortwave cloud feedback, which is further linked to the climatological pattern of cloud shortwave effect. The observed pattern of cloud effect thus constrains both sensitivities and consequently constrains ?P ¯/P ¯. The 5%-95% uncertainty range of ?P ¯/P ¯ from 1979-2005 to 2080-2100 under the high-emission (moderate-emission) scenario is constrained from 6.34±3.53% (4.19±2.28%) in the raw ensemble-model projection to 7.03±2.59% (4.63±1.71%). The constraint thus suggests a higher most-likely ?P ¯/P ¯ and reduces the uncertainty by ~25%, providing valuable information for impact assessments.

Zhou, Wenyu↗

Impact of ion fluxes across thylakoid membranes on photosynthetic electron transport and photoprotection

In photosynthetic thylakoid membranes the proton motive force (pmf) not only drives ATP synthesis, in addition it is central to controlling and regulating energy conversion. As a consequence, dynamic fine-tuning of the two pmf components, electrical (Δψ) and chemical (ΔpH), is an essential element for adjusting photosynthetic light reactions to changing environmental conditions. Good evidence exists that the Δψ/ΔpH partitioning is controlled by thylakoid potassium and chloride ion transporters and channels. However, a detailed mechanistic understanding of how these thylakoid ion transporter/channels control pmf partitioning is lacking. In this work, we combined functional measurements on potassium and chloride ion transporter and channel loss-of-function mutants with extended mathematical simulations of photosynthetic light reactions in thylakoid membranes to obtain detailed kinetic insights into the complex interrelationship between membrane energization and ion fluxes across thylakoid membranes. The data reveal that potassium and chloride fluxes in the thylakoid lumen determined by the K + /H + antiporter KEA3 and the voltage-gated Cl – channel VCCN1/Best1 have distinct kinetic responses that lead to characteristic and light-intensity-dependent Δψ/ΔpH oscillations. These oscillations fine-tune photoprotective mechanisms and electron transport which are particularly important during the first minutes of illumination and under fluctuating light conditions. By employing the predictive power of the model, we unravelled the functional consequences of changes in KEA3 and VCCN1 abundance and regulatory/enzymatic parameters on membrane energization and photoprotection.

59 BASIC BIOLOGICAL SCIENCES↗

Potential-pH diagrams considering complex oxide solution phases for understanding aqueous corrosion of multi-principal element alloys

The potential-pH diagram, a graphical representation of the thermodynamically predominant reaction products in aqueous corrosion, is originally proposed for the corrosion of pure metals. The original approach only leads to stoichiometric oxides and hydroxides as the oxidation products. However, numerous experiments show that non-stoichiometric oxide scales are prevalent in the aqueous corrosion of alloys. In the present study, a room temperature potential-pH diagram considering oxide solid solutions, as a generalization of the traditional potential-pH diagram with stoichiometric oxides, is constructed for an FCC single-phase multi-principal element alloy (MPEA) based on the CALculation of PHAse Diagram method. The predominant reaction products, the ions in aqueous solution, and the cation distribution in oxides are predicted. The oxide solid solution is stabilized by the mixing free energy (or mixing entropy) and the stabilizing effect becomes more significant as the temperature increases. Consequently, solid solution oxides are stable in large regions of the potential-pH diagram and the mixing free energy mostly affects the equilibrium composition of the stable oxides, while the shape of stable regions for oxides is mostly determined by the structure of the stable oxides. Agreements are found for Ni 2+ , Fe 2+ , and Mn 2+ between the atomic emission spectroelectrochemistry measurements and thermodynamic calculations, while deviations exist for Cr 3+ and Co 2+ possibly due to surface complexation with species such as Cl - and the oxide dissolution. By incorporating the solution models of oxides, the current work presents a general and more accurate way to analyze the reaction products during aqueous corrosion of MPEAs.

Materials Science↗

Accelerated vortex dynamics across the magnetic 3D-to-2D crossover in disordered superconductors

Disorder can have remarkably disparate consequences in superconductors, driving superconductor–insulator transitions in ultrathin films by localizing electron pairs and boosting the supercurrent carrying capacity of thick films by localizing vortices (magnetic flux lines). Though the electronic 3D-to-2D crossover at material thicknesses d ~ ξ (coherence length) is well studied, a similarly consequential magnetic crossover at d ~ L c (pinning length) that should drastically alter material properties remains largely underexamined. According to collective pinning theory, vortex segments of length L c bend to adjust to energy wells provided by point defects. Consequently, if d truncates L c , a change from elastic to rigid vortex dynamics should increase the rate of thermally activated vortex motion S. Here, we characterize the dependence of S on sample thickness in Nb and cuprate films. The results for Nb are consistent with collective pinning theory, whereas creep in the cuprate is strongly influenced by sparse large precipitates. In conclusion, we leverage the sensitivity of S to d to determine the generally unknown scale L c , establishing a new route for extracting pinning lengths in heterogeneously disordered materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The path to 1.5 °C requires ratcheting of climate pledges

Using model simulations of high-ambition emissions pathways, we show that ratcheting—or increasing—climate ambition through 2030 will be crucial to limiting global peak temperature changes this century. Although updated pledges offered in advance of the Glasgow climate conference in 2021 meaningfully strengthened global ambition in 2030 compared to the 2015 Paris pledges, here, our study underscores the importance of countries ratcheting their 2030 pledges further to reduce the magnitude of temperature overshoot and consequently reduce the risks of irreversible and adverse consequences to natural and human systems.

54 ENVIRONMENTAL SCIENCES↗

Atomic Origins of Water-Vapour-Promoted Alloy Oxidation

The presence of water vapor, intentional or unavoidable, is crucial to many materials applications, such as steam generator, turbine engine, fuel cell, catalyst, and corrosion 1-6. Phenomenologically, water vapor has been noticed to accelerate oxidation of metals/alloys 7,8, however, the atomistic mechanisms remain elusive. Herein, through direct in situ atomic-scale transmission electron microscopy observation and density functional theory calculation, we reveal that water vapor enhanced oxidation of Ni-Cr alloy is associated with proton dissolution promoted vacancy formation, migration and clustering. Protons derived from water dissociation occupy interstitial position in the oxide lattice, which consequently leads to the lowering of both vacancy formation energy and the cation diffusion barrier. The atomic scale observations reveal a water vapor derived proton mediated oxide growth mechanism, which provides insights for reckoning many technological processes concerning materials in moist environment at elevated temperatures.

Luo, Langli (ORCID:000000026311051X)↗

Decoupling the role of stress and corrosion in the intergranular cracking of noble-metal alloys

Intergranular stress-corrosion cracking (IGSCC) is a form of environmentally induced crack propagation causing premature failure of elemental metals and alloys. It is believed to require the simultaneous presence of tensile stress and corrosion; however, the exact nature of this synergy has eluded experimental identification. For noble metal alloys such as Ag–Au, IGSCC is a consequence of dealloying corrosion, forming a nanoporous gold layer that is believed to have the ability to transmit cracks into grain boundaries in un-dealloyed parent phase via a pure mechanical process. Here using atomic-scale techniques and statistical characterizations for this alloy system, we show that the separate roles of stress and anodic dissolution can be decoupled and that the apparent synergy exists owing to rapid time-dependent morphology changes at the dealloyed layer/parent phase interface. We discuss the applicability of our findings to the IGSCC of important engineering Fe- and Ni-based alloys in critical applications.

36 MATERIALS SCIENCE↗

Progressive growth of the solid–electrolyte interphase towards the Si anode interior causes capacity fading

The solid–electrolyte interphase (SEI), a layer formed on the electrode surface, is essential for electrochemical reactions in batteries and critically governs the battery stability. Active materials, especially those with extremely high energy density, such as silicon (Si), often inevitably undergo a large volume swing upon ion insertion and extraction, raising a critical question as to how the SEI interactively responds to and evolves with the material and consequently controls the cycling stability of the battery. Here, by integrating sensitive elemental tomography, an advanced algorithm and cryogenic scanning transmission electron microscopy, we unveil, in three dimensions, a correlated structural and chemical evolution of Si and SEI. Furthermore, corroborated with a chemomechanical model, we demonstrate progressive electrolyte permeation and SEI growth along the percolation channel of the nanovoids due to vacancy injection and condensation during the delithiation process. Consequently, the Si–SEI spatial configuration evolves from the classic ‘core–shell’ structure in the first few cycles to a ‘plum-pudding’ structure following extended cycling, featuring the engulfing of Si domains by the SEI, which leads to the disruption of electron conduction pathways and formation of dead Si, contributing to capacity loss. The spatially coupled interactive evolution model of SEI and active materials, in principle, applies to a broad class of high-capacity electrode materials, leading to a critical insight for remedying the fading of high-capacity electrodes.

36 MATERIALS SCIENCE↗

Plant functional trait change across a warming tundra biome

Trait-based ecology promises to predict community assembly1–3, ecosystem function4–6, and responses to environmental change4,7 across spatial and temporal scales. At the global scale the majority of plant trait variation is explained by just two dimensions8, corresponding to resource acquisition9 and plant size10,11. However, it is unknown whether (1) globally established trait relationships are maintained across biomes, (2) species level relationships could be invalidated by trait variation within species, and (3) trait variation is independent of scale. We tested these questions at the cold extremes of life on earth using the largest tundra plant trait database ever compiled. Here we show we found that tundra plants exhibited a two-axis spectrum consistent with global findings, and demonstrated remarkable consistency in the range of resource acquisition traits, but not size traits, compared to global trait distributions. The majority of trait variation occurred at the species level, but within-species variation comprised an important component of variation at local scales (<10 km2) and at low species richness (<10 species), implying that.... Our findings indicate that the dimensions of functional trait space are maintained in the coldest ecosystems on the planet despite strong environmental filtering of plant size, but that a greater focus on within-species trait variation is required to predict trait change at the community scale.

Bjorkman, Anne D.↗

Predator mass mortality events restructure food webs through trophic decoupling

Predators have a key role in structuring ecosystems. However, predator loss is accelerating globally, and predator mass-mortality events (MMEs)—rapid large-scale die-offs—are now emblematic of the Anthropocene epoch. Owing to their rare and unpredictable nature, we lack an understanding of how MMEs immediately impact ecosystems. Past predator-removal studies may be insufficient to understand the ecological consequences of MMEs because, in nature, dead predators decompose in situ and generate a resource pulse, which could alter ensuing ecosystem dynamics by temporarily enhancing productivity. Here we experimentally induce MMEs in tritrophic, freshwater lake food webs and report ecological dynamics that are distinct from predator losses or resource pulses alone, but that can be predicted from theory. MMEs led to the proliferation of diverse consumer and producer communities resulting from weakened top-down predator control and stronger bottom-up effects through predator decomposition. In contrast to predator removals alone, enhanced primary production after MMEs dampened the consumer community response. As a consequence, MMEs generated biomass dynamics that were most similar to those of undisturbed systems, indicating that they may be cryptic disturbances in nature. These biomass dynamics led to trophic decoupling, whereby the indirect beneficial effects of predators on primary producers are lost and later materialize as direct bottom-up effects that stimulate primary production amid intensified herbivory. Furthermore, these results reveal ecological signatures of MMEs and demonstrate the feasibility of forecasting novel ecological dynamics arising with intensifying global change.

Food webs↗

Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection

Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.

60 APPLIED LIFE SCIENCES↗

Enhanced thermoelectric performance in Cu-intercalated BiTeI by compensation weakening induced mobility improvement

The low weighted carrier mobility has long been considered to be the key challenge for improvement of thermoelectric (TE) performance in BiTeI. The Rashba-effect-induced two-dimensional density of states in this bulk semiconductor is beneficial for thermopower enhancement, which makes it a prospective compound for TE applications. In this report, we show that intercalation of minor Cu-dopants can substantially alter the equilibria of defect reactions, selectively mediate the donor-acceptor compensation, and tune the defect concentration in the carrier conductive network. Consequently, the potential fluctuations responsible for electron scattering are reduced and the carrier mobility in BiTeI can be enhanced by a factor of two to three between 10 K and 300 K. The carrier concentration can also be optimized by tuning the Te/I composition ratio, leading to higher thermopower in this Rashba system. Cu-intercalation in BiTeI gives rise to higher power factor, slightly lower lattice thermal conductivity, and consequently improved figure of merit. Compared with pristine BiTe 0.98 I 1.02 , the TE performance in Cu 0.05 BiTeI reveals a 150% and 20% enhancement at 300 and 520 K, respectively. Ultimately, these results demonstrate that defect equilibria mediated by selective doping in complex TE and energy materials could be an effective approach to carrier mobility and performance optimization.

36 MATERIALS SCIENCE↗

Chelation of Actinides. Chapter 6

Actinides, such as uranium, plutonium, or americium, are radioactive metals with no natural biological function. However, these elements are strongly retained by most organisms and can be extremely toxic due to their radioactive and chemical properties. In the event of an accidental or ill-intentional release of nuclear material into the environment, these radionuclides pose a severe health risk as contaminants. The only practical therapy to reduce the dramatic health consequences of internal actinide contamination is treatment with chelating agents that form excretable complexes, although the actinides are among the most intractable radionuclides to decorporate. In the last few years, a sense of urgency and a renewed interest in the study of actinide chemistry and biology have emerged, as threats of nuclear terrorism have become more plausible, and the risk of environmental contamination and human exposure to radioisotopes consequently increased. This chapter discusses available methods and recent progress in the development of new strategies for the chelation of actinides.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗