bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of Terrestrial Heat Flow in Songliao Basin Based on Deep Neural Network
Authors: Bai Lige , Li Jing , Zeng Zhaofa , Tao Deqiang
Published: December 2023

Heat flow is a geothermal parameter for indicating the heat source distribution and evaluating geothermal reservoirs. Only 1,230 heat flow points are distributed unevenly in China, mainly concentrated in high‐temperature geothermal and southeast regions. The Songliao Basin is a potential geothermal field in China. Still, only 20 measurement points are known, making evaluating the geothermal genetic mechanism difficult. Sparse data interpolation using deep learning methods is highly accurate and widely used in fields such as image processing. In this work, we propose a deep neural network for predicting heat flow in the Songliao Basin. More than 4,000 global heat flows and 23 geological and geophysical parameters are used as reference constraints for training. The uncertainty error of the prediction is estimated based on the correlation and distance‐based generalized sensitivity analysis. The results show that the maximum heat flow is 85 mW/m2, the average is 67.1 mW/m2, and the error with the measured data is 10.64%. The previous geophysical and geological interpretation results indicate that the heat flow is higher in the west and lower in the east, with high anomalies in the central region, which may be related to the uplift of the deep mantle and the depression of the shallow low‐velocity sedimentary layer. Some high‐temperature melt bodies are in the deep layers, forming the current potential geothermal field. The measured data validates that the DNN is an effective method for predicting regional‐scale heat flow, providing reliable heat source information for evaluating geothermal resources.
Induced Polarization Images the Plumbing System of Hydrothermal Vents in an Intracontinental Rift, Lake Abhé, Republic of Djibouti
Authors: Piolat L. , Geraud Y. , Revil A.
Published: December 2023

Recent developments in induced polarization allow for the characterization of alteration halos within hydrothermal systems. We explore the possibility of using electrical conductivity and normalized chargeability tomograms in concert to image hydrothermal conduits thanks to their high cation exchange capacities associated with alteration. The hydrothermal plumbing system of the late‐stage rift area of Lake Abhé (Republic of Djibouti) is used to test the ability of induced polarization to reveal such plumbing system associated with the prominent hydrothermal chimneys serving as vents for the hydrothermal fluids. We show that induced polarization can be used to provide an alteration tomogram, which highlights the flow path toward 2 chimneys in the top 70 m below the surface of the sediments at Lake Abhé.
Investigating Dynamic Weakening in Laboratory Faults Using Multi‐Scale Flash Heating Coupled With mm‐Scale Contact Evolution
Authors: Barbery M. R. , Chester F. M. , Chester J. S.
Published: December 2023

Flash‐weakening models typically show good agreement with the total magnitude of weakening in high‐speed rock friction experiments, however deviations during the acceleration and deceleration phases, and at low and intermediate sliding velocities, remain unresolved. Here, we incorporate inhomogeneous mm‐scale normal stress evolution into a model for flash heating and weakening to resolve outstanding transient and hysteretic friction observed in laboratory experiments and to identify unique solutions to constitutive parameters. We conduced 37 rock friction experiments on Westerly granite using a high‐speed biaxial apparatus outfitted with a high‐speed infrared camera. We initiated velocity steps from quasi‐static rates of 1 mm/s to sliding velocities ranging from 300 to 900 mm/s and conducted both constant‐ and decreasing‐velocity tests following the velocity step. Two sliding surfaces geometries were used to control mm‐scale life‐times and rest‐times. Constant‐strength sliding is achieved within 2–3 mm of initiating the velocity step in all constant‐velocity experiments. Macroscopic surface temperature is inhomogeneous and increases with slip distance, velocity, and decreasing rest‐time. Weakening increases with sliding velocity and decreasing rest‐time. We combine thermal models with measured surface temperatures to constrain the evolution of local normal stress at the mm‐scale and incorporate this evolution into a flash‐weakening model that considers weakening at both the µm‐ and mm‐scale. The flash‐weakening model improves when the effects of mm‐scale wear processes are incorporated and multi‐scale weakening is considered, however some transient friction remains undescribed. Models will be advanced by further incorporating wear processes and by considering processes at the mm‐scale and above.
Bayesian Hierarchical Modeling for Probabilistic Estimation of Tsunami Amplitude From Far‐Field Earthquake Sources
Authors: Boumis Georgios , Geist Eric L. , Lee Danhyang
Published: December 2023

Evaluation of tsunami disaster risk for a coastal region requires reliable estimation of tsunami hazard, for example, wave amplitude close to the shore. Observed tsunami data are scarce and have poor spatial coverage, and for this reason probabilistic tsunami hazard analysis (PTHA) traditionally relies on numerical simulation of “synthetic” tsunami generation and propagation toward the coast. Such an approach has been extensively studied in the past and it is widely recognized as an important disaster‐risk mitigation tool. PTHA can not only provide less uncertain and spatially coherent hazard estimates in comparison with classical empirical data analysis which is restricted at the tide gauge stations, but also local inundation information. In this paper, we explore a purely statistical alternative to traditional PTHA for evaluation of tsunami amplitude hazard. Here, we use tide gauge measurements of tsunami amplitude along the western United States, specifically California and Oregon, and develop a spatial Bayesian hierarchical model (BHM) to assess tsunami hazard from far‐field earthquake sources at various recurrence intervals. The configuration of our model incorporates latent Gaussian fields that utilize information on the distance between tide gauges as well as on the continental shelf width, that is, a covariate linked to potential dissipative effects on wave energy as the tsunami travels over shallow water. Through our BHM, we produce spatially continuous probabilistic maps of far‐field tsunami hazard which can aid comprehensive tsunami disaster risk reduction and management.
Antenatal and neonatal exposure to SARS-CoV-2 and children’s development: a systematic review and meta-analysis
Authors: Jackson Rebecca , Woodward Kathryn , Ireland Meg , Larkin Conor , Kurinczuk Jennifer J. , Knight Marian , Gale Chris , Johnson Samantha , Cornish Rosie , Chakkarapani Ela
Published: December 2023

Objectives

To conduct a systematic review of the impact of antenatal and neonatal exposure to SARS-CoV-2 on developmental outcomes in preterm and term-born infants.

Methods

We searched Embase, Emcare, MEDLINE, PsycINFO, Web of Science and grey literature on May 27, 2022 and updated on May 8, 2023. Studies defining exposure with a positive SARS-CoV-2 protein or genetic material, used a contemporaneous non-exposed cohort, and reported developmental outcomes up to 2 years of age were included.

Results

Four out of 828 screened studies were included. Meta-analysis included 815 infants screened for developmental delay (n = 306 exposed; n = 509 non-exposed) between 3- and 11-months of age. Among term-born infants, we did not find an increased risk of delay in communication (odd’s ratio: 0.73 (95% CI: 0.24–2.24)), gross motor (1.50 (0.62, 3.62)), fine motor (2.90 (0.58, 14.43)), problem-solving (1.19 (0.54, 2.66)) or personal-social development (1.93 (0.78, 4.75)) in exposed infants. The number of preterm-born infants in the exposed (n = 37) and comparison cohorts (n = 41) were too few to report meaningful comparisons.

Conclusion

Evidence regarding the potential impact of antenatal or neonatal exposure to SARS-CoV-2 infection on developmental outcomes in early infancy is limited and inconsistent. Larger cohorts with outcomes beyond the first year of life are needed.

Impact

The current evidence examining associations between SARS-CoV-2 exposure during the neonatal period and developmental outcomes in infancy is limited by there being few studies with extremely small sample sizes.

Based on sparse data there was no consistent association between antenatal or neonatal exposure to SARS-CoV-2 infection and an adverse impact on developmental outcomes below 12 months of age for babies born preterm or at term.

This study highlights that larger cohorts with outcomes assessed beyond the first year are needed to determine the potential longer-term impact of SARS-CoV-2 infection exposure on child development.
Gss deficiency causes age-related fertility impairment via ROS-triggered ferroptosis in the testes of mice
Authors: Zhu Haixia , Cheng Yin , Wang Xianmei , Yang Xing , Liu Min , Liu Jun , Liu Shuqiao , Wang Hongxiang , Zhang Aizhen , Li Runze , Ye Chao , Zhang Jian , Gao Jiangang , Fu Xiaolong , Wu Bin
Published: December 2023

Glutathione synthetase (GSS) catalyzes the final step in the synthesis of glutathione (GSH), a well-established antioxidant. Research on the specific roles of the Gss gene during spermatogenesis remains limited due to the intricate structure of testis. In this study, we identified pachytene spermatocytes as the primary site of GSS expression and generated a mouse model with postnatal deletion of Gss using Stra8-Cre (S8) to investigate the role of GSS in germ cells. The impact of Gss knockout on reducing male fertility is age-dependent and caused by ferroptosis in the testis. The 2-month-old S8/Gss−/− male mice exhibited normal fertility, due to a compensatory increase in GPX4, which prevented the accumulation of ROS. With aging, there was a decline in GPX4 and an increase in ALOX15 levels observed in 8-month-old S8/Gss−/− mice, resulting in the accumulation of ROS, lipid peroxidation, and ultimately testicular ferroptosis. We found that testicular ferroptosis did not affect spermatogonia, but caused meiosis disruption and acrosome heterotopia. Then the resulting aberrant sperm showed lower concentration and abnormal morphology, leading to reduced fertility. Furthermore, these injuries could be functionally rescued by inhibiting ferroptosis through intraperitoneal injection of GSH or Fer-1. In summary, Gss in germ cells play a crucial role in the resistance to oxidative stress injury in aged mice. Our findings deepen the understanding of ferroptosis during spermatogenesis and suggest that inhibiting ferroptosis may be a potential strategy for the treatment of male infertility.
Upregulation of Hsp27 via further inhibition of histone H2A ubiquitination confers protection against myocardial ischemia/reperfusion injury by promoting glycolysis and enhancing mitochondrial function
Authors: Shi Pilong , Wu Jiawei , Li Minghui , Cao Yonggang , Wu Jiabi , Ren Ping , Liu Kai , Zhou Jiajun , Sha Yuetong , Zhang Qianhui , Sun Hongli
Published: December 2023

Research suggests that ischemic glycolysis improves myocardial tolerance to anoxia and low-flow ischemia. The rate of glycolysis during ischemia reflects the severity of the injury caused by ischemia and subsequent functional recovery following reperfusion. Histone H2AK119 ubiquitination (H2Aub) is a common modification that is primarily associated with gene silencing. Recent studies have demonstrated that H2Aub contributes to the development of cardiovascular diseases. However, the underlying mechanism remains unclear. This study identified Hsp27 (heat shock protein 27) as a H2Aub binding protein and explored its involvement in mediating glycolysis and mitochondrial function. Functional studies revealed that inhibition of PRC1 (polycomb repressive complex 1) decreased H2Aub occupancy and promoted Hsp27 expression through inhibiting ubiquitination. Additionally, it increased glycolysis by activating the NF-κB/PFKFB3 signaling pathway during myocardial ischemia. Furthermore, Hsp27 reduced mitochondrial ROS production by chaperoning COQ9, and suppressed ferroptosis during reperfusion. A delivery system was developed based on PCL-PEG-MAL (PPM)-PCM-SH (CWLSEAGPVVTVRALRGTGSW) to deliver PRT4165 (PRT), a potent inhibitor of PRC1, to damaged myocardium, resulting in decreased H2Aub. These findings revealed a novel epigenetic mechanism connecting glycolysis and ferroptosis in protecting the myocardium against ischemia/reperfusion injury.
An RNA excited conformational state at atomic resolution
Authors: Geng Ainan , Ganser Laura , Roy Rohit , Shi Honglue , Pratihar Supriya , Case David A. , Al-Hashimi Hashim M.
Published: December 2023

Sparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational modeling, we determined the 3D structural ensemble formed by a short-lived (lifetime ~2.1 ms) lowly-populated (~0.4%) conformational state in HIV-1 TAR RNA. Through a strand register shift, the excited conformational state completely remodels the 3D structure of the ground state (RMSD from the ground state = 7.2 ± 0.9 Å), forming a surprisingly more ordered conformational ensemble rich in non-canonical mismatches. The structure impedes the formation of the motifs recognized by Tat and the super elongation complex, explaining why this alternative TAR conformation cannot activate HIV-1 transcription. The ability to determine the 3D structures of fleeting RNA states using the presented methodology holds great promise for our understanding of RNA biology, disease mechanisms, and the development of RNA-targeting therapeutics.
RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing
Authors: Maurin Michelle , Ranjouri Mohammadreza , Megino-Luque Cristina , Newberg Justin Y. , Du Dongliang , Martin Katelyn , Miner Robert E. , Prater Mollie S. , Wee Dave Keng Boon , Centeno Barbara , Pruett-Miller Shondra M. , Stewart Paul , Fleming Jason B. , Yu Xiaoqing , Bravo-Cordero Jose Javier , Guccione Ernesto , Black Michael A. , Mann Karen M.
Published: December 2023

RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.
Folk arts-inspired twice-coagulated configuration-editable tough aerogels enabled by transformable gel precursors
Authors: Li Lishan , Yang Guandu , Lyu Jing , Sheng Zhizhi , Ma Fengguo , Zhang Xuetong
Published: December 2023

Aerogels, as famous lightweight and porous nanomaterials, have attracted considerable attention in various emerging fields in recent decades, however, both low density and weak mechanical performance make their configuration-editing capability challenging. Inspired by folk arts, herein we establish a highly efficient twice-coagulated (TC) strategy to fabricate configuration-editable tough aerogels enabled by transformable gel precursors. As a proof of concept, aramid nanofibers (ANFs) and polyvinyl alcohol (PVA) are selected as the main components of aerogel, among which PVA forms a flexible configuration-editing gel network in the first coagulation process, and ANF forms a configuration-locking gel network in the second coagulation process. TC strategy guarantees the resulting aerogels with both high toughness and feasible configuration editing capability individually or simultaneously. Altogether, the resulting tough aerogels with special configuration through soft to hard modulation provide great opportunities to break through the performance limits of the aerogels and expand application areas of aerogels.
Structural dynamics of the CROPs domain control stability and toxicity of Paeniclostridium sordellii lethal toxin
Authors: Zhou Yao , Zhan Xiechao , Luo Jianhua , Li Diyin , Zhou Ruoyu , Zhang Jiahao , Pan Zhenrui , Zhang Yuanyuan , Jia Tianhui , Zhang Xiaofeng , Li Yanyan , Tao Liang
Published: December 2023

Paeniclostridium sordellii lethal toxin (TcsL) is a potent exotoxin that causes lethal toxic shock syndrome associated with fulminant bacterial infections. TcsL belongs to the large clostridial toxin (LCT) family. Here, we report that TcsL with varied lengths of combined repetitive oligopeptides (CROPs) deleted show increased autoproteolysis as well as higher cytotoxicity. We next present cryo-EM structures of full-length TcsL, at neutral (pH 7.4) and acidic (pH 5.0) conditions. The TcsL at neutral pH exhibits in the open conformation, which resembles reported TcdB structures. Low pH induces the conformational change of partial TcsL to the closed form. Two intracellular interfaces are observed in the closed conformation, which possibly locks the cysteine protease domain and hinders the binding of the host receptor. Our findings provide insights into the structure and function of TcsL and reveal mechanisms for CROPs-mediated modulation of autoproteolysis and cytotoxicity, which could be common across the LCT family.
A hard molecular nanomagnet from confined paramagnetic 3d-4f spins inside a fullerene cage
Authors: Huang Chenli , Sun Rong , Bao Lipiao , Tian Xinyue , Pan Changwang , Li Mengyang , Shen Wangqiang , Guo Kun , Wang Bingwu , Lu Xing , Gao Song
Published: December 2023

Reducing inter-spin distance can enhance magnetic interactions and allow for the realization of outstanding magnetic properties. However, achieving reduced distances is technically challenging. Here, we construct a 3d-4f metal cluster (Dy2VN) inside a C80 cage, affording a heretofore unseen metallofullerene containing both paramagnetic 3d and 4f metal ions. The significantly suppressed 3d-4f (Dy-V) distances, due to the unique cage confinement effect, were observed by crystallographic and theoretical analysis of Dy2VN@Ih(7)-C80. These reduced distances result in an enhanced magnetic coupling (Jtotal, Dy-V = 53.30 cm−1; Jtotal, Dy-Dy = −6.25 cm−1), leading to a high magnetic blocking temperature compared to reported 3d-4f single-molecule magnets and strong coercive field of 2.73 Tesla. Our work presents a new class of single-molecule magnets with both paramagnetic 3d and 4f metals confined in a fullerene cage, offering superior and tunable magnetic properties due to the unique cage confinement effect and the diverse composition of the entrapped magnetic core.
Mendelian randomization study supports the causal effects of air pollution on longevity via multiple age-related diseases
Authors: Qiu Shizheng , Hu Yang , Liu Guiyou
Published: December 2023

Growing evidence suggests that exposure to fine particulate matter (PM2.5) may reduce life expectancy; however, the causal pathways of PM2.5 exposure affecting life expectancy remain unknown. Here, we assess the causal effects of genetically predicted PM2.5 concentration on common chronic diseases and longevity using a Mendelian randomization (MR) statistical framework based on large-scale genome-wide association studies (GWAS) (>400,000 participants). After adjusting for other types of air pollution and smoking, we find significant causal relationships between PM2.5 concentration and angina pectoris, hypercholesterolaemia and hypothyroidism, but no causal relationship with longevity. Mediation analysis shows that although the association between PM2.5 concentration and longevity is not significant, PM2.5 exposure indirectly affects longevity via diastolic blood pressure (DBP), hypertension, angina pectoris, hypercholesterolaemia and Alzheimer’s disease, with a mediated proportion of 31.5, 70.9, 2.5, 100, and 24.7%, respectively. Our findings indicate that public health policies to control air pollution may help improve life expectancy.
Effects of caffeine and blue-enriched light on spare visual attention during simulated space teleoperation
Authors: Liu Andrew M. , Galvan-Garza Raquel C. , Flynn-Evans Erin E. , Rueger Melanie , Natapoff Alan , Lockley Steven W. , Oman Charles M.
Published: December 2023

Safe and successful operation of the International Space Station robotic arm is a complex task requiring difficult bimanual hand coordination and spatial reasoning skills, adherence to operating procedures and rules, and systems knowledge. These task attributes are all potentially affected by chronic sleep loss and circadian misalignment. In a randomized, placebo-controlled, cross-over trial examining the impact of regularly timed low-dose caffeine (0.3 mg kg−1 h−1) and moderate illuminance blue-enriched white light (~90 lux, ~88 melEDI lux, 6300 K), 16 participants performed 3 types of realistic robotic arm tasks using a high-fidelity desktop simulator overnight. Our goal was to determine how these countermeasures, separately and combined, impacted telerobotic task performance and the ability to allocate attention to an unrelated secondary visual task. We found that all participants maintained a similar level of robotic task performance throughout the primary task but the application of caffeine separately and with blue-enriched light significantly decreased response time to a secondary visual task by −9% to −13%, whereas blue-enriched light alone changed average response times between −4% and +2%. We conclude that, for sleep-restricted individuals, caffeine improved their ability to divide their visual attention, while the effect of blue-enriched light alone was limited. Light and caffeine together was most effective. Use of these countermeasures should improve the margin of safety if astronauts perform familiar tasks under degraded conditions or novel tasks where task workload is increased.
Compact description of quantum phase slip junctions
Authors: Koliofoti Christina , Riwar Roman-Pascal
Published: December 2023

Quantum circuit theory is a powerful tool to describe superconducting circuits. In its language, quantum phase slips (QPSs) are considered to be the exact dual to the Josephson effect. This duality renders the integration of QPS junctions into a unified theoretical framework challenging. As we argue, different existing formalisms may be inconsistent, and the correct inclusion of time-dependent flux driving requires introducing a large number of auxiliary, nonphysical degrees of freedom. We resolve these issues by describing QPS junctions as inductive rather than capacitive elements, and reducing the Hilbert space to account for a compact superconducting phase. Our treatment provides an approach to circuit quantization exclusively in terms of node-flux-node variables, and eliminates spurious degrees of freedom. Finally, the inductive treatment reveals the possibility of a voltage-dependent renormalization of the QPS amplitude, by accounting for spatial variations of the electric field built up across the junction.
How much schizophrenia do famines cause?
Authors: Ó Gráda Cormac , Li Chihua , Lumey L. H.
Published: December 2023

Since the 1970s, famines have been widely invoked as natural experiments in research into the long-term impact of foetal exposure to nutritional shocks. That research has produced compelling evidence for a robust link between foetal exposure and the odds of developing schizophrenia. However, the implications of that research for the human cost of famines in the longer run have not been investigated. We address the connection between foetal origins and schizophrenia with that question in mind. The impact turns out to be very modest—much less than one per cent of the associated famine death tolls—across a selection of case studies.
Essential amino acid supplements ingestion has a positive effect on executive function after moderate-intensity aerobic exercise
Authors: Dora Kento , Tsukamoto Hayato , Suga Tadashi , Tomoo Keigo , Suzuki Asuka , Adachi Yusuke , Takeshita Masamichi , Kato Yumiko , Kawasaki Mika , Sato Wataru , Imaizumi Akira , Karakawa Sachise , Uchida Hirohisa , Hashimoto Takeshi
Published: December 2023

Aerobic exercise acutely improves cognitive function (e.g., executive function (EF); memory recognition (MR)) and increases circulating brain-derived neurotrophic factor (BDNF). In addition, branched-chain amino acids (BCAA) ingestion acutely shortens the choice reaction time and increases brain BDNF. We examined whether the ingestion of essential amino acid (EAA) supplements (mainly composed of BCAA) would positively impact on cognitive function and circulating BDNF after moderate-intensity aerobic exercise. Twenty-two healthy young men received either an EAA supplements or the placebo (PL) 30 min before undergoing aerobic exercise. The participants performed a cycling exercise at 60% of peak oxygen uptake for 30 min. EF after aerobic exercise was better after the EAA treatment than after the PL treatment (P = 0.02). MR (P = 0.38 for response accuracy;P = 0.15 for reaction time) and circulating BDNF (P = 0.59) were not altered by EAA supplements. EF improvement was correlated with increases in some amino acids (leucine, isoleucine, valine, lysine, phenylalanine; allPs < 0.05) that are potential substrates for synthesizing neurotransmitters in the brain. These results suggest that EAA supplements ingestion had a positive effect on EF after moderate-intensity aerobic exercise, while MR and BDNF were not altered.
Solving the spectral gap problem with a four-mirror bow-tie cavity in waveguide free-electron laser oscillators
Authors: Xia Mengqi , Xu Yuanfang , Zhao Zhouyu , Li Heting
Published: December 2023

The generation of intense coherent radiation pulses in the far-infrared and terahertz regimes is of considerable interest to the free-electron laser (FEL) radiation user community. At long wavelengths, the diffraction effect can be quite severe, therefore, an optical waveguide is required to confine the radiation field. However, it will also bring about some new phenomena, and the most noteworthy one is the spectral gap phenomenon: at some particular wavelengths, regardless of electron beam adjustments, the coupling efficiency and output power of waveguide FEL oscillators drop significantly. Such spectral gap has an adverse effect on experimental results since numerous experiments require continuous spectral scanning. In this paper, we propose to utilize a bow-tie cavity instead of conventional cavities to the waveguide FEL to solve the spectral gap problem. The simulation was carried out based on the parameters of FELiChEM, a newly built user facility in China. Numerical simulation code OPC combining with modified GENESIS is used to enable the modelling, for the first time, of a bow-tie cavity based FEL in the far-infrared wavelength regime. The simulation results indicate that this novel structure can effectively eliminate the spectral gaps and substantially enhance long-wavelength laser performance.
Susceptible-Infected-Susceptible type COVID-19 spread with collective effects
Authors: Crocker Amanda , Strömbom Daniel
Published: December 2023

Many models developed to forecast and attempt to understand the COVID-19 pandemic are highly complex, and few take collective behavior into account. As the pandemic progressed individual recurrent infection was observed and simpler susceptible-infected type models were introduced. However, these do not include mechanisms to model collective behavior. Here, we introduce an extension of the SIS model that accounts for collective behavior and show that it has four equilibria. Two of the equilibria are the standard SIS model equilibria, a third is always unstable, and a fourth where collective behavior and infection prevalence interact to produce either node-like or oscillatory dynamics. We then parameterized the model using estimates of the transmission and recovery rates for COVID-19 and present phase diagrams for fixed recovery rate and free transmission rate, and both rates fixed. We observe that regions of oscillatory dynamics exist in both cases and that the collective behavior parameter regulates their extent. Finally, we show that the system exhibits hysteresis when the collective behavior parameter varies over time. This model provides a minimal framework for explaining oscillatory phenomena such as recurring waves of infection and hysteresis effects observed in COVID-19, and other SIS-type epidemics, in terms of collective behavior.
Atmospheric modes fiddling the simulated ENSO impact on tropical cyclone genesis over the Northwest Pacific
Authors: Zhao Jiuwei , Zhan Ruifen , Murakami Hiroyuki , Wang Yuqing , Xie Shang-Ping , Zhang Leying , Guo Yipeng
Published: December 2023

The El Niño-Southern Oscillation (ENSO) is crucial to the interannual variability of tropical cyclone (TC) genesis over the western North Pacific (WNP). However, most state-of-the-art climate models exhibit a consistent pattern of uncertainty in the simulated TC genesis frequency (TCGF) over the WNP in ENSO phases. Here, we analyze large ensemble simulations of TC-resolved climate models to identify the source of this uncertainty. Results show that large uncertainty appears in the South China Sea and east of the Philippines, primarily arising from two distinct atmospheric modes: the Matsuno-Gill-mode (MG-mode) and the Pacific-Japan-like pattern (PJ-mode). These two modes are closely associated with anomalous diabatic heating linked to tropical precipitation bias in model simulations. By conditionally constraining either of the modes, we can significantly reduce model uncertainty in simulating the dipole structure of the TCGF anomalies, confirming that it is the atmospheric circulation bias in response to tropical precipitation bias that causes uncertainty in the simulated WNP TCGF.
Psychedelic concentrations of nitrous oxide reduce functional differentiation in frontoparietal and somatomotor cortical networks
Authors: Dai Rui , Huang Zirui , Larkin Tony E. , Tarnal Vijay , Picton Paul , Vlisides Phillip E. , Janke Ellen , McKinney Amy , Hudetz Anthony G. , Harris Richard E. , Mashour George A.
Published: December 2023

Despite the longstanding use of nitrous oxide and descriptions of its psychological effects more than a century ago, there is a paucity of neurobiological investigation of associated psychedelic experiences. We measure the brain’s functional geometry (through analysis of cortical gradients) and temporal dynamics (through analysis of co-activation patterns) using human resting-state functional magnetic resonance imaging data acquired before and during administration of 35% nitrous oxide. Both analyses demonstrate that nitrous oxide reduces functional differentiation in frontoparietal and somatomotor networks. Importantly, the subjective psychedelic experience induced by nitrous oxide is inversely correlated with the degree of functional differentiation. Thus, like classical psychedelics acting on serotonin receptors, nitrous oxide flattens the functional geometry of the cortex and disrupts temporal dynamics in association with psychoactive effects.
Resurgence of superconductivity and the role of dxy hole band in FeSe1−xTex
Authors: Morfoot Archie B. , Kim Timur K. , Watson Matthew D. , Haghighirad Amir A. , Singh Shiv J. , Bultinck Nick , Coldea Amalia I.
Published: December 2023

Iron-chalcogenide superconductors display rich phenomena caused by orbital-dependent band shifts and electronic correlations. Additionally, they are potential candidates for topological superconductivity due to the band inversion between the Fe d bands and the chalcogen pz band. Here we present a detailed study of the electronic structure of the nematic superconductors FeSe1−xTex (0 < x < 0.4) using angle-resolved photoemission spectroscopy to understand the role of orbital-dependent band shifts, electronic correlations and the chalcogen band. We assess the changes in the effective masses using a three-band low energy model, and the band renormalization via comparison with DFT band structure calculations. The effective masses decrease for all three-hole bands inside the nematic phase, followed by a strong increase for the band with dxy orbital character. Interestingly, this nearly-flat dxy band becomes more correlated as it shifts towards the Fermi level with increasing Te concentrations and as the second superconducting dome emerges. Our findings suggests that the dxy hole band, which is very sensitive to the chalcogen height, could be involved in promoting an additional pairing channel and increasing the density of states to stabilize the second superconducting dome in FeSe1−xTex. This simultaneous shift of the dxy hole band and enhanced superconductivity is in contrast with FeSe1−xSx.
The state of food systems worldwide in the countdown to 2030
Authors: Schneider Kate R. , Fanzo Jessica , Haddad Lawrence , Herrero Mario , Moncayo Jose Rosero , Herforth Anna , Remans Roseline , Guarin Alejandro , Resnick Danielle , Covic Namukolo , Béné Christophe , Cattaneo Andrea , Aburto Nancy , Ambikapathi Ramya , Aytekin Destan , Barquera Simon , Battersby Jane , Beal Ty , Molina Paulina Bizzoto , Cafiero Carlo , Campeau Christine , Caron Patrick , Conforti Piero , Damerau Kerstin , Di Girolamo Michael , DeClerck Fabrice , Dewi Deviana , Elouafi Ismahane , Fabi Carola , Foley Pat , Frazier Tyler J. , Gephart Jessica , Golden Christopher , Fischer Carlos Gonzalez , Hendriks Sheryl , Honorati Maddalena , Huang Jikun , Kennedy Gina , Laar Amos , Lal Rattan , Lidder Preetmoninder , Loken Brent , Marshall Quinn , Masuda Yuta J. , McLaren Rebecca , Miachon Lais , Muñoz Hernán , Nordhagen Stella , Qayyum Naina , Saisana Michaela , Suhardiman Diana , Sumaila U. Rashid , Cullen Maximo Torero , Tubiello Francesco N. , Vivero-Pol Jose-Luis , Webb Patrick , Wiebe Keith
Published: December 2023

This Analysis presents a recently developed food system indicator framework and holistic monitoring architecture to track food system transformation towards global development, health and sustainability goals. Five themes are considered: (1) diets, nutrition and health; (2) environment, natural resources and production; (3) livelihoods, poverty and equity; (4) governance; and (5) resilience. Each theme is divided into three to five indicator domains, and indicators were selected to reflect each domain through a consultative process. In total, 50 indicators were selected, with at least one indicator available for every domain. Harmonized data of these 50 indicators provide a baseline assessment of the world’s food systems. We show that every country can claim positive outcomes in some parts of food systems, but none are among the highest ranked across all domains. Furthermore, some indicators are independent of national income, and each highlights a specific aspiration for healthy, sustainable and just food systems. The Food Systems Countdown Initiative will track food systems annually to 2030, amending the framework as new indicators or better data emerge.
Millions of seafloor pits, not pockmarks, induced by vertebrates in the North Sea
Authors: Schneider von Deimling Jens , Hoffmann Jasper , Geersen Jacob , Koschinski Sven , Lohrberg Arne , Gilles Anita , Belkin Igor , Böttner Christoph , Papenmeier Svenja , Krastel Sebastian
Published: December 2023

Seabed pockmarks are among the most prominent morphologic structures in the oceans. They are usually interpreted as surface manifestation of hydrocarbon fluids venting from sediments. Here we suggest an alternative hypothesis of pockmark formation based on latest multibeam echosounder data with a centimeter resolution. In the North Sea, >40,000 enigmatically shaped shallow depressions or ‘pits’ with a mean depth of 0.11 m were documented, that do not resemble known pockmark morphologies. Combining the new echosounder data with information from behavioral biology, physical oceanography, satellite remote sensing and habitat mapping, we conclude that harbor porpoises excavate sediments during benthic foraging. By grubbing the seabed, they cause sandeels to escape from the sediment and initiate the formation of seafloor pits. Time-lapse data reveals that the initially feeding pits serve as nuclei for scouring and eventually merge into larger scour-pits. With the immense number of vertebrates in the ocean, such megafauna-driven macro-bioturbation reshapes the seafloor, modulates sediment transport, and ultimately impacts associated ecosystems on a global scale.
How lowermost mantle viscosity controls the chemical structure of Earth’s deep interior
Authors: Dannberg Juliane , Chotalia Kiran , Gassmöller Rene
Published: December 2023

Determining the fate of subducted oceanic crust is critical for understanding material cycling through Earth’s deep interior and sources of mantle heterogeneity. A key control on the distribution of subducted slabs over long timescales is the bridgmanite to post-perovskite phase transition in the lowermost mantle, thought to cause rheological weakening. Using high-resolution computational models, we show that the ubiquitous presence of weak post-perovskite at the core-mantle boundary can facilitate or prevent the accumulation of basaltic oceanic crust, depending on the amount of weakening and the crustal thickness. Moderately weak post-perovskite ( ~ 10–100× weaker) facilitates segregation of crust from subducted slabs, increasing basalt accumulation in dense piles. Conversely, very weak post-perovskite (more than 100× weaker) promotes vigorous plumes that entrain more crustal material, decreasing basalt accumulation. Our results reconcile the contradicting conclusions of previous studies and provide insights into the accumulation of subducted crust in the lowermost mantle throughout Earth’s history.
Global trends of fronts and chlorophyll in a warming ocean
Authors: Yang Kai , Meyer Amelie , Strutton Peter G. , Fischer Andrew M.
Published: December 2023

Ocean fronts affect phytoplankton and higher trophic levels, including commercially important fisheries. As the oceans warm, uncertainty remains around the trends in fronts. Here we examine changes in sea surface temperature fronts (frequency, density, and intensity) and the concentration of chlorophyll, over recent satellite records (2003 – 2020) in ocean warming hotspots - areas that are warming faster than other parts of the ocean. Commonalities exist across hotspots with comparable dynamics. Most equatorial and subtropical gyre hotspots experienced a decline in frontal activity (frequency, density, strength) and chlorophyll concentration, while in high-latitude hotspots, frontal activity and chlorophyll concentration mostly increased. Continued warming may accentuate the impacts, changing both total biomass and the distribution of marine species. Areas with changing fronts and phytoplankton also correspond to areas of important global fish catch, highlighting the potential societal significance of these changes in the context of climate change.
Fertile upper mantle peridotite xenoliths indicate no wholesale destruction of cratonic root in East Asia
Authors: Samuel Vinod O. , Kwon Sanghoon , Jang Yirang , Kil Youngwoo , Santosh M. , Park Chaewon , Yi Keewook
Published: December 2023

A major question in geodynamic evolution of the Earth is whether the continental keel evolved geochemically or were delaminated and replaced by a new mantle. Here we present direct evidence for the geochemical evolution of continental keel from lherzolite xenoliths preserved in the Cenozoic alkali basalts from Jeju Island, Korea. Our findings, using detailed petrography and geochemical methods, reveal distinct textures and compositional changes (represented by olivine with magnesium number 91–87, 86–61 respectively) of two stages of geochemical alteration. The first stage involved a parental kimberlite melt that penetrated during the Paleozoic, and the second was caused by alkali basalt during Cenozoic. Our findings suggest that the Archean depleted harzburgitic upper mantle partially evolved to lherzolitic through interaction with melts/fluids that originated from the deep mantle, implying no wholesale delamination of the upper mantle root of East Asian continents.
Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon
Authors: Crossley Joel A , Allen William J , Watkins Daniel W , Sabir Tara , Radford Sheena E , Tuma Roman , Collinson Ian , Fessl Tomas
Published: December 2023

The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex—SecYEG in the inner membrane—is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome
Authors: Yang Lei , Metzger Genevieve A , Padilla Del Valle Ricky , Delgadillo Rubalcaba Diego , McLaughlin Richard N
Published: December 2023

Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
Vision on gyrate atrophy: why treat the eye?
Authors: Bergen Arthur A , Buijs Mark JN , ten Asbroek Anneloor LMA , Balfoort Berith M , Boon Camiel JF ,   The Dutch GACR “Bird’s Eye View” Consortium, Diederen Roselie RMH , Ferdinandusse Sacha , Ferreira Elise A , Schultink Patrick , Timmer Corrie , Vaz Frédéric M , Verhaagen Joost , Wagenmakers Margreet AEM , Waterham Hans R , Wijburg Frits , Brands Marion M , Wanders Ronald JA , van Karnebeek Clara DM , Houtkooper Riekelt H
Published: December 2023

In the April issue of this Journal, Boffa and coworkers put forward a new therapeutic approach for Gyrate Atrophy of the Choroid and Retina (GACR; OMIM 258870) (Boffa et al, 2023). The authors propose to apply gene therapy to the liver for GACR, a metabolic disease primarily affecting eyesight due to retinal degeneration. Their vision is enthusiastically supported by a News and Views comment in the same issue (Seker Yilmaz and Gissen, 2023). However, based on disease pathology, patient’s needs, ethical considerations, therapeutic developmental time lines, and current state of the art of gene therapy for liver and eye, we have a different view on this issue: We argue below that local treatment of the eye is the preferred option for GACR.
Chromosomal instability in aneuploid acute lymphoblastic leukemia associates with disease progression
Authors: Molina Oscar , Ortega-Sabater Carmen , Thampi Namitha , Fernández-Fuentes Narcís , Guerrero-Murillo Mercedes , Martínez-Moreno Alba , Vinyoles Meritxell , Velasco-Hernández Talía , Bueno Clara , Trincado Juan L , Granada Isabel , Campos Diana , Giménez Carles , Boer Judith M , den Boer Monique L , Calvo Gabriel F , Camós Mireia , Fuster Jose-Luis , Velasco Pablo , Ballerini Paola , Locatelli Franco , Mullighan Charles G , Spierings Diana C J , Foijer Floris , Pérez-García Víctor M , Menéndez Pablo
Published: December 2023

Chromosomal instability (CIN) lies at the core of cancer development leading to aneuploidy, chromosomal copy-number heterogeneity (chr-CNH) and ultimately, unfavorable clinical outcomes. Despite its ubiquity in cancer, the presence of CIN in childhood B-cell acute lymphoblastic leukemia (cB-ALL), the most frequent pediatric cancer showing high frequencies of aneuploidy, remains unknown. Here, we elucidate the presence of CIN in aneuploid cB-ALL subtypes using single-cell whole-genome sequencing of primary cB-ALL samples and by generating and functionally characterizing patient-derived xenograft models (cB-ALL-PDX). We report higher rates of CIN across aneuploid than in euploid cB-ALL that strongly correlate with intraclonal chr-CNH and overall survival in mice. This association was further supported by in silico mathematical modeling. Moreover, mass-spectrometry analyses of cB-ALL-PDX revealed a “CIN signature” enriched in mitotic-spindle regulatory pathways, which was confirmed by RNA-sequencing of a large cohort of cB-ALL samples. The link between the presence of CIN in aneuploid cB-ALL and disease progression opens new possibilities for patient stratification and offers a promising new avenue as a therapeutic target in cB-ALL treatment.
Real-time kinetic analysis and detection of glycated hemoglobin A1c using a quartz crystal microbalance-based aptasensor
Authors: Sriondee Yossawadee , Vijitvarasan Pasara , Rattanachata Arunothai , Nakajima Hideki , Oaew Sukunya , Cheunkar Sarawut
Published: December 2023

A quartz crystal microbalance-based aptasensor was developed for real-time kinetic analysis and detection of glycated hemoglobin (HbA1c), an important biomarker for long-term diagnosis and monitoring of diabetes mellitus.
Compressive Raman imaging by combining scattering-projection interleaving with context-aware excitation
Authors: Wang Yakun , Yuan Hang , Zhao Xuan , Zhang Pengfei , Wang Guiwen , Gao Feng
Published: December 2023

Introducing context-aware excitation into SIRI significantly improves signal intensity, SNR, and spectral resolution.