bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrieving Seismic Source Characteristics Using Seismic and Infrasound Data: The 2020 ML 4.1 Kiruna Minequake, Sweden
Authors: Turquet Antoine , Brissaud Quentin , Alvizuri Celso , Näsholm Sven Peter , Le Pichon Alexis , Kero Johan 
Published: June 2024

AbstractA minequake of magnitude ML 4.1 occurred on 18 May 2020 early in the morning at the LKAB underground iron ore mine in Kiruna, Sweden. This is the largest mining‐induced earthquake in Scandinavia. It generated acoustic signals observed at three infrasound arrays at 9.3 (KRIS, Sweden), 155 (IS37, Norway), and 286 km (ARCI, Norway) distance. We perform full‐waveform focal mechanism inversion based on regional seismic data and local infrasound data. These independently highlight that this event was dominated by a shallow‐depth collapse in agreement with in‐mine seismic station data. However, regional infrasound data cannot inform the inversion process without an accurate model of atmospheric winds and temperatures. Yet, our numerical simulations demonstrate a potential of using local and regional infrasound data to constrain an event's focal mechanism and depth.
High‐Frequency Ground Motions of Earthquakes Correlate With Fault Network Complexity
Authors: Chatterjee Avigyan , Trugman Daniel T. , Hirth Greg , Lee Jaeseok , Tsai Victor C. 
Published: June 2024

AbstractUnderstanding the generation of damaging, high‐frequency ground motions during earthquakes is essential both for fundamental science and for effective hazard preparation. Various theories exist regarding the origin of high‐frequency ground motions, including the standard paradigm linked to slip heterogeneity on the rupture plane, and alternative perspectives associated with fault complexity. To assess these competing hypotheses, we measure ground motion amplitudes in different frequency bands for 3 ≤ M ≤ 5.8 earthquakes in Southern California and compare them to empirical ground motion models. We utilize a Bayesian inference technique called the Integrated Nested Laplace Approximation (INLA) to identify earthquake source regions that produce higher or lower ground motions than expected. Our analysis reveals a strong correlation between fault complexity measurements and the high‐frequency ground motion event terms identified by INLA. These findings suggest that earthquakes on complex faults (or fault networks) lead to stronger‐than‐expected ground motions at high frequencies.
Molecular mechanisms of circular RNA translation
Authors: Hwang Hyun Jung , Kim Yoon Ki 
Published: June 2024

AbstractCircular RNAs (circRNAs) are covalently closed single-stranded RNAs without a 5′ cap structure and a 3′ poly(A) tail typically present in linear mRNAs of eukaryotic cells. CircRNAs are predominantly generated through a back-splicing process within the nucleus. CircRNAs have long been considered non-coding RNAs seemingly devoid of protein-coding potential. However, many recent studies have challenged this idea and have provided substantial evidence that a subset of circRNAs can associate with polysomes and indeed be translated. Therefore, in this review, we primarily highlight the 5’ cap-independent internal initiation of translation that occurs on circular RNAs. Several molecular features of circRNAs, including the internal ribosome entry site, N6-methyladenosine modification, and the exon junction complex deposited around the back-splicing junction after back-splicing event, play pivotal roles in their efficient internal translation. We also propose a possible relationship between the translatability of circRNAs and their stability, with a focus on nonsense-mediated mRNA decay and nonstop decay, both of which are well-characterized mRNA surveillance mechanisms. An in-depth understanding of circRNA translation will reshape and expand our current knowledge of proteomics.
Adhesion pilus retraction powers twitching motility in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius
Authors: Charles-Orszag Arthur , van Wolferen Marleen , Lord Samuel J. , Albers Sonja-Verena , Mullins R. Dyche 
Published: June 2024

AbstractType IV pili are filamentous appendages found in most bacteria and archaea, where they can support functions such as surface adhesion, DNA uptake, aggregation, and motility. In most bacteria, PilT-family ATPases disassemble adhesion pili, causing them to rapidly retract and produce twitching motility, important for surface colonization. As archaea do not possess PilT homologs, it was thought that archaeal pili cannot retract and that archaea do not exhibit twitching motility. Here, we use live-cell imaging, automated cell tracking, fluorescence imaging, and genetic manipulation to show that the hyperthermophilic archaeon Sulfolobus acidocaldarius exhibits twitching motility, driven by retractable adhesion (Aap) pili, under physiologically relevant conditions (75 °C, pH 2). Aap pili are thus capable of retraction in the absence of a PilT homolog, suggesting that the ancestral type IV pili in the last universal common ancestor (LUCA) were capable of retraction.
Scanless two-photon voltage imaging
Authors: Sims Ruth R. , Bendifallah Imane , Grimm Christiane , Lafirdeen Aysha S. Mohamed , Domínguez Soledad , Chan Chung Yuen , Lu Xiaoyu , Forget Benoît C. , St-Pierre François , Papagiakoumou Eirini , Emiliani Valentina 
Published: June 2024

AbstractTwo-photon voltage imaging has long been heralded as a transformative approach capable of answering many long-standing questions in modern neuroscience. However, exploiting its full potential requires the development of novel imaging approaches well suited to the photophysical properties of genetically encoded voltage indicators. We demonstrate that parallel excitation approaches developed for scanless two-photon photostimulation enable high-SNR two-photon voltage imaging. We use whole-cell patch-clamp electrophysiology to perform a thorough characterization of scanless two-photon voltage imaging using three parallel illumination approaches and lasers with different repetition rates and wavelengths. We demonstrate voltage recordings of high-frequency spike trains and sub-threshold depolarizations from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-Kv. Using a low repetition-rate laser, we perform multi-cell recordings from up to fifteen targets simultaneously. We co-express JEDI-2P-Kv and the channelrhodopsin ChroME-ST and capitalize on their overlapping two-photon absorption spectra to simultaneously evoke and image action potentials using a single laser source. We also demonstrate in vivo scanless two-photon imaging of multiple cells simultaneously up to 250 µm deep in the barrel cortex of head-fixed, anaesthetised mice.
Nanoalignment by critical Casimir torques
Authors: Wang Gan , Nowakowski Piotr , Farahmand Bafi Nima , Midtvedt Benjamin , Schmidt Falko , Callegari Agnese , Verre Ruggero , Käll Mikael , Dietrich S. , Kondrat Svyatoslav , Volpe Giovanni 
Published: June 2024

AbstractThe manipulation of microscopic objects requires precise and controllable forces and torques. Recent advances have led to the use of critical Casimir forces as a powerful tool, which can be finely tuned through the temperature of the environment and the chemical properties of the involved objects. For example, these forces have been used to self-organize ensembles of particles and to counteract stiction caused by Casimir-Liftshitz forces. However, until now, the potential of critical Casimir torques has been largely unexplored. Here, we demonstrate that critical Casimir torques can efficiently control the alignment of microscopic objects on nanopatterned substrates. We show experimentally and corroborate with theoretical calculations and Monte Carlo simulations that circular patterns on a substrate can stabilize the position and orientation of microscopic disks. By making the patterns elliptical, such microdisks can be subject to a torque which flips them upright while simultaneously allowing for more accurate control of the microdisk position. More complex patterns can selectively trap 2D-chiral particles and generate particle motion similar to non-equilibrium Brownian ratchets. These findings provide new opportunities for nanotechnological applications requiring precise positioning and orientation of microscopic objects.
Dan forms condensates in neuroblasts and regulates nuclear architecture and progenitor competence in vivo
Authors: Benchorin Gillie , Cho Richard Jangwon , Li Maggie Jiaqi , Molotkova Natalia , Kohwi Minoree 
Published: June 2024

AbstractGenome organization is thought to underlie cell type specific gene expression, yet how it is regulated in progenitors to produce cellular diversity is unknown. In Drosophila, a developmentally-timed genome reorganization in neural progenitors terminates competence to produce early-born neurons. These events require downregulation of Distal antenna (Dan), part of the conserved pipsqueak DNA-binding superfamily. Here we find that Dan forms liquid-like condensates with high protein mobility, and whose size and subnuclear distribution are balanced with its DNA-binding. Further, we identify a LARKS domain, a structural motif associated with condensate-forming proteins. Deleting just 13 amino acids from LARKS abrogates Dan’s ability to retain the early-born neural fate gene, hunchback, in the neuroblast nuclear interior and maintain competence in vivo. Conversely, domain-swapping with LARKS from known phase-separating proteins rescues Dan’s effects on competence. Together, we provide in vivo evidence for condensate formation and the regulation of progenitor nuclear architecture underlying neuronal diversification.
International and regional spread of carbapenem-resistant Klebsiella pneumoniae in Europe
Authors: Budia-Silva Mabel , Kostyanev Tomislav , Ayala-Montaño Stefany , Bravo-Ferrer Acosta Jose , Garcia-Castillo Maria , Cantón Rafael , Goossens Herman , Rodriguez-Baño Jesus , Grundmann Hajo , Reuter Sandra 
Published: June 2024

AbstractCarbapenem-resistant Klebsiella pneumoniae (CRKP) are of particular concern due to the spread of antibiotic resistance genes associated with mobile genetic elements. In this study, we collected 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018). We identified 11 major clonal lineages, with most isolates belonging to the high-risk clones ST258/512, ST101, ST11, and ST307. blaKPC-like was the most prevalent carbapenemase-encoding gene (46%), with blaOXA-48 present in 39% of isolates. Through the combination and comparison of this EURECA collection with the previous EuSCAPE collection (2013-2014), we investigated the spread of high-risk clones circulating in Europe exhibiting regional differences. We particularly found blaKPC-like ST258/512 in Greece, Italy, and Spain, blaOXA-48 ST101 in Serbia and Romania, blaNDM ST11 in Greece, and blaOXA-48-like ST14 in Türkiye. Genomic surveillance across Europe thus provides crucial insights for local risk mapping and informs necessary adaptions for implementation of control strategies.
Uncovering the dynamics of precise repair at CRISPR/Cas9-induced double-strand breaks
Authors: Ben-Tov Daniela , Mafessoni Fabrizio , Cucuy Amit , Honig Arik , Melamed-Bessudo Cathy , Levy Avraham A. 
Published: June 2024

AbstractCRISPR/Cas9 is widely used for precise mutagenesis through targeted DNA double-strand breaks (DSBs) induction followed by error-prone repair. A better understanding of this process requires measuring the rates of cutting, error-prone, and precise repair, which have remained elusive so far. Here, we present a molecular and computational toolkit for multiplexed quantification of DSB intermediates and repair products by single-molecule sequencing. Using this approach, we characterize the dynamics of DSB induction, processing and repair at endogenous loci along a 72 h time-course in tomato protoplasts. Combining this data with kinetic modeling reveals that indel accumulation is determined by the combined effect of the rates of DSB induction processing of broken ends, and precise versus error repair. In this study, 64–88% of the molecules were cleaved in the three targets analyzed, while indels ranged between 15–41%. Precise repair accounts for most of the gap between cleavage and error repair, representing up to 70% of all repair events. Altogether, this system exposes flux in the DSB repair process, decoupling induction and repair dynamics, and suggesting an essential role of high-fidelity repair in limiting the efficiency of CRISPR-mediated mutagenesis.
Income and racial disparity in household publicly available electric vehicle infrastructure accessibility
Authors: Lou Jiehong , Shen Xingchi , Niemeier Deb A. , Hultman Nathan 
Published: June 2024

AbstractPublicly available electric vehicle (EV) infrastructure is pivotal for the United States EV transition by 2030. Existing infrastructure lacks equitably distribution to low-income and underrepresented communities, impeding mass adoption. Our study, utilizing 2021 micro-level data from 121 million United States households, comprehensively examines income and racial disparities in EV infrastructure accessibility. Our analysis of national averages indicates that lower-income groups face less accessibility to public EV infrastructure in both urban and rural geographies. Black households experience less rural accessibility, but greater urban accessibility compared to White households conditioning on income. However, our localized analysis uncovers significant variations in accessibility gaps among counties, rural and urban settings, and dwelling types. While Black households experience greater urban accessibility nationally, a closer look at the county level reveals diminishing advantages. This study identifies areas with pronounced inequality and urgent needs for enhanced accessibility, emphasizing the necessity for tailored solutions by local governments to enhance equitable access to EV infrastructure.
Atomic scale disorder and reconstruction in bulk infinite-layer nickelates lacking superconductivity
Authors: Hu Kejun , Li Qing , Song Dongsheng , Jia Yingze , Liang Zhiyao , Wang Shuai , Du Haifeng , Wen Hai-Hu , Ge Binghui 
Published: June 2024

AbstractThe recent discovery of superconductivity in infinite-layer nickelate films has sparked significant interest and expanded the realm of superconductors, in which the infinite-layer structure and proper chemical doping are both of the essence. Nonetheless, the reasons for the absence of superconductivity in bulk infinite-layer nickelates remain puzzling. Herein, we investigate atomic defects and electronic structures in bulk infinite-layer Nd0.8Sr0.2NiO2 using scanning transmission electron microscopy. Our observations reveal the presence of three-dimensional (3D) block-like structural domains resulting from intersecting defect structures, disrupting the continuity within crystal grains, which could be a crucial factor in giving rise to the insulating character and inhibiting the emergence of superconductivity. Moreover, the infinite-layer structure, without complete topotactic reduction, retains interstitial oxygen atoms on the Nd atomic plane in bulk nickelates, possibly further aggravating the local distortions of NiO2 planes and hindering the superconductivity. These findings shed light on the existence of structural and atomic defects in bulk nickelates and provide valuable insights into the influence of proper topotactic reduction and structural orders on superconductivity.
Association between antibody responses post-vaccination and severe COVID-19 outcomes in Scotland
Authors: Macdonald Calum , Palmateer Norah , McAuley Andrew , Lindsay Laura , Hasan Taimoor , Hameed Safraj Shahul , Hall Elliot , Jeffrey Karen , Grange Zoë , Gousias Petros , Mavin Sally , Jarvis Lisa , Cameron J. Claire , Daines Luke , Tibble Holly , Simpson Colin R. , McCowan Colin , Katikireddi Srinivasa Vittal , Rudan Igor , Fagbamigbe Adeniyi Francis , Ritchie Lewis , Swallow Ben , Moss Paul , Robertson Chris , Sheikh Aziz , Murray Josie 
Published: June 2024

AbstractSeveral population-level studies have described individual clinical risk factors associated with suboptimal antibody responses following COVID-19 vaccination, but none have examined multimorbidity. Others have shown that suboptimal post-vaccination responses offer reduced protection to subsequent SARS-CoV-2 infection; however, the level of protection from COVID-19 hospitalisation/death remains unconfirmed. We use national Scottish datasets to investigate the association between multimorbidity and testing antibody-negative, examining the correlation between antibody levels and subsequent COVID-19 hospitalisation/death among double-vaccinated individuals. We found that individuals with multimorbidity ( ≥ five conditions) were more likely to test antibody-negative post-vaccination and 13.37 [6.05–29.53] times more likely to be hospitalised/die from COVID-19 than individuals without conditions. We also show a dose-dependent association between post-vaccination antibody levels and COVID-19 hospitalisation or death, with those with undetectable antibody levels at a significantly higher risk (HR 9.21 [95% CI 4.63–18.29]) of these serious outcomes compared to those with high antibody levels.
Economic nanobubbles by RFB and promoted PEF with yolk@double-shell structural photocatalyst for degradation of pharmaceutical pollutants
Authors: Shirazian Saeed , Alshehri Sameer , A. Khasawneh Mohammad , Habibi Zare Masoud , Mehrabani-Zeinabad Arjomand 
Published: June 2024

AbstractIn this research, the generation of nanobubbles was carried out using a structure of vortex pump based on the relative blockage of flow (without the use of venturi and orifices, which consume a lot of energy to generate nanobubbles), which has made this process economical and commercial. In addition, the use of advanced synthesized nanoreactors with the Yolk@Shell structure, which forms a photoanode by coating the anode electrode and can operate in the visible light range, has highlighted this research work. An in-depth study of the synergistic effect of advanced photoelectrofenton oxidation methods in addition to the hydrodynamic reactor has shown that the intelligent selection of these three types of advanced oxidation methods together has improved the performance of each other and solved their negative aspects, including the use of hydrogen peroxide, divalent iron ion, and the removal of sludge generated by the electrofenton method. The use of hollow cylindrical electrodes allowed adequate loading of the advanced synthesized nanoreactors with Yolk@Shell structure. The investigation of the effects of micro (advanced synthesized nanoreactors with Yolk@Shell structure) and macro (vortex structure based on relative blockage of the flow) processes on the degradation of pharmaceutical pollutants, both separately and in combination, is a focus of this work. At the end, the energy consumption for each of these processes and this system in general was studied, which showed that the operating cost of this combined system according to the energy consumption requirements for the almost complete removal of the pollutant naproxen and the 90% reduction of its chemical oxygen demand is 6530 Rials/L.h (or 0.15525 USD/L.h), which presents this system as an economical method with industrialization capability. The degradability index (DI) of the introduced system under optimal operating conditions was 3.38, which shows that the development of the system based on the combination of advanced oxidation methods is a suitable method used in this research work due to its environmental friendliness, absence of side effluent production, efficiency and high degradation performance, ability to recover the nanocatalyst and consequently economic efficiency.
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting
Authors: Hu Xiaodi , Hoffmann David S. , Wang Mai , Schuhmacher Lars , Stroe Maria C. , Schreckenberger Birgit , Elstner Marcus , Fischer Reinhard 
Published: June 2024

AbstractInitiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A. flagrans develops adhesive traps and recognizes its prey, Caenorhabditis elegans, through nematode-specific pheromones (ascarosides). Gene-expression analyses revealed that ascarosides activate the fungal GPCR, GprC, at the plasma membrane and together with the G-protein alpha subunit GasA, reprograms the cell. However, GprC and GasA also reside in mitochondria and boost respiration. This dual localization of GprC in A. flagrans resembles the localization of the cannabinoid receptor CB1 in humans. The C. elegans ascaroside-sensing GPCR, SRBC66 and GPCRs of many fungi are also predicted for dual localization, suggesting broad evolutionary conservation. An SRBC64/66-GprC chimaeric protein was functional in A. flagrans, and C. elegans SRBC64/66 and DAF38 share ascaroside-binding sites with the fungal GprC receptor, suggesting 400-million-year convergent evolution.
Development of a novel rodent model for dog heartworm microfilaremia using the severe-combined immunodeficiency mouse
Authors: Mizuseki Mihoko , Ikeda Nao , Shirozu Takahiro , Yamagishi Maki , Oshiro Sugao , Fukumoto Shinya 
Published: June 2024

AbstractDirofilaria immitis is a mosquito-borne parasitic nematode that causes fatal heartworm disease in canids. The microfilariae are essential for research, including drug screening and mosquito-parasite interactions. However, no reliable methods for maintaining microfilaria long-term are currently available. Therefore, we used severe combined immunodeficiency (SCID) mice to develop a reliable method for maintaining D. immitis microfilaria. SCID mice were injected intravenously with microfilariae isolated from a D. immitis-infected dog. Microfilariae were detected in blood collected from the tail vein 218 days post-inoculation (dpi) and via cardiac puncture 296 dpi. Microfilariae maintained in and extracted from SCID mice showed infectivity and matured into third-stage larvae (L3s) in the vector mosquito Aedes aegypti. L3s can develop into the fourth stage larvae in vitro. Microfilariae from SCID mice respond normally to ivermectin in vitro. The microfilariae in SCID mice displayed periodicity in the peripheral circulation. The SCID mouse model aided in the separation of microfilariae from cryopreserved specimens. The use of SCID mice enabled the isolation and sustained cultivation of microfilariae from clinical samples. These findings highlight the usefulness of the SCID mouse model for studying D. immitis microfilaremia in canine heartworm research.