bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guiding Fuzzy Cognitive Mapping With Structured Decision Making to Inform Complex Natural Resource Management Problems in Waiʻanae Hawaiʻi
Authors: Cleveland Rachael , Trauernicht Clay , Bremer Leah , Pickett Elizabeth , Oleson Kirsten L. L. 
Published: April 2024

AbstractFire is one example of a larger class of wicked environmental management problems that require community‐based management for long‐term success. This study aimed to support participatory decision making in a data poor and complex system by using Fuzzy Cognitive Mapping (FCM) within the decision‐making framework Structured Decision Making (SDM) to develop a community‐based wildfire management plan in partnership with a local group in Wai‘anae Hawaiʻi. SDM is an organized process to create and evaluate decisions that can clarify trade‐offs and increase transparency. FCM is a semi‐quantitative method to describe system relationships that can handle low data and high uncertainty. We used SDM to define the problem, articulate community concerns related to wildfire, and identify management actions. We then used FCM to model how these actions affected valued ecosystem services and other stakeholder‐identified objectives. Modeling results highlighted the trade‐offs across three valued ecosystem services from three community‐led wildfire management actions. We found that native species outplanting was the most beneficial action to each of the three valued ecosystem services. Through this participatory research, we conclude that the SDM and FCM pairing provided an inclusive and cost‐effective way to engage with a specific wildfire management context, and that the process effectively engaged stakeholders while tackling uncertainty. This process also aided consensus‐building and group member communication. This pairing can be used to aid community decision‐making across diverse management problems as it provides a way to elicit objectives and model trade‐offs, even under uncertainty and data limitations, while including stakeholders impacted by such decisions.
Three‐Dimensional Teleseismic Elastic Reverse‐Time Migration With Deconvolution Imaging Condition and Its Application to Southwest Japan
Authors: Zou Peng , Cheng Jiubing , Wang Tengfei , Zhang Haijiang 
Published: April 2024

AbstractWe have developed a novel deconvolution‐based reverse time migration method to image lithospheric structures using teleseismic data recorded by dense seismic arrays. Unlike traditional approaches that rely on the retrieval of Green's functions (or receiver functions), the new method directly utilizes the recorded three‐component (3‐C) seismic waveforms to reconstruct subsurface wavefields, which has the advantage of avoiding the estimation and removal of source time function. Importantly, it enables the asymptotic estimation of P‐to‐S transmission conversion coefficients at the elastic discontinuities and enhances resolving power for the fine‐scale heterogeneities. Taking these improvements, we have obtained a full three‐dimensional (3‐D) high‐resolution image of the subduction zone beneath southwest Japan. This image provides a comprehensive configuration of the severely deformed subducting plate beneath the Kii Channel and Kinki Peninsula.
Costs of Dust Collection by Trichodesmium: Effect on Buoyancy and Toxic Metal Release
Authors: Wang Siyuan , Zhang Futing , Koedooder Coco , Qafoku Odeta , Basu Subhajit , Krisch Stephan , Visser Anna‐Neva , Eichner Meri , Kessler Nivi , Boiteau Rene M. , Gledhill Martha , Shaked Yeala 
Published: April 2024

AbstractThe marine cyanobacterium Trichodesmium has the remarkable ability to interact with and utilize air‐borne dust as a nutrient source. However, dust may adversely affect Trichodesmium through buoyancy loss and exposure to toxic metals. Our study explored the effect of desert dust on buoyancy and mortality of natural Red Sea puff‐shaped Trichodesmium thiebautii. Sinking velocities and ability of individual colonies to stay afloat with increasing dust loads were studied in sedimentation chambers. Low dust loads of up to ∼400 ng per colony did not impact initial sinking velocity and colonies remained afloat in the chamber. Above this threshold, sinking velocity increased linearly with the colony dust load at a slope matching prediction based on Stoke's law. The potential toxicity of dust was assessed with regards to metal dissolution kinetics, differentiating between rapidly released metals, which may impact surface blooms, and gradually released metals that may impact dust‐centering colonies. Incubations with increasing dust concentrations revealed colony death, but the observed lethal dose far exceeded dust concentrations measured in coastal and open ocean systems. Removal of toxic particles as a mechanism to reduce toxicity was explored using SEM‐EDX imaging of colonies incubated with Cu‐minerals, yet observations did not support this pathway. Combining our current and former experiments, we suggest that in natural settings the nutritional benefits gained by Trichodesmium via dust collection outweigh the risks of buoyancy loss and toxicity. Our data and concepts feed into the growing recognition of the significance of dust for Trichodesmium's ecology and subsequently to ocean productivity.
Brittle‐Ductile Rheological Behavior in Subduction Zones: Effects of Strength Ratio Between Strong and Weak Phases in a Bi‐Phase System
Authors: Maitre A. , Gueydan F. , Thieulot C. , Oliot E. 
Published: April 2024

AbstractThe brittle‐ductile rheological behavior in subduction zones is commonly proposed to explain deep transient slips. Generally observed at large scales in tectonic “mélanges”, here we show that it is also observed at the grain scale in exhumed blueschist metagabbros. In these rocks, petrologic and microstructural observations show a bi‐phase material constituted by strong microfractured magmatic pyroxene clasts located in a weak and ductile lawsonite‐rich metamorphic matrix. To constrain the mechanical conditions allowing the brittle deformation of a clast in a ductile matrix, we used two‐dimensional simple shear numerical experiments. Results show four behaviors: (a) entirely brittle; (b) brittle‐ductile with clast fracturing in a ductile matrix; (c) ductile‐dominant with limited plastic deformation at clast edges; and (d) entirely ductile. We propose that the conditions of the brittle‐ductile behavior, commonly associated with deep transient slips, are controlled by the strength ratio between the strong brittle phase and the weak ductile phase.
Gradient-induced long-range optical pulling force based on photonic band gap
Authors: Lu Wenlong , Krasavin Alexey V. , Lan Sheng , Zayats Anatoly V. , Dai Qiaofeng 
Published: April 2024

AbstractOptical pulling provides a new degree of freedom in optical manipulation. It is generally believed that long-range optical pulling forces cannot be generated by the gradient of the incident field. Here, we theoretically propose and numerically demonstrate the realization of a long-range optical pulling force stemming from a self-induced gradient field in the manipulated object. In analogy to potential barriers in quantum tunnelling, we use a photonic band gap design in order to obtain the intensity gradients inside a manipulated object placed in a photonic crystal waveguide, thereby achieving a pulling force. Unlike the usual scattering-type optical pulling forces, the proposed gradient-field approach does not require precise elimination of the reflection from the manipulated objects. In particular, the Einstein-Laub formalism is applied to design this unconventional gradient force. The magnitude of the force can be enhanced by a factor of up to 50 at the optical resonance of the manipulated object in the waveguide, making it insensitive to absorption. The developed approach helps to break the limitation of scattering forces to obtain long-range optical pulling for manipulation and sorting of nanoparticles and other nano-objects. The developed principle of using the band gap to obtain a pulling force may also be applied to other types of waves, such as acoustic or water waves, which are important for numerous applications.
Exercise mitigates a gut microbiota-mediated reduction in adult hippocampal neurogenesis and associated behaviours in rats
Authors: Nicolas Sarah , Dohm-Hansen Sebastian , Lavelle Aonghus , Bastiaanssen Thomaz F. S. , English Jane A. , Cryan John F. , Nolan Yvonne M. 
Published: April 2024

AbstractLifestyle factors, especially exercise, impact the manifestation and progression of psychiatric and neurodegenerative disorders such as depression and Alzheimer’s disease, mediated by changes in hippocampal neuroplasticity. The beneficial effects of exercise may be due to its promotion of adult hippocampal neurogenesis (AHN). Gut microbiota has also been showed to be altered in a variety of brain disorders, and disturbances of the microbiota have resulted in alterations in brain and behaviour. However, whether exercise can counteract the negative effects of altered gut microbiota on brain function remains under explored. To this end, chronic disruption of the gut microbiota was achieved using an antibiotic cocktail in rats that were sedentary or allowed voluntary access to running wheels. Sedentary rats with disrupted microbiota displayed impaired performance in hippocampal neurogenesis-dependent tasks: the modified spontaneous location recognition task and the novelty suppressed feeding test. Performance in the elevated plus maze was also impaired due to antibiotics treatment. These behaviours, and an antibiotics-induced reduction in AHN were attenuated by voluntary exercise. The effects were independent of changes in the hippocampal metabolome but were paralleled by caecal metabolomic changes. Taken together these data highlight the importance of the gut microbiota in AHN-dependent behaviours and demonstrate the power of lifestyle factors such as voluntary exercise to attenuate these changes.
Cell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity
Authors: Fredin Haslum Johan , Lardeau Charles-Hugues , Karlsson Johan , Turkki Riku , Leuchowius Karl-Johan , Smith Kevin , Müllers Erik 
Published: April 2024

AbstractIdentifying active compounds for a target is a time- and resource-intensive task in early drug discovery. Accurate bioactivity prediction using morphological profiles could streamline the process, enabling smaller, more focused compound screens. We investigate the potential of deep learning on unrefined single-concentration activity readouts and Cell Painting data, to predict compound activity across 140 diverse assays. We observe an average ROC-AUC of 0.744 ± 0.108 with 62% of assays achieving ≥0.7, 30% ≥0.8, and 7% ≥0.9. In many cases, the high prediction performance can be achieved using only brightfield images instead of multichannel fluorescence images. A comprehensive analysis shows that Cell Painting-based bioactivity prediction is robust across assay types, technologies, and target classes, with cell-based assays and kinase targets being particularly well-suited for prediction. Experimental validation confirms the enrichment of active compounds. Our findings indicate that models trained on Cell Painting data, combined with a small set of single-concentration data points, can reliably predict the activity of a compound library across diverse targets and assays while maintaining high hit rates and scaffold diversity. This approach has the potential to reduce the size of screening campaigns, saving time and resources, and enabling primary screening with more complex assays.
Kalium channelrhodopsins effectively inhibit neurons
Authors: Ott Stanislav , Xu Sangyu , Lee Nicole , Hong Ivan , Anns Jonathan , Suresh Danesha Devini , Zhang Zhiyi , Zhang Xianyuan , Harion Raihanah , Ye Weiying , Chandramouli Vaishnavi , Jesuthasan Suresh , Saheki Yasunori , Claridge-Chang Adam 
Published: April 2024

AbstractThe analysis of neural circuits has been revolutionized by optogenetic methods. Light-gated chloride-conducting anion channelrhodopsins (ACRs)—recently emerged as powerful neuron inhibitors. For cells or sub-neuronal compartments with high intracellular chloride concentrations, however, a chloride conductance can have instead an activating effect. The recently discovered light-gated, potassium-conducting, kalium channelrhodopsins (KCRs) might serve as an alternative in these situations, with potentially broad application. As yet, KCRs have not been shown to confer potent inhibitory effects in small genetically tractable animals. Here, we evaluated the utility of KCRs to suppress behavior and inhibit neural activity in Drosophila, Caenorhabditiselegans, and zebrafish. In direct comparisons with ACR1, a KCR1 variant with enhanced plasma-membrane trafficking displayed comparable potency, but with improved properties that include reduced toxicity and superior efficacy in putative high-chloride cells. This comparative analysis of behavioral inhibition between chloride- and potassium-selective silencing tools establishes KCRs as next-generation optogenetic inhibitors for in vivo circuit analysis in behaving animals.
Quantum critical phase of FeO spans conditions of Earth’s lower mantle
Authors: Ho Wai-Ga D. , Zhang Peng , Haule Kristjan , Jackson Jennifer M. , Dobrosavljević Vladimir , Dobrosavljevic Vasilije V. 
Published: April 2024

AbstractSeismic and mineralogical studies have suggested regions at Earth’s core-mantle boundary may be highly enriched in FeO, reported to exhibit metallic behavior at extreme pressure-temperature (P–T) conditions. However, underlying electronic processes in FeO remain poorly understood. Here we explore the electronic structure of B1-FeO at extreme conditions with large-scale theoretical modeling using state-of-the-art embedded dynamical mean field theory (eDMFT). Fine sampling of the phase diagram reveals that, instead of sharp metallization, compression of FeO at high temperatures induces a gradual orbitally selective insulator-metal transition. Specifically, at P–T conditions of the lower mantle, FeO exists in an intermediate quantum critical state, characteristic of strongly correlated electronic matter. Transport in this regime, distinct from insulating or metallic behavior, is marked by incoherent diffusion of electrons in the conducting t2g orbital and a band gap in the eg orbital, resulting in moderate electrical conductivity (~105 S/m) with modest P–T dependence as observed in experiments. Enrichment of solid FeO can thus provide a unifying explanation for independent observations of low seismic velocities and elevated electrical conductivities in heterogeneities at Earth’s mantle base.
Flexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope
Authors: Feng Xu , Xu Ruyi , Liao Jianglan , Zhao Jingyu , Zhang Baochang , Xu Xiaoxiao , Zhao Pengpeng , Wang Xiaoning , Yao Jianyun , Wang Pengxia , Wang Xiaoxue , Han Wenyuan , She Qunxin 
Published: April 2024

AbstractTnpBs encoded by the IS200/IS605 family transposon are among the most abundant prokaryotic proteins from which type V CRISPR-Cas nucleases may have evolved. Since bacterial TnpBs can be programmed for RNA-guided dsDNA cleavage in the presence of a transposon-adjacent motif (TAM), these nucleases hold immense promise for genome editing. However, the activity and targeting specificity of TnpB in homology-directed gene editing remain unknown. Here we report that a thermophilic archaeal TnpB enables efficient gene editing in the natural host. Interestingly, the TnpB has different TAM requirements for eliciting cell death and for facilitating gene editing. By systematically characterizing TAM variants, we reveal that the TnpB recognizes a broad range of TAM sequences for gene editing including those that do not elicit apparent cell death. Importantly, TnpB shows a very high targeting specificity on targets flanked by a weak TAM. Taking advantage of this feature, we successfully leverage TnpB for efficient single-nucleotide editing with templated repair. The use of different weak TAM sequences not only facilitates more flexible gene editing with increased cell survival, but also greatly expands targeting scopes, and this strategy is probably applicable to diverse CRISPR-Cas systems.
Chromosome organization shapes replisome dynamics in Caulobacter crescentus
Authors: Zhang Chen , Joseph Asha Mary , Casini Laurent , Collier Justine , Badrinarayanan Anjana , Manley Suliana 
Published: April 2024

AbstractDNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome β-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture.
Rapid autopsies to enhance metastatic research: the UPTIDER post-mortem tissue donation program
Authors: Geukens Tatjana , De Schepper Maxim , Van Den Bogaert Wouter , Van Baelen Karen , Maetens Marion , Pabba Anirudh , Mahdami Amena , Leduc Sophia , Isnaldi Edoardo , Nguyen Ha-Linh , Bachir Imane , Hajipirloo Maysam , Zels Gitte , Van Cauwenberge Josephine , Borremans Kristien , Vandecaveye Vincent , Weynand Birgit , Vermeulen Peter , Leucci Eleonora , Baietti Maria Francesca , Sflomos George , Battista Laura , Brisken Cathrin , Derksen Patrick W. B. , Koorman Thijs , Visser Daan , Scheele Colinda L. G. J. , Thommen Daniela S. , Hatse Sigrid , Fendt Sarah-Maria , Vanderheyden Evy , Van Brussel Thomas , Schepers Rogier , Boeckx Bram , Lambrechts Diether , Marano Giuseppe , Biganzoli Elia , Smeets Ann , Nevelsteen Ines , Punie Kevin , Neven Patrick , Wildiers Hans , Richard François , Floris Giuseppe , Desmedt Christine 
Published: April 2024

AbstractResearch on metastatic cancer has been hampered by limited sample availability. Here we present the breast cancer post-mortem tissue donation program UPTIDER and show how it enabled sampling of a median of 31 (range: 5-90) metastases and 5-8 liquids per patient from its first 20 patients. In a dedicated experiment, we show the mild impact of increasing time after death on RNA quality, transcriptional profiles and immunohistochemical staining in tumor tissue samples. We show that this impact can be counteracted by organ cooling. We successfully generated ex vivo models from tissue and liquid biopsies from distinct histological subtypes of breast cancer. We anticipate these and future findings of UPTIDER to elucidate mechanisms of disease progression and treatment resistance and to provide tools for the exploration of precision medicine strategies in the metastatic setting.
Optimizing self-organized study orders: combining refutations and metacognitive prompts improves the use of interleaved practice
Authors: Onan Erdem , Biwer Felicitas , Abel Roman , Wiradhany Wisnu , de Bruin Anique 
Published: April 2024

AbstractDuring category learning, students struggle to create an optimal study order: They often study one category at a time (i.e., blocked practice) instead of alternating between different categories (i.e., interleaved practice). Several interventions to improve self-study of categorical learning have been proposed, but these interventions have only been tested in learning tasks where students did not create the study order themselves. Instead, they decided which type of study order to follow. This pre-registered experiment examined whether an intervention that combines refutations and metacognitive prompts can enhance students’ engagement in interleaved practice, specifically when they organize the learning materials themselves. Ninety-one undergraduate students were randomized into the intervention and control condition and learned visual categories. Prior to the intervention, students used more blocked practice. After the intervention, the use of interleaved practice significantly increased in both immediate and delayed-transfer tasks. More interleaved practice was associated with better classification performance. Our findings indicate that refutations and metacognitive prompts form a strong intervention that corrects students’ erroneous beliefs and increases their engagement in interleaved practice.
Age and sex influence antibody profiles associated with tuberculosis progression
Authors: Davies Leela R. L. , Wang Chuangqi , Steigler Pia , Bowman Kathryn A. , Fischinger Stephanie , Hatherill Mark , Fisher Michelle , Mbandi Stanley Kimbung , Rodo Miguel , Ottenhoff Tom H. M. , Dockrell Hazel M. , Sutherland Jayne S. , Mayanja-Kizza Harriet , Boom W. Henry , Walzl Gerhard , Kaufmann Stefan H. E. , Nemes Elisa , Scriba Thomas J. , Lauffenburger Douglas , Alter Galit , Fortune Sarah M. 
Published: April 2024

AbstractAntibody features vary with tuberculosis (TB) disease state. Whether clinical variables, such as age or sex, influence associations between Mycobacterium tuberculosis-specific antibody responses and disease state is not well explored. Here we profiled Mycobacterium tuberculosis-specific antibody responses in 140 TB-exposed South African individuals from the Adolescent Cohort Study. We identified distinct response features in individuals progressing to active TB from non-progressing, matched controls. A multivariate antibody score differentially associated with progression (SeroScore) identified progressors up to 2 years before TB diagnosis, earlier than that achieved with the RISK6 transcriptional signature of progression. We validated these antibody response features in the Grand Challenges 6–74 cohort. Both the SeroScore and RISK6 correlated better with risk of TB progression in adolescents compared with adults, and in males compared with females. This suggests that age and sex are important, underappreciated modifiers of antibody responses associated with TB progression.