bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting fatty acid synthase in preclinical models of TNBC brain metastases synergizes with SN-38 and impairs invasion
Authors: Serhan Habib A. , Bao Liwei , Cheng Xu , Qin Zhaoping , Liu Chia-Jen , Heth Jason A. , Udager Aaron M. , Soellner Matthew B. , Merajver Sofia D. , Morikawa Aki , Merrill Nathan M. 
Published: June 2024

AbstractFatty acid synthesis (FAS) has been shown to play a key role in the survival of brain-metastatic (BM) breast cancer. We demonstrate that the fatty acid synthase inhibitor TVB-2640 synergizes with the topoisomerase inhibitor SN-38 in triple-negative breast cancer (TNBC) BM cell lines, upregulates FAS and downregulates cell cycle progression gene expression, and slows the motility of TNBC BM cell lines. The combination of SN-38 and TVB-2640 warrants further consideration as a potential therapeutic option in TNBC BMs.
Dynamic mode decomposition of nonequilibrium electron-phonon dynamics: accelerating the first-principles real-time Boltzmann equation
Authors: Maliyov Ivan , Yin Jia , Yao Jia , Yang Chao , Bernardi Marco 
Published: June 2024

AbstractNonequilibrium dynamics governed by electron–phonon (e-ph) interactions plays a key role in electronic devices and spectroscopies and is central to understanding electronic excitations in materials. The real-time Boltzmann transport equation (rt-BTE) with collision processes computed from first principles can describe the coupled dynamics of electrons and atomic vibrations (phonons). Yet, a bottleneck of these simulations is the calculation of e–ph scattering integrals on dense momentum grids at each time step. Here we show a data-driven approach based on dynamic mode decomposition (DMD) that can accelerate the time propagation of the rt-BTE and identify dominant electronic processes. We apply this approach to two case studies, high-field charge transport and ultrafast excited electron relaxation. In both cases, simulating only a short time window of ~10% of the dynamics suffices to predict the dynamics from initial excitation to steady state using DMD extrapolation. Analysis of the momentum-space modes extracted from DMD sheds light on the microscopic mechanisms governing electron relaxation to a steady state or equilibrium. The combination of accuracy and efficiency makes our DMD-based method a valuable tool for investigating ultrafast dynamics in a wide range of materials.
A possible direct exposure of the Earth to the cold dense interstellar medium 2–3 Myr ago
Authors: Opher Merav , Loeb Abraham , Peek J. E. G. 
Published: June 2024

AbstractCold, dense clouds in the interstellar medium of our Galaxy are 4–5 orders of magnitude denser than their diffuse counterparts. Our Solar System has most likely encountered at least one of these dense clouds during its lifetime. However, evidence for such an encounter has not been studied in detail yet. Here we derive the velocity field of the Local Ribbon of Cold Clouds (LRCC) by modelling the 21 cm data from the HI4PI survey, finding that the Solar System may have passed through the LRCC in the constellation Lynx 2–3 million years ago. Using a state-of-the-art simulation of the heliosphere, we show that during the passage, the heliosphere shrinks to a scale of 0.22 au, smaller than the Earth’s orbit around the Sun. This would have put the Earth in direct contact with the dense interstellar medium for a period of time and exposed it to a neutral hydrogen density above 3,000 cm−3. Such a scenario agrees with geological evidence from 60Fe and 244Pu isotopes. The encounter and related increased radiation from Galactic cosmic rays might have had a substantial impact on the Earth’s system and climate.
A somatic genetic clock for clonal species
Authors: Yu Lei , Renton Jessie , Burian Agata , Khachaturyan Marina , Bayer Till , Kotta Jonne , Stachowicz John J. , DuBois Katherine , Baums Iliana B. , Werner Benjamin , Reusch Thorsten B. H. 
Published: June 2024

AbstractAge and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species.
Prominent misinformation interventions reduce misperceptions but increase scepticism
Authors: Hoes Emma , Aitken Brian , Zhang Jingwen , Gackowski Tomasz , Wojcieszak Magdalena 
Published: June 2024

AbstractCurrent interventions to combat misinformation, including fact-checking, media literacy tips and media coverage of misinformation, may have unintended consequences for democracy. We propose that these interventions may increase scepticism towards all information, including accurate information. Across three online survey experiments in three diverse countries (the United States, Poland and Hong Kong; total n = 6,127), we tested the negative spillover effects of existing strategies and compared them with three alternative interventions against misinformation. We examined how exposure to fact-checking, media literacy tips and media coverage of misinformation affects individuals’ perception of both factual and false information, as well as their trust in key democratic institutions. Our results show that while all interventions successfully reduce belief in false information, they also negatively impact the credibility of factual information. This highlights the need for further improved strategies that minimize the harms and maximize the benefits of interventions against misinformation.
Brillouin gain microscopy
Authors: Shaashoua Roni , Kasuker Lir , Kishner Mor , Levy Tal , Rotblat Barak , Ben-Zvi Anat , Bilenca Alberto 
Published: June 2024

AbstractOptical imaging techniques with mechanical contrast, including passive microrheology, optical coherence elastography and Brillouin microscopy, are critical for material and biological discovery owing to their less perturbative nature compared with traditional mechanical imaging methods. An emerging optical microscopy approach for mechanical imaging is stimulated Brillouin scattering microscopy, which has been shown to be useful for biomechanical imaging with high sensitivity and specificity. However, the excitation energy used is high and the temporal resolution remains limited by the need to acquire full spectra. Here we develop Brillouin gain microscopy that detects the Brillouin gain at a specific mechanically contrasting frequency corresponding to a Brillouin acoustic-vibrational mode of interest in the sample. Brillouin gain microscopy affords a 200-fold improvement in temporal resolution compared with stimulated Brillouin scattering microscopy, down to 100 μs at excitation energy as low as 23 μJ. Using Brillouin gain microscopy, we demonstrate cross-sectional, all-optical mechanical imaging of materials as well as of the structure and dynamics in living systems with low excitation energy and at high temporal resolution.
Systematic rare variant analyses identify RAB32 as a susceptibility gene for familial Parkinson’s disease
Authors: Hop Paul J. , Lai Dongbing , Keagle Pamela J. , Baron Desiree M. , Kenna Brendan J. , Kooyman Maarten , Shankaracharya  , Halter Cheryl , Straniero Letizia , Asselta Rosanna , Bonvegna Salvatore , Soto-Beasley Alexandra I. ,   Project MinE ALS Sequencing Consortium, Wszolek Zbigniew K. , Uitti Ryan J. , Isaias Ioannis Ugo , Pezzoli Gianni , Ticozzi Nicola , Ross Owen A. , Veldink Jan H. , Foroud Tatiana M. , Kenna Kevin P. , Landers John E. 
Published: June 2024

AbstractDespite substantial progress, causal variants are identified only for a minority of familial Parkinson’s disease (PD) cases, leaving high-risk pathogenic variants unidentified1,2. To identify such variants, we uniformly processed exome sequencing data of 2,184 index familial PD cases and 69,775 controls. Exome-wide analyses converged on RAB32 as a novel PD gene identifying c.213C > G/p.S71R as a high-risk variant presenting in ~0.7% of familial PD cases while observed in only 0.004% of controls (odds ratio of 65.5). This variant was confirmed in all cases via Sanger sequencing and segregated with PD in three families. RAB32 encodes a small GTPase known to interact with LRRK2 (refs. 3,4). Functional analyses showed that RAB32 S71R increases LRRK2 kinase activity, as indicated by increased autophosphorylation of LRRK2 S1292. Here our results implicate mutant RAB32 in a key pathological mechanism in PD—LRRK2 kinase activity5–7—and thus provide novel insights into the mechanistic connections between RAB family biology, LRRK2 and PD risk.
Fast and robust feature-based stitching algorithm for microscopic images
Authors: Mohammadi Fatemeh Sadat , Shabani Hasti , Zarei Mojtaba 
Published: June 2024

AbstractThe limited field of view of high-resolution microscopic images hinders the study of biological samples in a single shot. Stitching of microscope images (tiles) captured by the whole-slide imaging (WSI) technique solves this problem. However, stitching is challenging due to the repetitive textures of tissues, the non-informative background part of the slide, and the large number of tiles that impact performance and computational time. To address these challenges, we proposed the Fast and Robust Microscopic Image Stitching (FRMIS) algorithm, which relies on pairwise and global alignment. The speeded up robust features (SURF) were extracted and matched within a small part of the overlapping region to compute the transformation and align two neighboring tiles. In cases where the transformation could not be computed due to an insufficient number of matched features, features were extracted from the entire overlapping region. This enhances the efficiency of the algorithm since most of the computational load is related to pairwise registration and reduces misalignment that may occur by matching duplicated features in tiles with repetitive textures. Then, global alignment was achieved by constructing a weighted graph where the weight of each edge is determined by the normalized inverse of the number of matched features between two tiles. FRMIS has been evaluated on experimental and synthetic datasets from different modalities with different numbers of tiles and overlaps, demonstrating faster stitching time compared to existing algorithms such as the Microscopy Image Stitching Tool (MIST) toolbox. FRMIS outperforms MIST by 481% for bright-field, 259% for phase-contrast, and 282% for fluorescence modalities, while also being robust to uneven illumination.
Evaluating lignin degradation under limited oxygen conditions by bacterial isolates from forest soil
Authors: Sumranwanich Thitinun , Amosu Esther , Chankhamhaengdecha Surang , Phetruen Tanaporn , Loktumraks Wethaka , Ounjai Puey , Harnvoravongchai Phurt 
Published: June 2024

AbstractLignin, a heterogeneous aromatic polymer present in plant biomass, is intertwined with cellulose and hemicellulose fibrils, posing challenges to its effective utilization due to its phenolic nature and recalcitrance to degradation. In this study, three lignin utilizing bacteria, Klebsiella sp. LEA1, Pseudomonas sp. LEA2, and Burkholderia sp. LEA3, were isolated from deciduous forest soil samples in Nan province, Thailand. These isolates were capable of growing on alkali lignin and various lignin-associated monomers at 40 °C under microaerobic conditions. The presence of Cu2+ significantly enhanced guaiacol oxidation in Klebsiella sp. LEA1 and Pseudomonas sp. LEA2. Lignin-related monomers and intermediates such as 2,6-dimethoxyphenol, 4-vinyl guaiacol, 4-hydroxybenzoic acid, benzoic acid, catechol, and succinic acid were detected mostly during the late stage of incubation of Klebsiella sp. LEA1 and Pseudomonas sp. LEA2 in lignin minimal salt media via GC–MS analysis. The intermediates identified from Klebsiella sp. LEA1 degradation suggested that conversion and utilization occurred through the β-ketoadipate (ortho-cleavage) pathway under limited oxygen conditions. The ability of these bacteria to thrive on alkaline lignin and produce various lignin-related intermediates under limited oxygen conditions suggests their potential utility in oxygen-limited processes and the production of renewable chemicals from plant biomass.
Coral-seeding devices with fish-exclusion features reduce mortality on the Great Barrier Reef
Authors: Whitman T. N. , Hoogenboom M. O. , Negri A. P. , Randall C. J. 
Published: June 2024

AbstractRestoration methods that seed juvenile corals show promise as scalable interventions to promote population persistence through anthropogenic warming. However, challenges including predation by fishes can threaten coral survival. Coral-seeding devices with refugia from fishes offer potential solutions to limit predation-driven mortality. In an 8-month field study, we assessed the efficacy of such devices for increasing the survival of captive-reared Acropora digitifera (spat and microfragments) over control devices (featureless and caged). Devices with fish-exclusion features demonstrated a twofold increase in coral survival, while most corals seeded without protection suffered mortality within 48 h. Overall, spat faced more grazing and higher mortality compared to microfragments, and upward-facing corals were more vulnerable than side-facing corals. Grazing-induced mortality varied by site, with lower activity in locations abundant in mat-forming cyanobacteria or Scleractinian corals. Many scraping parrotfish were found feeding on or near the seeded corals; however, bites by Scarus globiceps explained the most site-related variation in grazing. Cyanobacteria may be preferred over corals as a nutritional resource for scraping parrotfish—advancing our understanding of their foraging ecology. Incorporating side-facing refugia in seeding devices and deploying to sites with nutrient-rich food sources for fish are potential strategies to enhance coral survival in restoration programs.
Salicylic acid and jasmonic acid-mediated different fate of nickel phytoremediation in two populations of Alyssum inflatum Nyár.
Authors: Modarresi Masoud , Karimi Naser , Chaichi Mehrdad , Chahardoli Azam , Najafi-Kakavand Shiva 
Published: June 2024

AbstractThis study investigates Ni phytoremediation and accumulation potential in the presence of salicylic acid (SA) (0, 50 and 200 μM) and jasmonic acid (JA) (0, 5 and 10 μM) in two populations of Alyssum inflatum under various nickel (Ni) doses (0, 100 and 400 μM). By measuring Ni levels in the shoots and roots, values of bioaccumulation coefficient (BAC), biological concentration factor (BCF) and translocation factor (TF) were calculated to quantify Ni accumulation and translocation between plant organs. Additionally, the amounts of histidine (His), citric acid (CA) and malic acid (MA) were explored. The results showed that plant dry weight (DW) [in shoot (29.8%, 8.74%) and in root (21.6%, 24.4%)] and chlorophyll [a (17.1%, 32.5%), b (10.1%, 30.9%)] declined in M and NM populations respectively, when exposed to Ni (400 μM). Conversely, the levels of MA [in shoot (37.0%, 32.0%) and in root (25.5%, 21.2%)], CA [in shoot (17.0%, 10.0%) and in root (47.9%, 37.2%)] and His [in shoot (by 1.59- and 1.34-fold) and in root (by 1.24- and 1.18-fold)] increased. Also, in the presence 400 μM Ni, the highest accumulation of Ni was observed in shoots of M (1392 μg/g DW) and NM (1382 μg/g DW). However, the application of SA and JA (especially in Ni 400 μM + SA 200 μM + JA 5 and 10 μM treatments) mitigated the harmful impact of Ni on physiological parameters. Also, a decreasing trend was observed in the contents of MA, CA, and His. The reduction of these compounds as important chelators of Ni caused a decrease in root-to-shoot Ni transfer and reducing accumulation in the shoots of both populations. The values of phytoremediation indices in both populations exposed to Ni (400 μM) were above one. In presence of the SA and JA, these indices showed a decreasing trend, although the values remained above one (BAC, BCF and TF > 1). Overall, the results indicated that SA and JA can reduce phytoremediation potential of the two populations through different mechanisms.
Extreme Tibetan Plateau cooling caused by tropical volcanism
Authors: Zhu Xian , Ji Zhenming , Liu Fei , Dong Wenjie , Gao Chaochao 
Published: June 2024

AbstractThe extreme cooling of the Tibetan Plateau (TP) during the boreal winter typically poses threats to the local environment and people’s safety, and it is usually attributed to internal climate variability. Here we demonstrate that the five recent large tropical volcanic eruptions since 1880 have caused an average extreme cooling of up to −0.80 K on the TP in observations during the first boreal winter following the eruptions. This cooling effect is much larger than the global average terrestrial cooling of −0.30 K after the eruptions. The multi-model ensemble mean (MME) of the Atmospheric Model Intercomparison Project (AMIP) runs from Phase 6 of the Coupled Model Intercomparison Project (CMIP6), in which realistic sea surface temperatures (SST) were specified, can simulate an extreme TP cooling response of up to −0.79 K, which is much larger than the direct aerosol cooling of −0.36 K simulated by the historical runs. The positive North Atlantic Oscillation (NAO) anomaly during the post-eruption winter after the eruptions plays a key role in amplifying the TP cooling through atmospheric teleconnection, which overwhelms the warming response associated with the frequently occurring El Niños. The results from this study provide a perspective on the potential contribution of volcanic activity or stratospheric sulfur injection scenarios to specific TP cooling.
Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world
Authors: Hylander Kristoffer , Nemomissa Sileshi , Fischer Joern , Zewdie Beyene , Ayalew Biruk , Tack Ayco J. M. 
Published: June 2024

AbstractThe reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.
An immobilized antibody-based affinity grid strategy for on-grid purification of target proteins enables high-resolution cryo-EM
Authors: Zhao Qiaoyu , Hong Xiaoyu , Wang Yanxing , Zhang Shaoning , Ding Zhanyu , Meng Xueming , Song Qianqian , Hong Qin , Jiang Wanying , Shi Xiangyi , Cai Tianxun , Cong Yao 
Published: June 2024

AbstractIn cryo-electron microscopy (cryo-EM), sample preparation poses a critical bottleneck, particularly for rare or fragile macromolecular assemblies and those suffering from denaturation and particle orientation distribution issues related to air-water interface. In this study, we develop and characterize an immobilized antibody-based affinity grid (IAAG) strategy based on the high-affinity PA tag/NZ-1 antibody epitope tag system. We employ Pyr-NHS as a linker to immobilize NZ-1 Fab on the graphene oxide or carbon-covered grid surface. Our results demonstrate that the IAAG grid effectively enriches PA-tagged target proteins and overcomes preferred orientation issues. Furthermore, we demonstrate the utility of our IAAG strategy for on-grid purification of low-abundance target complexes from cell lysates, enabling atomic resolution cryo-EM. This approach greatly streamlines the purification process, reduces the need for large quantities of biological samples, and addresses common challenges encountered in cryo-EM sample preparation. Collectively, our IAAG strategy provides an efficient and robust means for combined sample purification and vitrification, feasible for high-resolution cryo-EM. This approach holds potential for broader applicability in both cryo-EM and cryo-electron tomography (cryo-ET).
Design, modeling, and manufacturing of high strain composites for space deployable structures
Authors: Ma Xiaofei , An Ning , Cong Qiang , Bai Jiang-Bo , Wu Minger , Xu Yan , Zhou Jinxiong , Zhang Dayu , Zhang Taotao , Guo Ruiwen , Li Huanxiao , Wang Yizhe , Zhou Xiaotao , Zhu Jialong , Jin Xin , Feng Yuqing , Wu Di , Liu Tian-Wei , Yan Zhongxi , Wu Tong , Xi Haotian , Jia Qilong 
Published: June 2024

AbstractThe demand for larger and lighter mechanisms for next-generation space missions necessitates using deployable structures. High-strain fiber polymer composites show considerable promise for such applications due to their exceptional strength-to-weight ratio, manufacturing versatility, packaging efficiency, and capacity for self-deployment using stored strain energy. However, a significant challenge in using composite deployable structures for space applications arises from the unavoidable extended stowage periods before they are deployed into their operational configuration in orbit. During the stowage period, the polymers within the composites experience material degradation due to their inherent viscoelastic and/or plastic properties, causing stress relaxation and accumulation of plastic strains, thereby reducing the deployment capability and resulting in issues related to recovery accuracy. This paper aims to give a state-of-the-art review of recent advances in the design, modeling, and manufacturing of high-strain composites for deployable structures in space applications, emphasizing the long-term stowage effects. This review is intended to initiate discussion of future research to enable efficient, robust, and accurate design of composite deployable structures that account for the enduring challenges posed by long-term stowage effects.