bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal Emissions of Active Craters at Stromboli Volcano: Spatio‐Temporal Insights From 10 Years of Satellite Observations
Authors: Massimetti F. , Laiolo M. , Aiuppa A. , Aveni S. , Bitetto M. , Campus A. , Coltelli M. , Cristaldi A. , Delle Donne D. , Innocenti L. , Lacanna G. , Pistolesi M. , Privitera E. , Ripepe M. , Salerno G. , Coppola D. 
Published: August 2024

AbstractOpen‐vent volcanoes continuously emit magmatic products and frequently feature multiple adjacent craters. Temporal shifts of thermal emissions between craters are especially detectable by InfraRed satellites. Here, SENTINEL‐2 and LANDSAT‐8/9 Short Wave InfraRed (SWIR) high‐spatial resolution satellite data, are combined to investigate 10 years (2013–2023) of thermal activity at Stromboli volcano (Italy). The correlation between Volcanic Radiative Power (VRP, in Watts) and Volcanic Radiative Energy (VRE, in Joules), retrieved by moderate MODIS and VIIRS Middle InfraRed (MIR) data, with the Thermal Index SWIR (TISWIR) data, allows us to quantify long‐term series of heat fluxes (VRPSWIR) and energy (VRESWIR). Combining moderate and higher spatial resolution data and fitting cumulative trends of TISWIR with VREMIR allows to measure thermal activity sourced by single craters during Strombolian activity. Long‐term results highlight that thermal emissions are clustered in the northern and southern parts of the crater terrace, with total energy emitted (∼12 × 1014 J) equally distributed. The thermal increase since April 2017 marked a reactivation of shallow magma transportation and an intensification of the activity after the 2014 eruption. Distinct thermal behaviors are shown by the NE, C, and SW craters, related to mechanisms of explosions. We found that short‐term thermal variations match well those resolved by ground‐based signals, and the NE crater as the most sensitive to the transition to higher‐intensity activity. Our multispatial/multisensory investigation allows, for the first time, the long‐term quantification of heat flux from Stromboli's craters, with an improved understanding of open‐vent dynamics and a new approach to monitor multiple active craters.
A New Climatology of Depth of Nitracline in the Bay of Bengal for Improving Model Simulations
Authors: Sridevi B. , Ashitha M. K. , Sarma V. V. S. S. , Udaya Bhaskar T. V. S. , Chakraborty Kunal , Bhavani I. V. G. , Valsala V. 
Published: August 2024

AbstractThe dissolved nitrate is one of the major essential nutrients for primary production in the tropical ocean and it is brought to the surface though mixing. The depth of nitracline determines how much of nitrate enters to the upper ocean through mixing. The depth of nitracline is traditionally estimated using nitrate concentrations measured at standard depths that introduces significant error due to interpolation of data. Based nitrate profiles measured at 5 m interval using nitrate sensors onboard Argo, the exact depth of nitracline was derived in the Bay of Bengal that displayed a significant linear relationship with depth of 26°C isotherm (D26). Based on climatological D26, the temporal and spatial variations in the depth of nitracline was estimated for the entire Bay of Bengal. The depth of nitracline varied between 5 and 80 m with large spatial and temporal variability in the Bay of Bengal and it is 5–20 m deeper than simulations of numerical models. The relationship between the depth of nitracline and photic zone integrated primary production indicates that 7.5 ± 3 mgC m−2 d−1 of primary production increases due to shallowing of 1 m of depth of nitracline. Therefore, models seem to be over estimating the photic zone integrated primary production by 5%–25% in the Bay of Bengal. The numerical models may improve the simulation of primary production and carbon cycling by accounting the accurate estimation of depth of nitracline in the model initialization.
Impact of clonal TP53 mutations with loss of heterozygosity on adjuvant chemotherapy and immunotherapy in gastric cancer
Authors: Gu Yun , Sun Mengyao , Fang Hanji , Shao Fei , Lin Chao , Liu Hao , Li He , He Hongyong , Li Ruochen , Wang Jieti , Zhang Heng , Xu Jiejie 
Published: August 2024

Abstract
Background
This study aimed to reveal the effect of TP53 status on clinical outcomes and underlying mechanism in gastric cancer (GC) patients.

Methods
TP53 status was divided into three groups according to genome sequencing, namely clonal mutations with LOH (C-LOH), clonal diploid or subclonal mutations (CD-SC), and wild type (WT). The p53 protein activity was divided into over-expression (OE), Null and WT according to immunohistochemical staining. Four cohorts, including the TCGA, SMC, ZSHS and FUSCC cohort, were analyzed for association between TP53 mutation status and clinical outcomes and the underlying mechanism.

Results
In TCGA cohort, TP53 CD-SC were associated with superior overall survival compared to TP53 C-LOH cases. GC patients could benefit from ACT only in TP53 CD-SC/ p53 OE and TP53/ p53 WT subgroups, and TP53 C-LOH subgroup demonstrated the worst response to pembrolizumab among three subgroups. Genomic and immunophenotypic deconvolution revealed that TP53 C-LOH, CD-SC and WT differed for genomic and immune-related features.

Conclusions
TP53 C-LOH GCs with genomic instability and immune evasion phenotype have poor clinical outcomes in patients treated with ACT or immunotherapy.
A common druggable signature of oncogenic c-Myc, mutant KRAS and mutant p53 reveals functional redundancy and competition among oncogenes in cancer
Authors: Grześ Maria , Jaiswar Akanksha , Grochowski Marcin , Wojtyś Weronika , Kaźmierczak Wojciech , Olesiński Tomasz , Lenarcik Małgorzata , Nowak-Niezgoda Magdalena , Kołos Małgorzata , Canarutto Giulia , Piazza Silvano , Wiśniewski Jacek R. , Walerych Dawid 
Published: August 2024

AbstractThe major driver oncogenes MYC, mutant KRAS, and mutant TP53 often coexist and cooperate to promote human neoplasia, which results in anticancer therapeutic opportunities within their downstream molecular programs. However, little research has been conducted on whether redundancy and competition among oncogenes affect their programs and ability to drive neoplasia. By CRISPR‒Cas9-mediated downregulation we evaluated the downstream proteomics and transcriptomics programs of MYC, mutant KRAS, and mutant TP53 in a panel of cell lines with either one or three of these oncogenes activated, in cancers of the lung, colon and pancreas. Using RNAi screening of the commonly activated molecular programs, we found a signature of three proteins - RUVBL1, HSPA9, and XPO1, which could be efficiently targeted by novel drug combinations in the studied cancer types. Interestingly, the signature was controlled by the oncoproteins in a redundant or competitive manner rather than by cooperation. Each oncoprotein individually upregulated the target genes, while upon oncogene co-expression each target was controlled preferably by a dominant oncoprotein which reduced the influence of the others. This interplay was mediated by redundant routes of target gene activation - as in the case of mutant KRAS signaling to c-Jun/GLI2 transcription factors bypassing c-Myc activation, and by competition - as in the case of mutant p53 and c-Myc competing for binding to target promoters. The global transcriptomics data from the cell lines and patient samples indicate that the redundancy and competition of oncogenic programs are broad phenomena, that may constitute even a majority of the genes dependent on oncoproteins, as shown for mutant p53 in colon and lung cancer cell lines. Nevertheless, we demonstrated that redundant oncogene programs harbor targets for efficient anticancer drug combinations, bypassing the limitations for direct oncoprotein inhibition.
Temperature and volumetric effects on structural and dielectric properties of hybrid perovskites
Authors: Nowok Andrzej , Sobczak Szymon , Roszak Kinga , Szeremeta Anna Z. , Mączka Mirosław , Katrusiak Andrzej , Pawlus Sebastian , Formalik Filip , Barros dos Santos Antonio José , Paraguassu Waldeci , Sieradzki Adam 
Published: August 2024

AbstractThree-dimensional organic-inorganic perovskites are rapidly evolving materials with diverse applications. This study focuses on their two representatives - acetamidinium manganese(II) formate (AceMn) and formamidinium manganese(II) formate (FMDMn) – subjected to varying temperature and pressure. We show that AceMn undergoes atypical pressure-induced structural transformations at room temperature, increasing the symmetry from ambient-pressure P21/n phase II to the high-pressure Pbca phase III. In turn, FMDMn in its C2/c phase II displays temperature- and pressure-induced ordering of cage cations that proceeds without changing the phase symmetry or energy barriers. The FMD+ cations do not order under constant volume across the pressure-temperature plane, despite similar pressure and temperature evolution of the unit-cell parameters. Temperature and pressure affect the cage cations differently, which is particularly pronounced in their relaxation dynamics seen by dielectric spectroscopy. Their motion require a rearrangement of the metal-formate framework, resulting in the energy and volumetric barriers defined by temperature-independent activation energy and activation volume parameters. As this process is phonon-assisted, the relaxation time is strongly temperature-dependent. Consequently, relaxation times do not scale with unit-cell volume nor H-bond lengths in formates, offering the possibility of tuning their electronic properties by external stimuli (like temperature or pressure) even without any structural changes.
A framework for the emergence and analysis of language in social learning agents
Authors: Wieczorek Tobias J. , Tchumatchenko Tatjana , Wert-Carvajal Carlos , Eggl Maximilian F. 
Published: August 2024

AbstractNeural systems have evolved not only to solve environmental challenges through internal representations but also, under social constraints, to communicate these to conspecifics. In this work, we aim to understand the structure of these internal representations and how they may be optimized to transmit pertinent information from one individual to another. Thus, we build on previous teacher-student communication protocols to analyze the formation of individual and shared abstractions and their impact on task performance. We use reinforcement learning in grid-world mazes where a teacher network passes a message to a student to improve task performance. This framework allows us to relate environmental variables with individual and shared representations. We compress high-dimensional task information within a low-dimensional representational space to mimic natural language features. In coherence with previous results, we find that providing teacher information to the student leads to a higher task completion rate and an ability to generalize tasks it has not seen before. Further, optimizing message content to maximize student reward improves information encoding, suggesting that an accurate representation in the space of messages requires bi-directional input. These results highlight the role of language as a common representation among agents and its implications on generalization capabilities.
Towards higher frequencies in a compact prebunched waveguide THz-FEL
Authors: Fisher Andrew , Lenz Maximilian , Ody Alex , Yang Yining , Pennington Chad , Maxson Jared , Hodgetts Tara , Agustsson Ronald , Murokh Alex , Musumeci Pietro 
Published: August 2024

AbstractFree-electron-lasers fill a critical gap in the space of THz-sources as they can reach high average and peak powers with spectral tunability. Using a waveguide in a THz FEL significantly increases the coupling between the relativistic electrons and electromagnetic field enabling large amounts of radiation to be generated in a single passage of electrons through the undulator. In addition to transversely confining the radiation, the dispersive properties of the waveguide critically affect the velocity and slippage of the radiation pulse which determine the central frequency and bandwidth of the generated radiation. In this paper, we characterize the spectral properties of a compact waveguide THz FEL including simultaneous lasing at two different frequencies and demonstrating tuning of the radiation wavelength in the high frequency branch by varying the beam energy and ensuring that the electrons injected into the undulator are prebunched on the scale of the resonant radiation wavelength.
Competitive processes shape multi-synapse plasticity along dendritic segments
Authors: Chater Thomas E. , Eggl Maximilian F. , Goda Yukiko , Tchumatchenko Tatjana 
Published: August 2024

AbstractNeurons receive thousands of inputs onto their dendritic arbour, where individual synapses undergo activity-dependent plasticity. Long-lasting changes in postsynaptic strengths correlate with changes in spine head volume. The magnitude and direction of such structural plasticity - potentiation (sLTP) and depression (sLTD) - depend upon the number and spatial distribution of stimulated synapses. However, how neurons allocate resources to implement synaptic strength changes across space and time amongst neighbouring synapses remains unclear. Here we combined experimental and modelling approaches to explore the elementary processes underlying multi-spine plasticity. We used glutamate uncaging to induce sLTP at varying number of synapses sharing the same dendritic branch, and we built a model incorporating a dual role Ca2+-dependent component that induces spine growth or shrinkage. Our results suggest that competition among spines for molecular resources is a key driver of multi-spine plasticity and that spatial distance between simultaneously stimulated spines impacts the resulting spine dynamics.
The heart is a resident tissue for hematopoietic stem and progenitor cells in zebrafish
Authors: Bornhorst Dorothee , Hejjaji Amulya V. , Steuter Lena , Woodhead Nicole M. , Maier Paul , Gentile Alessandra , Alhajkadour Alice , Santis Larrain Octavia , Weber Michael , Kikhi Khrievono , Guenther Stefan , Huisken Jan , Tamplin Owen J. , Stainier Didier Y. R. , Gunawan Felix 
Published: August 2024

AbstractThe contribution of endocardial cells (EdCs) to the hematopoietic lineages has been strongly debated. Here, we provide evidence that in zebrafish, the endocardium gives rise to and maintains a stable population of hematopoietic cells. Using single-cell sequencing, we identify an endocardial subpopulation expressing enriched levels of hematopoietic-promoting genes. High-resolution microscopy and photoconversion tracing experiments uncover hematopoietic cells, mainly hematopoietic stem and progenitor cells (HSPCs)/megakaryocyte-erythroid precursors (MEPs), derived from EdCs as well as the dorsal aorta stably attached to the endocardium. Emergence of HSPCs/MEPs in hearts cultured ex vivo without external hematopoietic sources, as well as longitudinal imaging of the beating heart using light sheet microscopy, support endocardial contribution to hematopoiesis. Maintenance of these hematopoietic cells depends on the adhesion factors Integrin α4 and Vcam1 but is at least partly independent of cardiac trabeculation or shear stress. Finally, blocking primitive erythropoiesis increases cardiac-residing hematopoietic cells, suggesting that the endocardium is a hematopoietic reservoir. Altogether, these studies uncover the endocardium as a resident tissue for HSPCs/MEPs and a de novo source of hematopoietic cells.
Direct coupling of light to valley current
Authors: Sharma S. , Gill D. , Krishna J. , Dewhurst J. K. , Shallcross S. 
Published: August 2024

AbstractThe coupling of circularly polarized light to local band structure extrema ("valleys”) in two dimensional semiconductors promises a new electronics based on the valley degree of freedom. Such pulses, however, couple only to valley charge and not to the valley current, precluding lightwave manipulation of this second vital element of valleytronic devices. Contradicting this established wisdom, we show that the few cycle limit of circularly polarized light is imbued with an emergent vectorial character that allows direct coupling to the valley current. The underlying physical mechanism involves the emergence of a momentum space valley dipole, the orientation and magnitude of which allows complete control over the direction and magnitude of the valley current. We demonstrate this effect via minimal tight-binding models both for the visible spectrum gaps of the transition metal dichalcogenides (generation time ~ 1 fs) as well as the infrared gaps of biased bilayer graphene ( ~ 14 fs); we further verify our findings with state-of-the-art time-dependent density functional theory incorporating transient excitonic effects. Our findings both mark a striking example of emergent physics in the ultrafast limit of light-matter coupling, as well as allowing the creation of valley currents on time scales that challenge quantum decoherence in matter.
Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome
Authors: Duller Stefanie , Vrbancic Simone , Szydłowski Łukasz , Mahnert Alexander , Blohs Marcus , Predl Michael , Kumpitsch Christina , Zrim Verena , Högenauer Christoph , Kosciolek Tomasz , Schmitz Ruth A. , Eberhard Anna , Dragovan Melanie , Schmidberger Laura , Zurabischvili Tamara , Weinberger Viktoria , Moser Adrian Mathias , Kolb Dagmar , Pernitsch Dominique , Mohammadzadeh Rokhsareh , Kühnast Torben , Rattei Thomas , Moissl-Eichinger Christine 
Published: August 2024

AbstractArchaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes’ adaptability in critical microbiome contexts.
Membrane filter removal in FTIR spectra through dictionary learning for exploring explainable environmental microplastic analysis
Authors: Buaruk Suphachok , Somnuake Pattara , Gulyanon Sarun , Deepaisarn Somrudee , Laitrakun Seksan , Opaprakasit Pakorn 
Published: August 2024

AbstractMicroplastic analysis is a crucial step for locating the environmental contamination sources and controlling plastic contamination. A popular tool like Fourier transform infrared (FTIR) spectroscopy is capable of identifying plastic types and can be carried out through a variety of containers. Unfortunately, sample collection from water sources like rivers usually involves filtration so the measurements inevitably include the membrane filter that also has its own FTIR characteristic bands. Furthermore, when plastic particles are small, the membrane filter’s spectrum may overwhelm the desired plastics’ spectrum. In this study, we proposed a novel preprocessing method based on the dictionary learning technique for decomposing the variations within the acquired FTIR spectra and capturing the membrane filter’s characteristic bands for the effective removal of these unwanted signals. We break down the plastic analysis task into two subtasks — membrane filter removal and plastic classification — to increase the explainability of the method. In the experiments, our method demonstrates a 1.5-fold improvement compared with baseline, and yields comparable results compared to other state-of-the-art methods such as UNet when applied to noisy spectra with low signal-to-noise ratio (SNR), but offers explainability, a crucial quality that is missing in other state-of-the-art methods. The limitations of the method are studied by testing against generated spectra with different levels of noise, with SNR ranging from 0 to – 30dB, as well as samples collected from the lab. The components/atoms learned from the dictionary learning technique are also scrutinized to describe the explainability and demonstrate the effectiveness of our proposed method in practical applications.
A novel lipophilic amiloride derivative efficiently kills chemoresistant breast cancer cells
Authors: Hu Michelle , Liu Ruiwu , Castro Noemi , Loza Sanchez Liliana , Rueankham Lapamas , Learn Julie A. , Huang Ruiqi , Lam Kit S. , Carraway Kermit L. 
Published: August 2024

AbstractDerivatives of the potassium-sparing diuretic amiloride are preferentially cytotoxic toward tumor cells relative to normal cells, and have the capacity to target tumor cell populations resistant to currently employed therapeutic agents. However, a major barrier to clinical translation of the amilorides is their modest cytotoxic potency, with estimated IC50 values in the high micromolar range. Here we report the synthesis of ten novel amiloride derivatives and the characterization of their cytotoxic potency toward MCF7 (ER/PR-positive), SKBR3 (HER2-positive) and MDA-MB-231 (triple negative) cell line models of breast cancer. Comparisons of derivative structure with cytotoxic potency toward these cell lines underscore the importance of an intact guanidine group, and uncover a strong link between drug-induced cytotoxicity and drug lipophilicity. We demonstrate that our most potent derivative called LLC1 is preferentially cytotoxic toward mouse mammary tumor over normal epithelial organoids, acts in the single digit micromolar range on breast cancer cell line models representing all major subtypes, acts on cell lines that exhibit both transient and sustained resistance to chemotherapeutic agents, but exhibits limited anti-tumor effects in a mouse model of metastatic breast cancer. Nonetheless, our observations offer a roadmap for the future optimization of amiloride-based compounds with preferential cytotoxicity toward breast tumor cells.
The molecular basis of the anticancer effect of statins
Authors: Buccioli Giovanni , Testa Carolina , Jacchetti Emanuela , Pinoli Pietro , Carelli Stephana , Ceri Stefano , Raimondi Manuela T. 
Published: August 2024

AbstractStatins, widely used cardiovascular drugs that lower cholesterol by inhibiting HMG-CoA reductase, have been increasingly recognized for their potential anticancer properties. This study elucidates the underlying mechanism, revealing that statins exploit Synthetic Lethality, a principle where the co-occurrence of two non-lethal events leads to cell death. Our computational analysis of approximately 37,000 SL pairs identified statins as potential drugs targeting genes involved in SL pairs with metastatic genes. In vitro validation on various cancer cell lines confirmed the anticancer efficacy of statins. This data-driven drug repurposing strategy provides a molecular basis for the anticancer effects of statins, offering translational opportunities in oncology.