bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic-scale observation of localized phonons at FeSe/SrTiO3 interface
Authors: Shi Ruochen , Li Qize , Xu Xiaofeng , Han Bo , Zhu Ruixue , Liu Fachen , Qi Ruishi , Zhang Xiaowen , Du Jinlong , Chen Ji , Yu Dapeng , Zhu Xuetao , Guo Jiandong , Gao Peng 
Published: April 2024

AbstractIn single unit-cell FeSe grown on SrTiO3, the superconductivity transition temperature features a significant enhancement. Local phonon modes at the interface associated with electron-phonon coupling may play an important role in the interface-induced enhancement. However, such phonon modes have eluded direct experimental observations. The complicated atomic structure of the interface brings challenges to obtain the accurate structure-phonon relation knowledge. Here, we achieve direct characterizations of atomic structure and phonon modes at the FeSe/SrTiO3 interface with atomically resolved imaging and electron energy loss spectroscopy in an electron microscope. We find several phonon modes highly localized (~1.3 nm) at the unique double layer Ti-O terminated interface, one of which (~ 83 meV) engages in strong interactions with the electrons in FeSe based on ab initio calculations. This finding of the localized interfacial phonon associated with strong electron-phonon coupling provides new insights into understanding the origin of superconductivity enhancement at the FeSe/SrTiO3 interface.
Autonomous self-healing supramolecular polymer transistors for skin electronics
Authors: Vo Ngoc Thanh Phuong , Nam Tae Uk , Jeong Min Woo , Kim Jun Su , Jung Kyu Ho , Lee Yeongjun , Ma Guorong , Gu Xiaodan , Tok Jeffrey B.-H. , Lee Tae Il , Bao Zhenan , Oh Jin Young 
Published: April 2024

AbstractSkin-like field-effect transistors are key elements of bio-integrated devices for future user-interactive electronic-skin applications. Despite recent rapid developments in skin-like stretchable transistors, imparting self-healing ability while maintaining necessary electrical performance to these transistors remains a challenge. Herein, we describe a stretchable polymer transistor capable of autonomous self-healing. The active material consists of a blend of an electrically insulating supramolecular polymer with either semiconducting polymers or vapor-deposited metal nanoclusters. A key feature is to employ the same supramolecular self-healing polymer matrix for all active layers, i.e., conductor/semiconductor/dielectric layers, in the skin-like transistor. This provides adhesion and intimate contact between layers, which facilitates effective charge injection and transport under strain after self-healing. Finally, we fabricate skin-like self-healing circuits, including NAND and NOR gates and inverters, both of which are critical components of arithmetic logic units. This work greatly advances practical self-healing skin electronics.
Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast
Authors: Jiang Lihui , Zhang Xiaoyan , Zhao Yiting , Zhu Haiyan , Fu Qijing , Lu Xinqi , Huang Wuying , Yang Xinyue , Zhou Xuan , Wu Lixia , Yang Ao , He Xie , Dong Man , Peng Ziai , Yang Jing , Guo Liwei , Wen Jiancheng , Huang Huichuan , Xie Yong , Zhu Shusheng , Li Chengyun , He Xiahong , Zhu Youyong , Friml Jiří , Du Yunlong 
Published: April 2024

AbstractPhytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.
Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis
Authors: Serra Moncadas Lucas , Hofer Cyrill , Bulzu Paul-Adrian , Pernthaler Jakob , Andrei Adrian-Stefan 
Published: April 2024

AbstractThe emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
Targeting NRAS via miR-1304-5p or farnesyltransferase inhibition confers sensitivity to ALK inhibitors in ALK-mutant neuroblastoma
Authors: Pucci Perla , Lee Liam C. , Han Miaojun , Matthews Jamie D. , Jahangiri Leila , Schlederer Michaela , Manners Eleanor , Sorby-Adams Annabel , Kaggie Joshua , Trigg Ricky M. , Steel Christopher , Hare Lucy , James Emily R. , Prokoph Nina , Ducray Stephen P. , Merkel Olaf , Rifatbegovic Firkret , Luo Ji , Taschner-Mandl Sabine , Kenner Lukas , Burke G. A. Amos , Turner Suzanne D. 
Published: April 2024

AbstractTargeting Anaplastic lymphoma kinase (ALK) is a promising therapeutic strategy for aberrant ALK-expressing malignancies including neuroblastoma, but resistance to ALK tyrosine kinase inhibitors (ALK TKI) is a distinct possibility necessitating drug combination therapeutic approaches. Using high-throughput, genome-wide CRISPR-Cas9 knockout screens, we identify miR-1304-5p loss as a desensitizer to ALK TKIs in aberrant ALK-expressing neuroblastoma; inhibition of miR-1304-5p decreases, while mimics of this miRNA increase the sensitivity of neuroblastoma cells to ALK TKIs. We show that miR-1304-5p targets NRAS, decreasing cell viability via induction of apoptosis. It follows that the farnesyltransferase inhibitor (FTI) lonafarnib in addition to ALK TKIs act synergistically in neuroblastoma, inducing apoptosis in vitro. In particular, on combined treatment of neuroblastoma patient derived xenografts with an FTI and an ALK TKI complete regression of tumour growth is observed although tumours rapidly regrow on cessation of therapy. Overall, our data suggests that combined use of ALK TKIs and FTIs, constitutes a therapeutic approach to treat high risk neuroblastoma although prolonged therapy is likely required to prevent relapse.
Room-temperature stabilizing strongly competing ferrielectric and antiferroelectric phases in PbZrO3 by strain-mediated phase separation
Authors: Yu Ziyi , Fan Ningbo , Fu Zhengqian , He Biao , Yan Shiguang , Cai Henghui , Chen Xuefeng , Zhang Linlin , Zhang Yuanyuan , Xu Bin , Wang Genshui , Xu Fangfang 
Published: April 2024

AbstractPbZrO3 has been broadly considered as a prototypical antiferroelectric material for high-power energy storage. A recent theoretical study suggests that the ground state of PbZrO3 is threefold-modulated ferrielectric, which challenges the generally accepted antiferroelectric configuration. However, such a novel ferrielectric phase was predicted only to be accessible at low temperatures. Here, we successfully achieve the room-temperature construction of the strongly competing ferrielectric and antiferroelectric state by strain-mediated phase separation in PbZrO3/SrTiO3 thin film. We demonstrate that the phase separation occurs spontaneously in quasi-periodic stripe-like patterns under a compressive misfit strain and can be tailored by varying the film thickness. The ferrielectric phase strikingly exhibitsa threefold modulation period with a nearly up-up-down configuration, which could be stabilized and manipulated by the formation and evolution of interfacial defects under applied strain. The present results construct a fertile ground for further exploring the physical properties and applications based on the novel ferrielectric phase.
Temporal coordination of the transcription factor response to H2O2 stress
Authors: Jose Elizabeth , March-Steinman Woody , Wilson Bryce A. , Shanks Lisa , Parkinson Chance , Alvarado-Cruz Isabel , Sweasy Joann B. , Paek Andrew L. 
Published: April 2024

AbstractOxidative stress from excess H2O2 activates transcription factors that restore redox balance and repair oxidative damage. Although many transcription factors are activated by H2O2, it is unclear whether they are activated at the same H2O2 concentration, or time. Dose-dependent activation is likely as oxidative stress is not a singular state and exhibits dose-dependent outcomes including cell-cycle arrest and cell death. Here, we show that transcription factor activation is both dose-dependent and coordinated over time. Low levels of H2O2 activate p53, NRF2 and JUN. Yet under high H2O2, these transcription factors are repressed, and FOXO1, NF-κB, and NFAT1 are activated. Time-lapse imaging revealed that the order in which these two groups of transcription factors are activated depends on whether H2O2 is administered acutely by bolus addition, or continuously through the glucose oxidase enzyme. Finally, we provide evidence that 2-Cys peroxiredoxins control which group of transcription factors are activated.
Designer peptide–DNA cytoskeletons regulate the function of synthetic cells
Authors: Daly Margaret L. , Nishi Kengo , Klawa Stephen J. , Hinton Kameryn Y. , Gao Yuan , Freeman Ronit 
Published: April 2024

AbstractThe bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide–DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide–DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide–DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
Measurements of dune erosion processes during the RealDune/REFLEX experiments
Authors: van Wiechen Paul , Rutten Jantien , de Vries Sierd , Tissier Marion , Mieras Ryan , Anarde Katherine , Baker Christine , Reniers Ad , Mol Jan-Willem 
Published: April 2024

AbstractNearshore hydro- and morphodynamic data were collected during a field experiment under calm conditions, moderate conditions, and storm conditions with dune erosion in the collision regime. The experiment was conducted on the Sand Engine near Kijkduin, the Netherlands, from October 18, 2021, to January 7, 2022. Two artificial unvegetated dunes were constructed just above the high water line to measure storm erosion and dune impacts from higher water levels and waves. During the experiment, three storms occurred that resulted in significant erosion of both dunes. The collected hydrodynamic data include pressure sensor and velocimeter data along two cross-shore transects. The collected morphodynamic data include bathymetry and topography surveys, optical backscatter sensor data in the inner surf zone, and a continuous cross-shore line-scanning lidar data set of the dune face. This comprehensive data set can be used to (1) study relevant nearshore hydrodynamic and morphodynamic processes that occur during calm conditions, moderate conditions, and storm conditions with dune erosion in the collision regime, and (2) validate existing dune erosion models.
RASMI: Global ranges of building material intensities differentiated by region, structure, and function
Authors: Fishman Tomer , Mastrucci Alessio , Peled Yoav , Saxe Shoshanna , van Ruijven Bas 
Published: April 2024

AbstractThe construction materials used in buildings have large and growing implications for global material flows and emissions. Material Intensity (MI) is a metric that measures the mass of construction materials per unit of a building’s floor area. MIs are used to model buildings’ materials and assess their resource use and environmental performance, critical to global climate commitments. However, MI data availability and quality are inconsistent, incomparable, and limited, especially for regions in the Global South. To address these challenges, we present the Regional Assessment of buildings’ Material Intensities (RASMI), a new dataset and accompanying method of comprehensive and consistent representative MI value ranges that embody the variability inherent in buildings. RASMI consists of 3072 MI ranges for 8 construction materials in 12 building structure and function types across 32 regions covering the entire world. The dataset is reproducible, traceable, and updatable, using synthetic data when required. It can be used for estimating historical and future material flows and emissions, assessing demolition waste and at-risk stocks, and evaluating urban mining potentials.
Large-scale annotated dataset for cochlear hair cell detection and classification
Authors: Buswinka Christopher J. , Rosenberg David B. , Simikyan Rubina G. , Osgood Richard T. , Fernandez Katharine , Nitta Hidetomi , Hayashi Yushi , Liberman Leslie W. , Nguyen Emily , Yildiz Erdem , Kim Jinkyung , Jarysta Amandine , Renauld Justine , Wesson Ella , Wang Haobing , Thapa Punam , Bordiga Pierrick , McMurtry Noah , Llamas Juan , Kitcher Siân R. , López-Porras Ana I. , Cui Runjia , Behnammanesh Ghazaleh , Bird Jonathan E. , Ballesteros Angela , Vélez-Ortega A. Catalina , Edge Albert S. B. , Deans Michael R. , Gnedeva Ksenia , Shrestha Brikha R. , Manor Uri , Zhao Bo , Ricci Anthony J. , Tarchini Basile , Basch Martín L. , Stepanyan Ruben , Landegger Lukas D. , Rutherford Mark A. , Liberman M. Charles , Walters Bradley J. , Kros Corné J. , Richardson Guy P. , Cunningham Lisa L. , Indzhykulian Artur A. 
Published: April 2024

AbstractOur sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5–15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 107,000 hair cells which have been identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.
Chromosome-level genome assembly of the predatory stink bug Arma custos
Authors: Wang Yuqin , Luo Yunfei , Ge Yunkang , Liu Sha , Liang Wenkai , Wu Chaoyan , Wei Shujun , Zhu Jiaying 
Published: April 2024

AbstractThe stink bug Arma custos (Hemiptera: Pentatomidae) is a predatory enemy successfully used for biocontrol of lepidopteran and coleopteran pests in notorious invasive species. In this study, a high-quality chromosome-scale genome assembly of A. custos was achieved through a combination of Illumina sequencing, PacBio HiFi sequencing, and Hi-C scaffolding techniques. The final assembled genome was 969.02 Mb in size, with 935.94 Mb anchored to seven chromosomes, and a scaffold N50 length of 135.75 Mb. This genome comprised 52.78% repetitive elements. The detected complete BUSCO score was 99.34%, indicating its completeness. A total of 13,708 protein-coding genes were predicted in the genome, and 13219 of them were annotated. This genome provides an invaluable resource for further research on various aspects of predatory bugs, such as biology, genetics, and functional genomics.
Overexpression of cyclin F/CCNF as an independent prognostic factor for poor survival in clear cell renal cell carcinoma
Authors: Kwiatkowski Maciej , Krajewski Adrian , Durślewicz Justyna , Buchholz Karolina , Grzanka Dariusz , Gagat Maciej , Zabrzyński Jan , Klimaszewska-Wiśniewska Anna 
Published: April 2024

AbstractCyclin F (encoded by CCNF gene) has been reported to be implicated in the pathobiology of several human cancers. However, its potential clinical significance in clear cell renal cell carcinoma (ccRCC) remains unknown. The present study aimed to evaluate the potential significance of cyclin F, assessed by immunohistochemical (IHC) staining and molecular (bioinformatics) techniques, as a prognostic marker in ccRCC in relation to clinicopathological features and outcomes. IHC staining was performed using two independent ccRCC tissue array cohorts, herein called tissue macroarray (TMA)_1 and tissue microarray (TMA)_2, composed of 108 ccRCCs and 37 histologically normal tissues adjacent to the tumor (NAT) and 192 ccRCCs and 16 normal kidney samples, respectively. The mRNA expression data were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) public datasets, followed by bioinformatics analysis of biological mechanisms underlying prognosis. The relationship between immune cell infiltration level and CCNF expression in ccRCC was investigated using the Tumor Immune Estimation Resource 2.0 (TIMER2) and Gene Expression Profiling Interactive Analysis 2 (GEPIA2). Cyclin F expression was significantly elevated in ccRCC lesions compared to both NAT and normal renal tissues. Likewise, CCNF mRNA was markedly increased in ccRCCs relative to non-cancerous tissues. In all analyzed cohorts, tumors with features of more aggressive behavior were more likely to display cyclin F/CCNF-high expression than low. Furthermore, patients with high cyclin F/CCNF expression had shorter overall survival (OS) times than those with low expression. In addition, multivariable analysis revealed that cyclin F/CCNF-high expression was an independent prognostic factor for poor OS in ccRCC. Enrichment analysis for mechanistically relevant processes showed that CCNF and its highly correlated genes initiate the signaling pathways that eventually result in uncontrolled cell proliferation. CCNF expression was also correlated with immune cell infiltration and caused poor outcomes depending on the abundance of tumor-infiltrating immune cells in ccRCC. Our findings suggest that cyclin F/CCNF expression is likely to have an essential role in ccRCC pathobiology through regulating multiple oncogenic signaling pathways and affecting the tumor immune microenvironment and may serve as prognostic biomarker and promising therapeutic target in ccRCC.
Exposure to environmental pharmaceuticals affects the macromolecular composition of mussels digestive glands
Authors: Mezzelani Marica , Notarstefano Valentina , Panni Michela , Giorgini Elisabetta , Gorbi Stefania , Regoli Francesco 
Published: April 2024

AbstractHuman pharmaceuticals represent a major challenge in natural environment. A better knowledge on their mechanisms of action and adverse effects on cellular pathways is fundamental to predict long-term consequences for marine wildlife. The FTIRI Imaging (FTIRI) spectroscopy represents a vibrational technique allowing to map specific areas of non-homogeneous biological samples, providing a unique biochemical and ultrastructural fingerprint of the tissue. In this study, FTIRI technique has been applied, for the first time, to characterize (i) the chemical building blocks of digestive glands of Mytilus galloprovincialis, (ii) alterations and (iii) resilience of macromolecular composition, after a 14-days exposure to 0.5 µg/L of carbamazepine (CBZ), valsartan (VAL) and their mixture, followed by a 14-days recovery period. Spectral features of mussels digestive glands provided insights on composition and topographical distribution of main groups of biological macromolecules, such as proteins, lipids, and glycosylated compounds. Pharmaceuticals caused an increase in the total amount of protein and a significant decrease of lipids levels. Changes in macromolecular features reflected the modulation of specific molecular and biochemical pathways thus supporting our knowledge on mechanisms of action of such emerging pollutants. Overall, the applied approach could represent an added value within integrated strategies for the effects-based evaluation of environmental contaminants.