bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scale‐Dependent Influence of Permafrost on Riverbank Erosion Rates
Authors: Rowland Joel C. , Schwenk Jonathan P. , Shelef Eitan , Muss Jordan , Ahrens Daniel , Stauffer Sophie , Pilliouras Anastasia , Crosby Benjamin , Chadwick Austin , Douglas Madison M. , Kemeny Preston C. , Lamb Michael P. , Li Gen K. , Vulis Lawrence 
Published: July 2023

AbstractWhether permafrost systematically alters the rate of riverbank erosion is a fundamental geomorphic question with significant importance to infrastructure, water quality, and biogeochemistry of high‐latitude watersheds. For over four decades, this question has remained unanswered due to a lack of data. Using remotely sensed imagery, we addressed this knowledge gap by quantifying riverbank erosion rates across the Arctic and subarctic. To compare these rates to non‐permafrost rivers, we assembled a global data set of published riverbank erosion rates. We found that erosion rates in rivers influenced by permafrost are on average nine times lower than non‐permafrost systems; erosion rate differences increase up to 40 times for the largest rivers. To test alternative hypotheses for the observed erosion rate difference, we examined differences in total water yield and erosional efficiency between these rivers and non‐permafrost rivers. Neither of these factors nor differences in river sediment loads provided compelling alternative explanations, leading us to conclude that permafrost limits riverbank erosion rates. This conclusion was supported by field investigations of rates and patterns of erosion along three rivers flowing through discontinuous permafrost in Alaska. Our results show that permafrost limits maximum bank erosion rates on rivers with stream powers greater than 900 Wm−1. On smaller rivers, however, hydrology rather than thaw rate may be the dominant control on bank erosion. Our findings suggest that Arctic warming and hydrological changes should increase bank erosion rates on large rivers but may reduce rates on rivers with drainage areas less than a few thousand km2.
Decorin: a potential therapeutic candidate for ligamentum flavum hypertrophy by antagonizing TGF-β1
Authors: Wang Shanxi , Qu Yunkun , Fang Xuan , Ding Qing , Zhao Hongqi , Yu Xiaojun , Xu Tao , Lu Rui , Jing Shaoze , Liu Chaoxu , Wu Hua , Liu Yang 
Published: July 2023

AbstractLigamentum flavum hypertrophy (LFH) is the main physiological and pathological mechanism of lumbar spinal canal stenosis (LSCS). The specific mechanism for LFH has not been completely clarified. In this study, bioinformatic analysis, human ligamentum flavum (LF) tissues collection and analysis, and in vitro and in vivo experiments were conducted to explore the effect of decorin (DCN) on LFH pathogenesis. Here, we found that TGF-β1, collagen I, collagen III, α-SMA and fibronectin were significantly upregulated in hypertrophic LF samples. The DCN protein expression in hypertrophic LF samples was higher than that in non-LFH samples, but the difference was not significant. DCN inhibited the expression of TGF-β1-induced fibrosis-associated proteins in human LF cells, including collagen I, collagen III, α-SMA, and fibronectin. ELISAs showed that TGF-β1 can upregulate PINP and PIIINP in the cell supernatant, and this effect was inhibited after DCN administration. Mechanistic studies revealed that DCN suppressed TGF-β1-induced fibrosis by blocking the TGF-β1/SMAD3 signaling pathway. In addition, DCN ameliorated mechanical stress-induced LFH in vivo. In summary, our findings indicated that DCN ameliorated mechanical stress-induced LFH by antagonizing the TGF-β1/SMAD3 signaling pathway in vitro and in vivo. These findings imply that DCN is a potential therapeutic candidate for ligamentum flavum hypertrophy.
PHF6 maintains acute myeloid leukemia via regulating NF-κB signaling pathway
Authors: Hou Shuaibing , Wang Xiaomin , Guo Tengxiao , Lan Yanjie , Yuan Shengnan , Yang Shuang , Zhao Fei , Fang Aizhong , Liu Na , Yang Wanzhu , Chu Yajing , Jiang Erlie , Cheng Tao , Sun Xiaojian , Yuan Weiping 
Published: July 2023

AbstractAcute myeloid leukemia (AML) is a major hematopoietic malignancy characterized by the accumulation of immature and abnormally differentiated myeloid cells in bone marrow. Here with in vivo and in vitro models, we demonstrate that the Plant homeodomain finger gene 6 (PHF6) plays an important role in apoptosis and proliferation in myeloid leukemia. Phf6 deficiency could delay the progression of RUNX1-ETO9a and MLL-AF9-induced AML in mice. PHF6 depletion inhibited the NF-κB signaling pathways by disrupting the PHF6-p50 complex and partially inhibiting the nuclear translocation of p50 to suppress the expression of BCL2. Treating PHF6 over-expressed myeloid leukemia cells with NF-κB inhibitor (BAY11-7082) significantly increased their apoptosis and decreased their proliferation. Taken together, in contrast to PHF6 as a tumor suppressor in T-ALL as reported, we found that PHF6 also plays a pro-oncogenic role in myeloid leukemia, and thus potentially to be a therapeutic target for treating myeloid leukemia patients.
Seasonal effect—an overlooked factor in neuroimaging research
Authors: Zhang Rui , Shokri-Kojori Ehsan , Volkow Nora D. 
Published: July 2023

AbstractIn neuroimaging research, seasonal effects are often neglected or controlled as confounding factors. However, seasonal fluctuations in mood and behavior have been observed in both psychiatric disorders and healthy participants. There are vast opportunities for neuroimaging studies to understand seasonal variations in brain function. In this study, we used two longitudinal single-subject datasets with weekly measures over more than a year to investigate seasonal effects on intrinsic brain networks. We found that the sensorimotor network displayed a strong seasonal pattern. The sensorimotor network is not only relevant for integrating sensory inputs and coordinating movement, but it also affects emotion regulation and executive function. Therefore, the observed seasonality effects in the sensorimotor network could contribute to seasonal variations in mood and behavior. Genetic analyses revealed seasonal modulation of biological processes and pathways relevant to immune function, RNA metabolism, centrosome separation, and mitochondrial translation that have a significant impact on human physiology and pathology. In addition, we revealed critical factors such as head motion, caffeine use, and scan time that could interfere with seasonal effects and need to be considered in future studies.
LncRNA miR663AHG represses the development of colon cancer in a miR663a-dependent manner
Authors: Yuan Hongfan , Ren Qianwen , Du Yantao , Ma Yuwan , Gu Liankun , Zhou Jing , Tian Wei , Deng Dajun 
Published: July 2023

AbstractThe MIR663AHG gene encodes both miR663AHG and miR663a. While miR663a contributes to the defense of host cells against inflammation and inhibits colon cancer development, the biological function of lncRNA miR663AHG has not been previously reported. In this study, the subcellular localization of lncRNA miR663AHG was determined by RNA-FISH. miR663AHG and miR663a were measured by qRT-PCR. The effects of miR663AHG on the growth and metastasis of colon cancer cells were investigated in vitro and in vivo. CRISPR/Cas9, RNA pulldown, and other biological assays were used to explore the underlying mechanism of miR663AHG. We found that miR663AHG was mainly distributed in the nucleus of Caco2 and HCT116 cells and the cytoplasm of SW480 cells. The expression level of miR663AHG was positively correlated with the level of miR663a (r = 0.179, P = 0.015) and significantly downregulated in colon cancer tissues relative to paired normal tissues from 119 patients (P < 0.008). Colon cancers with low miR663AHG expression were associated with advanced pTNM stage (P = 0.021), lymph metastasis (P = 0.041), and shorter overall survival (hazard ratio = 2.026; P = 0.021). Experimentally, miR663AHG inhibited colon cancer cell proliferation, migration, and invasion. The growth of xenografts from RKO cells overexpressing miR663AHG was slower than that of xenografts from vector control cells in BALB/c nude mice (P = 0.007). Interestingly, either RNA-interfering or resveratrol-inducing expression changes of miR663AHG or miR663a can trigger negative feedback regulation of transcription of the MIR663AHG gene. Mechanistically, miR663AHG could bind to miR663a and its precursor pre-miR663a, and prevent the degradation of miR663a target mRNAs. Disruption of the negative feedback by knockout of the MIR663AHG promoter, exon-1, and pri-miR663A-coding sequence entirely blocked these effects of miR663AHG, which was restored in cells transfected with miR663a expression vector in rescue experiment. In conclusion, miR663AHG functions as a tumor suppressor that inhibits the development of colon cancer through its cis-binding to miR663a/pre-miR663a. The cross talk between miR663AHG and miR663a expression may play dominant roles in maintaining the functions of miR663AHG in colon cancer development.
Lesion area progression in eyes with neovascular age-related macular degeneration treated using a proactive or a reactive regimen
Authors: Cozzi Mariano , Monteduro Davide , Esposito Raffaele Antonio , Spooner Kimberly L. , Fraser-Bell Samantha , Staurenghi Giovanni , Romano Francesco , Airaldi Matteo , Chang Andrew A. , Invernizzi Alessandro 
Published: July 2023

Abstract
Background
To compare the change in lesion area over 4 years of follow-up in eyes with neovascular age-related macular degeneration (nAMD) treated with anti-vascular endothelial growth factor (VEGF) agents using either a proactive or a reactive regimen in routine clinical practice.

Methods
This was a multicentre, retrospective comparative study. Totally, 202 treatment-naïve nAMD eyes (183 patients) received anti-VEGF therapy according to a proactive (n = 105) or reactive (n = 97) regimen. Eyes were included if they had received anti-VEGF injections for a period of at least 4 years and had baseline fluorescein angiography and annual optical coherence tomography (OCT) imaging. Two masked graders independently delineated the lesion’s margins from serial OCT images and growth rates were calculated.

Results
At baseline, the mean [SD] lesion area was 7.24 [5.6] mm2 in the proactive group and 6.33 [4.8] mm2 in the reactive group respectively (p = 0.22). After four years of treatment, the mean [SD] lesion area in the proactive group was 5.16 [4.5] mm2 showing a significant reduction compared to the baseline (p < 0.001). By contrast, the mean [SD] lesion area kept expanding in the reactive group during the follow-up and was 9.24 [6.0] mm2 at four years (p < 0.001). The lesion area at 4 years was significantly influenced by treatment regimen, baseline lesion area, and proportion of visits with active lesions.

Conclusions
Eyes treated using a reactive strategy had an increased lesion area and worse visual outcomes at 4 years. By contrast, the proactive regimen was associated with fewer recurrences of active disease, shrinkage of the lesion area, and better vision at four years.
Causal associations between cardiorespiratory fitness and type 2 diabetes
Authors: Cai Lina , Gonzales Tomas , Wheeler Eleanor , Kerrison Nicola D. , Day Felix R. , Langenberg Claudia , Perry John R. B. , Brage Soren , Wareham Nicholas J. 
Published: July 2023

AbstractHigher cardiorespiratory fitness is associated with lower risk of type 2 diabetes. However, the causality of this relationship and the biological mechanisms that underlie it are unclear. Here, we examine genetic determinants of cardiorespiratory fitness in 450k European-ancestry individuals in UK Biobank, by leveraging the genetic overlap between fitness measured by an exercise test and resting heart rate. We identified 160 fitness-associated loci which we validated in an independent cohort, the Fenland study. Gene-based analyses prioritised candidate genes, such as CACNA1C, SCN10A, MYH11 and MYH6, that are enriched in biological processes related to cardiac muscle development and muscle contractility. In a Mendelian Randomisation framework, we demonstrate that higher genetically predicted fitness is causally associated with lower risk of type 2 diabetes independent of adiposity. Integration with proteomic data identified N-terminal pro B-type natriuretic peptide, hepatocyte growth factor-like protein and sex hormone-binding globulin as potential mediators of this relationship. Collectively, our findings provide insights into the biological mechanisms underpinning cardiorespiratory fitness and highlight the importance of improving fitness for diabetes prevention.
A rapid cell-free expression and screening platform for antibody discovery
Authors: Hunt Andrew C. , Vögeli Bastian , Hassan Ahmed O. , Guerrero Laura , Kightlinger Weston , Yoesep Danielle J. , Krüger Antje , DeWinter Madison , Diamond Michael S. , Karim Ashty S. , Jewett Michael C. 
Published: July 2023

AbstractAntibody discovery is bottlenecked by the individual expression and evaluation of antigen-specific hits. Here, we address this bottleneck by developing a workflow combining cell-free DNA template generation, cell-free protein synthesis, and binding measurements of antibody fragments in a process that takes hours rather than weeks. We apply this workflow to evaluate 135 previously published antibodies targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including all 8 antibodies previously granted emergency use authorization for coronavirus disease 2019 (COVID-19), and demonstrate identification of the most potent antibodies. We also evaluate 119 anti-SARS-CoV-2 antibodies from a mouse immunized with the SARS-CoV-2 spike protein and identify neutralizing antibody candidates, including the antibody SC2-3, which binds the SARS-CoV-2 spike protein of all tested variants of concern. We expect that our cell-free workflow will accelerate the discovery and characterization of antibodies for future pandemics and for research, diagnostic, and therapeutic applications more broadly.
Jamming and unusual charge density fluctuations of strange metals
Authors: Thornton Stephen J. , Liarte Danilo B. , Abbamonte Peter , Sethna James P. , Chowdhury Debanjan 
Published: July 2023

AbstractThe strange metallic regime across a number of high-temperature superconducting materials presents numerous challenges to the classic theory of Fermi liquid metals. Recent measurements of the dynamical charge response of strange metals, including optimally doped cuprates, have revealed a broad, featureless continuum of excitations, extending over much of the Brillouin zone. The collective density oscillations of this strange metal decay into the continuum in a manner that is at odds with the expectations of Fermi liquid theory. Inspired by these observations, we investigate the phenomenology of bosonic collective modes and the particle-hole excitations in a class of strange metals by making an analogy to the phonons of classical lattices falling apart across an unconventional jamming-like transition associated with the onset of rigidity. By making comparisons to the experimentally measured dynamical response functions, we reproduce many of the qualitative features using the above framework. We conjecture that the dynamics of electronic charge density over an intermediate range of energy scales in a class of strongly correlated metals can be at the brink of a jamming-like transition.
Understanding the unique S-scheme charge migration in triazine/heptazine crystalline carbon nitride homojunction
Authors: Li Fang , Yue Xiaoyang , Liao Yulong , Qiao Liang , Lv Kangle , Xiang Quanjun 
Published: July 2023

AbstractUnderstanding charge transfer dynamics and carrier separation pathway is challenging due to the lack of appropriate characterization strategies. In this work, a crystalline triazine/heptazine carbon nitride homojunction is selected as a model system to demonstrate the interfacial electron-transfer mechanism. Surface bimetallic cocatalysts are used as sensitive probes during in situ photoemission for tracing the S-scheme transfer of interfacial photogenerated electrons from triazine phase to the heptazine phase. Variation of the sample surface potential under light on/off confirms dynamic S-scheme charge transfer. Further theoretical calculations demonstrate an interesting reversal of interfacial electron-transfer path under light/dark conditions, which also supports the experimental evidence of S-scheme transport. Benefiting from the unique merit of S-scheme electron transfer, homojunction shows significantly enhanced activity for CO2 photoreduction. Our work thus provides a strategy to probe dynamic electron transfer mechanisms and to design delicate material structures towards efficient CO2 photoreduction.
Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation
Authors: Calcagni’ Alessia , Staiano Leopoldo , Zampelli Nicolina , Minopoli Nadia , Herz Niculin J. , Di Tullio Giuseppe , Huynh Tuong , Monfregola Jlenia , Esposito Alessandra , Cirillo Carmine , Bajic Aleksandar , Zahabiyon Mahla , Curnock Rachel , Polishchuk Elena , Parkitny Luke , Medina Diego Luis , Pastore Nunzia , Cullen Peter J. , Parenti Giancarlo , De Matteis Maria Antonietta , Grumati Paolo , Ballabio Andrea 
Published: July 2023

AbstractBatten disease, one of the most devastating types of neurodegenerative lysosomal storage disorders, is caused by mutations in CLN3. Here, we show that CLN3 is a vesicular trafficking hub connecting the Golgi and lysosome compartments. Proteomic analysis reveals that CLN3 interacts with several endo-lysosomal trafficking proteins, including the cation-independent mannose 6 phosphate receptor (CI-M6PR), which coordinates the targeting of lysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking of CI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lysosomal reformation. Conversely, CLN3 overexpression promotes the formation of multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent, generating newly formed proto-lysosomes. Together, our findings reveal that CLN3 functions as a link between the M6P-dependent trafficking of lysosomal enzymes and lysosomal reformation pathway, explaining the global impairment of lysosomal function in Batten disease.
Dynamics of lattice disorder in perovskite materials, polarization nanoclusters and ferroelectric domain wall structures
Authors: Očenášek Jan , Minár Ján , Alcalá Jorge 
Published: July 2023

AbstractThe nexus between classic ferroelectricity and the structure of perovskite materials hinges on the concept of lattice disorder. Although the ordered perovskites display short-range displacements of the central cations around their equilibrium points, the lattice disorder dynamically unfolds to generate a myriad of distorted rhombohedral lattices characterized by the hopping of the central cations across <111> directions. It is discovered that the lattice disorder correlates with the emergence of minimum configuration energy <100> pathways for the central cations, resulting in spatially modulated ultrafast polarization nanocluster arrangements that are stabilized by the electric charge defects in the material. Through high-resolution phonon dispersion analyses encompassing molecular dynamics (MD) and density functional theory (DFT) simulations, we provide unequivocal evidence linking the hopping of central cations to the development of diffuse soft phonon modes observed throughout the phase transitions of the perovskite. Through massive MD simulations, we unveil the impact of lattice disorder on the structures of domain walls at finite-temperature vis-à-vis collective activation and deactivation of <100> pathways. Furthermore, our simulations demonstrate the development of hierarchical morphotropic phase boundary (MPB) nanostructures under the combined influence of externally applied pressure and stress relaxation, characterized by sudden emergence of zig-zagged monoclinic arrangements that involve dual <111> shifts of the central cations. These findings have implications for tailoring MPBs in thin-film structures and for the light-induced mobilization of DWs. Avenues are finally uncovered to the exploration of lattice disorder through gradual shear strain application.
Global volcanic rock classification of Holocene volcanoes
Authors: Oggier Frédérique , Widiwijayanti Christina , Costa Fidel 
Published: July 2023

AbstractThis data descriptor assigns the major and minor rock names from worldwide Holocene volcanoes of the Global Volcanism Program (GVP) using the Total Alkali-Silica diagram (TAS) for the chemical classification of volcanic rocks using the Geochemistry of Rocks of the Oceans and Continents (GEOROC) database. The precompiled files of the GEOROC database provide the chemical composition of volcanic rock samples, from which we computed major and minor rocks for global Holocene volcanoes reported in GVP. The combined dataset associates each volcano with the relative abundance of each volcanic sample type (whole rock, glass, melt inclusion) and provides the five major (more than 10% abundance) and minor rock names. In total, over 138,000 GEOROC volcanic rock samples were considered, for ~1000 Holocene volcanoes. The resulting major rock compositions are in general consistent with those given in GVP. The dataset provides a global panorama of rock composition for Holocene volcanoes.
Inventory of landslides triggered by an extreme rainfall event in Marche-Umbria, Italy, on 15 September 2022
Authors: Santangelo M. , Althuwaynee O. , Alvioli M. , Ardizzone F. , Bianchi C. , Bornaetxea T. , Brunetti M. T. , Bucci F. , Cardinali M. , Donnini M. , Esposito G. , Gariano S. L. , Grita S. , Marchesini I. , Melillo M. , Peruccacci S. , Salvati P. , Yazdani M. , Fiorucci F. 
Published: July 2023

AbstractSystematic and timely documentation of triggered (i.e. event) landslides is fundamental to build extensive datasets worldwide that may help define and/or validate trends in response to climate change. More in general, preparation of landslide inventories is a crucial activity since it provides the basic data for any subsequent analysis. In this work we present an event landslide inventory map (E-LIM) that was prepared through a systematic reconnaissance field survey in about 1 month after an extreme rainfall event hit an area of about 5000 km2 in the Marche-Umbria regions (central Italy). The inventory reports evidence of 1687 triggered landslides in an area of ~550 km2. All slope failures were classified according to type of movement and involved material, and documented with field pictures, wherever possible. The database of the inventory described in this paper as well as the collection of selected field pictures associated with each feature is publicly available at figshare.