bluuebunny/crossref_metadata_2025_split huggingface dataset:
The p53/ZEB1-PLD3 feedback loop regulates cell proliferation in breast cancer
Authors: Liu Bo-Wen , Sun Ning , Lin Hui , Zhou Xue-Jie , Ma Hai-Yan , Wang Xin , Cao Xu-Chen , Yu Yue 
Published: November 2023

AbstractBreast cancer is the most prevalent cancer globally, endangering women’s physical and mental health. Phospholipase D3 (PLD3) belongs to the phosphodiesterase family (PLD). PLD3 is related to insulin-mediated phosphorylation of the AKT pathway, suggesting that it may play a role in the occurrence and development of malignant tumors. This study may further explore the molecular mechanism of PLD3 inhibiting breast cancer cell proliferation. In this study, we demonstrated that PLD3 and miR-6796 are co-expressed in breast cancer. PLD3 can bind with CDK1 and inhibit its expression, leading to mitotic arrest and inhibiting breast cancer proliferation. Wild-type p53 regulates PLD3 and miR-6796 expression by competitively binding to the PLD3 promoter with ZEB1. DNMT3B, as the target gene of miR-6796, is recruited into the PLD3 promoter by combining with ZEB1 to regulate the DNA methylation of the PLD3 promoter and ultimately affect PLD3 and miR-6796 expression. In conclusion, we revealed the role and molecular mechanism of PLD3 and its embedded miR-6796 in breast cancer proliferation, providing clues and a theoretical foundation for future research and development of therapeutic targets and prognostic markers for breast cancer.
Imitation dynamics on networks with incomplete information
Authors: Wang Xiaochen , Zhou Lei , McAvoy Alex , Li Aming 
Published: November 2023

AbstractImitation is an important learning heuristic in animal and human societies. Previous explorations report that the fate of individuals with cooperative strategies is sensitive to the protocol of imitation, leading to a conundrum about how different styles of imitation quantitatively impact the evolution of cooperation. Here, we take a different perspective on the personal and external social information required by imitation. We develop a general model of imitation dynamics with incomplete information in networked systems, which unifies classical update rules including the death-birth and pairwise-comparison rule on complex networks. Under pairwise interactions, we find that collective cooperation is most promoted if individuals neglect personal information. If personal information is considered, cooperators evolve more readily with more external information. Intriguingly, when interactions take place in groups on networks with low degrees of clustering, using more personal and less external information better facilitates cooperation. Our unifying perspective uncovers intuition by examining the rate and range of competition induced by different information situations.
Electroconvective viscous fingering in a single polyelectrolyte fluid on a charge selective surface
Authors: Kim Jeonghwan , Kim Joonhyeon , Kim Minyoung , Kwak Rhokyun 
Published: November 2023

AbstractWhen a low-viscosity fluid displaces into a higher-viscosity fluid, the liquid-liquid interface becomes unstable causing finger-like patterns. This viscous fingering instability has been widely observed in nature and engineering systems with two adjoined fluids. Here, we demonstrate a hitherto-unrealizable viscous fingering in a single fluid-solid interface. In a single polyelectrolyte fluid on a charge selective surface, selective ion rejection through the surface initiates i) stepwise ion concentration and viscosity gradient boundaries in the fluid and ii) electroconvective vortices on the surface. As the vortices grow, the viscosity gradient boundary pushes away from the surface, resulting viscous fingering. Comparable to conventional one with two fluids, i) a viscosity ratio ($$M$$
M
) governs the onset of this electroconvective viscous fingering, and ii) the boundary properties (finger velocity and rheological effects) - represented by $$M$$
M
, electric Rayleigh ($${{Ra}}_{E}$$

R
a

E

), Schmidt ($${Sc}$$
S
c
), and Deborah ($${De}$$
D
e
) numbers - determine finger shapes (straight v.s. ramified, the onset length of fingering, and relative finger width). With controllable onset and shape, the mechanism of electroconvective viscous fingering offers new possibilities for manipulating ion transport and dendritic instability in electrochemical systems.
Tree mortality during long-term droughts is lower in structurally complex forest stands
Authors: Ma Qin , Su Yanjun , Niu Chunyue , Ma Qin , Hu Tianyu , Luo Xiangzhong , Tai Xiaonan , Qiu Tong , Zhang Yao , Bales Roger C. , Liu Lingli , Kelly Maggi , Guo Qinghua 
Published: November 2023

AbstractIncreasing drought frequency and severity in a warming climate threaten forest ecosystems with widespread tree deaths. Canopy structure is important in regulating tree mortality during drought, but how it functions remains controversial. Here, we show that the interplay between tree size and forest structure explains drought-induced tree mortality during the 2012-2016 California drought. Through an analysis of over one million trees, we find that tree mortality rate follows a “negative-positive-negative” piecewise relationship with tree height, and maintains a consistent negative relationship with neighborhood canopy structure (a measure of tree competition). Trees overshadowed by tall neighboring trees experienced lower mortality, likely due to reduced exposure to solar radiation load and lower water demand from evapotranspiration. Our findings demonstrate the significance of neighborhood canopy structure in influencing tree mortality and suggest that re-establishing heterogeneity in canopy structure could improve drought resiliency. Our study also indicates the potential of advances in remote-sensing technologies for silvicultural design, supporting the transition to multi-benefit forest management.
Th17-associated cytokines IL-17 and IL-23 in inflamed skin of Darier disease patients as potential therapeutic targets
Authors: Ettinger Monika , Burner Teresa , Sharma Anshu , Chang Yun-Tsan , Lackner Angelika , Prompsy Pacôme , Deli Isabella M. , Traxler Judith , Wahl Gerald , Altrichter Sabine , Langer Rupert , Tsai Yi-Chien , Varkhande Suraj R. , Schoeftner Leonie C. , Iselin Christoph , Gratz Iris K. , Kimeswenger Susanne , Guenova Emmanuella , Hoetzenecker Wolfram 
Published: November 2023

AbstractDarier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. DD patients often have skin involvement characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. The aim of this study was to characterize the cutaneous immune infiltrate in DD skin lesions in detail and to identify new therapeutic targets. Using gene and protein expression profiling assays including scRNA sequencing, we demonstrate enhanced expression of Th17-related genes and cytokines and increased numbers of Th17 cells in six DD patients. We provide evidence that targeting the IL-17/IL-23 axis in a case series of three DD patients with monoclonal antibodies is efficacious with significant clinical improvement. As DD is a chronic, relapsing disease, our findings might pave the way toward additional options for the long-term management of skin inflammation in patients with DD.
Synthetic genetic oscillators demonstrate the functional importance of phenotypic variation in pneumococcal-host interactions
Authors: Rueff Anne-Stéphanie , van Raaphorst Renske , Aggarwal Surya D. , Santos-Moreno Javier , Laloux Géraldine , Schaerli Yolanda , Weiser Jeffrey N. , Veening Jan-Willem 
Published: November 2023

AbstractPhenotypic variation is the phenomenon in which clonal cells display different traits even under identical environmental conditions. This plasticity is thought to be important for processes including bacterial virulence, but direct evidence for its relevance is often lacking. For instance, variation in capsule production in the human pathogen Streptococcus pneumoniae has been linked to different clinical outcomes, but the exact relationship between variation and pathogenesis is not well understood due to complex natural regulation. In this study, we use synthetic oscillatory gene regulatory networks (GRNs) based on CRISPR interference (CRISPRi) together with live cell imaging and cell tracking within microfluidics devices to mimic and test the biological function of bacterial phenotypic variation. We provide a universally applicable approach for engineering intricate GRNs using only two components: dCas9 and extended sgRNAs (ext-sgRNAs). Our findings demonstrate that variation in capsule production is beneficial for pneumococcal fitness in traits associated with pathogenesis providing conclusive evidence for this longstanding question.
SEPTIN2 suppresses an IFN-γ-independent, proinflammatory macrophage activation pathway
Authors: Fu Beibei , Xiong Yan , Sha Zhou , Xue Weiwei , Xu Binbin , Tan Shun , Guo Dong , Lin Feng , Wang Lulu , Ji Jianjian , Luo Yang , Lin Xiaoyuan , Wu Haibo 
Published: November 2023

AbstractInterferon-gamma (IFN-γ) signaling is necessary for the proinflammatory activation of macrophages but IFN-γ-independent pathways, for which the initiating stimuli and downstream mechanisms are lesser known, also contribute. Here we identify, by high-content screening, SEPTIN2 (SEPT2) as a negative regulation of IFN-γ-independent macrophage autoactivation. Mechanistically, endoplasmic reticulum (ER) stress induces the expression of SEPT2, which balances the competition between acetylation and ubiquitination of heat shock protein 5 at position Lysine 327, thereby alleviating ER stress and constraining M1-like polarization and proinflammatory cytokine release. Disruption of this negative feedback regulation leads to the accumulation of unfolded proteins, resulting in accelerated M1-like polarization, excessive inflammation and tissue damage. Our study thus uncovers an IFN-γ-independent macrophage proinflammatory autoactivation pathway and suggests that SEPT2 may play a role in the prevention or resolution of inflammation during infection.
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Authors: Wang Cong , Yu Qing-Yi , Ji Niu-Niu , Zheng Yong , Taylor John W. , Guo Liang-Dong , Gao Cheng 
Published: November 2023

AbstractBacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.
Actomyosin and CSI1/POM2 cooperate to deliver cellulose synthase from Golgi to cortical microtubules in Arabidopsis
Authors: Liu Lu , Wang Ting , Bai Yifan , Yan Pengcheng , Dai Liufeng , Du Pingzhou , Persson Staffan , Zhang Yi 
Published: November 2023

AbstractAs one of the major components of plant cell walls, cellulose is crucial for plant growth and development. Cellulose is synthesized by cellulose synthase (CesA) complexes (CSCs), which are trafficked and delivered from the Golgi apparatus to the plasma membrane. How CesAs are released from Golgi remains largely unclear. In this study, we observed that STELLO (STL) family proteins localized at a group of small CesA-containing compartments called Small CesA compartments (SmaCCs) or microtubule-associated CesA compartments (MASCs). The STL-labeled SmaCCs/MASCs were directly derived from Golgi through a membrane-stretching process: membrane-patches of Golgi attached to cortical microtubules, which led to emergence of membrane-tails that finally ruptured to generate SmaCCs/MASCs associated with the cortical microtubules. While myosin propelled the movement of Golgi along actin filaments to stretch the tails, the CesA-microtubule linker protein, CSI1/POM2 was indispensable for the tight anchor of the membrane-tail ends at cortical microtubules. Together, our data reveal a non-canonical delivery route to the plasma membrane of a major enzyme complex in plant biology.
Semantic segmentation of methane plumes with hyperspectral machine learning models
Authors: Růžička Vít , Mateo-Garcia Gonzalo , Gómez-Chova Luis , Vaughan Anna , Guanter Luis , Markham Andrew 
Published: November 2023

AbstractMethane is the second most important greenhouse gas contributor to climate change; at the same time its reduction has been denoted as one of the fastest pathways to preventing temperature growth due to its short atmospheric lifetime. In particular, the mitigation of active point-sources associated with the fossil fuel industry has a strong and cost-effective mitigation potential. Detection of methane plumes in remote sensing data is possible, but the existing approaches exhibit high false positive rates and need manual intervention. Machine learning research in this area is limited due to the lack of large real-world annotated datasets. In this work, we are publicly releasing a machine learning ready dataset with manually refined annotation of methane plumes. We present labelled hyperspectral data from the AVIRIS-NG sensor and provide simulated multispectral WorldView-3 views of the same data to allow for model benchmarking across hyperspectral and multispectral sensors. We propose sensor agnostic machine learning architectures, using classical methane enhancement products as input features. Our HyperSTARCOP model outperforms strong matched filter baseline by over 25% in F1 score, while reducing its false positive rate per classified tile by over 41.83%. Additionally, we demonstrate zero-shot generalisation of our trained model on data from the EMIT hyperspectral instrument, despite the differences in the spectral and spatial resolution between the two sensors: in an annotated subset of EMIT images HyperSTARCOP achieves a 40% gain in F1 score over the baseline.
Cigarette smoking and disproportionate changes of thoracic skeletal muscles in low-dose chest computed tomography
Authors: Lim Woo Hyeon , Jeong Suhyun , Park Chang Min 
Published: November 2023

AbstractAssociation between smoking intensity and the quantity and quality of thoracic skeletal muscles (TSMs) remains unexplored. Skeletal muscle index (SMI; skeletal muscle area/height2) and percentage of normal attenuation muscle area (NAMA%) were measured to represent the quantity and quality of the skeletal muscles, respectively, and quantification was performed in pectoralis muscle at aortic arch (AA-PM), TSM at carina (C-TSM), erector spinae muscle at T12 (T12-ESM), and skeletal muscle at L1 (L1-SM). Among the 258 men (median age, 62 years [IQR: 58–69]), 183 were current smokers (median smoking intensity, 40 pack-years [IQR: 30–46]). SMI and NAMA% of AA-PM significantly decreased with pack-year (β =  − 0.028 and − 0.076; P < 0.001 and P = 0.021, respectively). Smoking intensity was inversely associated with NAMA% of C-TSM (β =  − 0.063; P = 0.001), whereas smoking intensity showed a borderline association with SMI of C-TSM (β =  − 0.023; P = 0.057). Smoking intensity was associated with the change in NAMA% of L1-SM (β =  − 0.040; P = 0.027), but was not associated with SMI of L1-SM (P > 0.05). Neither NAMA% nor SMI of T12-ESM was affected by smoking intensity (P > 0.05). In conclusion, smoking intensity was associated with the change of TSMs. Its association varied according to the location of TSMs, with the most associated parts being the upper (AA-PM) and middle TSMs (C-TSM).
Tracking tsunami propagation and Island’s collapse after the Hunga Tonga Hunga Ha’apai 2022 volcanic eruption from multi-space observations
Authors: Shrivastava Mahesh N. , Sunil A. S. , Maurya Ajeet K. , Aguilera Felipe , Orrego Simón , Sunil P. S. , Cienfuegos Rodrigo , Moreno Marcos 
Published: November 2023

AbstractThe quantity and accuracy of satellite-geodetic measurements have increased over time, revolutionizing the monitoring of tectonic processes. Global Navigation Satellite System (GNSS) and satellite radar signals provide observations beyond ground deformation, including how earthquake and tsunami processes affect variations in the ionosphere. Here, we study the Hunga Tonga Hunga Ha’apai (HTHH) volcanic eruption 2022 and its associated tsunami propagation with the analysis GNSS derived Total Electron Content (TEC), Synthetic Aperture Radar (SAR) Sentinel-1 data, complemented with tide gauge observations. We utilize GNSS sites data within a ~ 5000 km radius from the volcanic eruption for estimating the ionospheric perturbation as Vertical TEC. We give evidence on the detection of acoustic gravity, internal gravity, and atmospheric Lamb waves signatures in the TEC perturbation. In particular, the internal gravity waves that concentrated in the southwest of Tonga, directly correlates with the observed tsunami propagation direction as accounted by the tide gauge measurements. However, the acoustic gravity wave signature in the TEC is dominant in the north direction suggesting a surface deformation, which could be verified using Sentinel-1A SAR amplitude data. The analysis presented herein shows that within 5 h of the volcanic eruption, the central part of the HTHH island landscape disappeared with the biggest explosion. The unprecedented detail resolved by integrating satellite data yields previously unknown details of the deformation of the 2022 HTHH volcano eruption.
Trajectory analysis and optimization of sea buckthorn fruit vibration separation manipulator based on I-PSO algorithm
Authors: Liang Bingqin , Lin Xinzhang , Liu Ganghui , Lei Jin , Wang Weibing 
Published: November 2023

AbstractIn this paper, the optimal time planning of vibration separation trajectory of Hippophae rhamnoides fruit is studied for space manipulator using the I-PSO algorithm. The first step is to analyze the motion of the robotic arm's joints, which are limited in range and speed, in combination with a 3–5–3 polynomial interpolation, an improved Particle swarm optimization with adaptive inertia weight and asynchronous learning factor is proposed, and the specific process is given. Experimental images and data show that the improved particle swarm optimization algorithm can ensure the continuity of joint acceleration and velocity, and the optimal vibration trajectory time is 0.536539094 s Compared with the planned system trajectory time of 0.71022 s, the speed increased by 24.5%. The results of the orthogonal experiment show that the average fruit drop rate reaches 96.19%, which verifies the validity and reliability of the I-PSO algorithm for optimal time planning of seabuckthorn fruit separation vibration trajectory.
A 2 °C difference affecting the spatiotemporal distribution of small demersal fish assemblages in shallow tropical and subtropical waters of Western Taiwan
Authors: Chen Kuo-Shu , Chen Chiee-Young , Chang Yi , Chen Hsu-Sen , Chen Meng-Hsien 
Published: November 2023

AbstractTwo OR3 research vessel cruises were conducted at seven nearshore sites from north to south in the western coastal waters off Taiwan in May (late spring) and November (late autumn) 2019 in order to gain insights into the 2 °C difference in the tropical-subtropical fish fauna. Totally, 37 families, 72 genera, and 99 taxas were recorded for the 1809 fishes. Three fish assemblages, the North, South, and Fall-Zhuoshui River (ZRf) groups, were identified as eurythermal, stenothermal, and croaker communities. Their dominants, in rank order, were Tarphops oligolepis, Liachirus melanospilosa, Ostorhinchus fasciatus, and Trachinocephalus myops for the Northern eurythermal group, Arnoglossus tenuis, Eubleekeria splendens, and Ostorhinchus pleuron for the Southern stenothermal group, and Johnius taiwanensis, Chrysochir aureus, and Pennahia macrocephalus for the croaker-ZRf group. Their distribution was markedly correlated with the bottom water temperature, seafloor grain size, and concentration of suspended solids. The influence of a 2 °C difference on the tropical and subtropical demersal fish could indicate how rising temperatures due to climate change are shaping fish communities. The flatfish, Liachirus melanospilos, was distributed northward by 0.5oN and is suggested to be considered as an ecological indicator of the tropicalization of subtropical marine ecosystems in the future.
UAV-based individual Chinese cabbage weight prediction using multi-temporal data
Authors: Aguilar-Ariza Andrés , Ishii Masanori , Miyazaki Toshio , Saito Aika , Khaing Hlaing Phyoe , Phoo Hnin Wint , Kondo Tomohiro , Fujiwara Toru , Guo Wei , Kamiya Takehiro 
Published: November 2023

AbstractThe use of unmanned aerial vehicles (UAVs) has facilitated crop canopy monitoring, enabling yield prediction by integrating regression models. However, the application of UAV-based data to individual-level harvest weight prediction is limited by the effectiveness of obtaining individual features. In this study, we propose a method that automatically detects and extracts multitemporal individual plant features derived from UAV-based data to predict harvest weight. We acquired data from an experimental field sown with 1196 Chinese cabbage plants, using two cameras (RGB and multi-spectral) mounted on UAVs. First, we used three RGB orthomosaic images and an object detection algorithm to detect more than 95% of the individual plants. Next, we used feature selection methods and five different multi-temporal resolutions to predict individual plant weights, achieving a coefficient of determination (R2) of 0.86 and a root mean square error (RMSE) of 436 g/plant. Furthermore, we achieved predictions with an R2 greater than 0.72 and an RMSE less than 560 g/plant up to 53 days prior to harvest. These results demonstrate the feasibility of accurately predicting individual Chinese cabbage harvest weight using UAV-based data and the efficacy of utilizing multi-temporal features to predict plant weight more than one month prior to harvest.