bluuebunny/crossref_metadata_2025_split huggingface dataset:
Going Local: How Coastal Environmental Settings Can Help Improve Global Mangrove Carbon Storage and Flux Estimates
Authors: Taillardat Pierre 
Published: November 2022

AbstractThe magnitude and variability of mangrove carbon storage are uncertain and still being discussed. In a recent article, Breithaupt and Steinmuller (2022, https://doi.org/10.1029/2022GL100177) completed a literature review and compared mangrove organic carbon burial rates between different coastal environmental settings (CES) that integrate sedimentary supply (terrigenous vs. carbonate) and hydrogeomorphic settings (delta, estuary, lagoon, open coast). They found greater burial rates in terrigenous delta and estuaries while lower rates were reported in lagoons and carbonate settings. Surprisingly, these CES relationships do not strictly match previous mangrove soil carbon stock estimates but were consistent with biomass stocks. The CES approach used by Breithaupt and Steinmuller should be used for other mangrove carbon stocks and fluxes estimates to refine our understanding of mangrove carbon cycling and storage.
Survey of Electron Heating and Implications for Wave‐Particle Interactions Near the Lunar Surface: ARTEMIS Observations
Authors: Sawyer R. P. , Halekas J. S. 
Published: November 2022

AbstractInteractions between the incident solar wind plasma and lunar crustal magnetic fields can lead to modifications in electron and ion dynamics that can result in the generation of electrostatic and electromagnetic waves. The resulting waves can then interact with the ambient electrons, leading to perpendicular and/or parallel electron heating. We analyze 10 years of data from the Acceleration, Reconnection, Turbulence, and Electrodynamics of Moon's Interaction with the Sun mission, when the spacecraft was within 200 km of the dayside lunar surface and within the solar wind, in order to characterize the near‐Moon plasma environment. We find that as the reflected ion density increases, electrostatic waves associated with plasma conditions favorable for the electron cyclotron drift instability play an increasingly important role in perpendicular electron heating, while electromagnetic interactions display the opposite trend. Additionally, we find that electrostatic waves associated with parallel heating exhibit plasma characteristics that are consistent with both the electron two‐stream instability and the modified two‐stream instability.
Protective effect of hepatocyte-enriched lncRNA-Mir122hg by promoting hepatocyte proliferation in acute liver injury
Authors: Yu Zhenjun , Li Yuhan , Shao Shuai , Guo Beichen , Zhang Mengxia , Zheng Lina , Zhang Kun , Zhou Feng , Zhang Li , Chen Chiyi , Jiang Wentao , Hong Wei , Han Tao 
Published: November 2022

AbstractSome long noncoding RNAs (lncRNAs), which harbor microRNAs in their gene sequence and are also known as microRNA host gene derived lncRNAs (lnc-MIRHGs), play a dominant role alongside miRNAs, or both perform biological functions synergistically or independently. However, only a small number of lnc-MIRHGs have been identified. Here, multiple liver injury datasets were analyzed to screen and identify the target lncRNA Mir122hg. Mir122hg was mainly enriched in liver tissues with human-mouse homology. In both CCl4-induced acute liver injury and Dgal/LPS-induced fulminant liver failure in mice, Mir122hg was sharply downregulated at the early stage, while a subsequent significant increase was only found in the CCl4 group with liver recovery. Overexpression and silencing assays confirmed that Mir122hg played a protective role in acute injury by promoting hepatocyte proliferation in vivo and in vitro. Consistent with the results of gene enrichment analysis, Mir122hg binding to C/EBPα affected its transcriptional repression, promoted gene transcription of downstream chemokines, Cxcl2, Cxcl3, and Cxcl5, and exerted pro-proliferative effects on hepatocytes through activation of the AKT/GSK-3β/p27 signaling pathway by CXC/CXCR2 complexes. This study identifies a novel lncRNA with protective effects in acute liver injury and demonstrates that the binding of Mir122hg-C/EBPα promotes hepatocyte proliferation via upregulation of CXC chemokine and activation of AKT signaling.
HDAC1/3-dependent moderate liquid–liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation
Authors: Li Meng , Li Mingying , Xia Yuan , Li Guosheng , Su Xiuhua , Wang Dongmei , Ye Jingjing , Lu Fei , Sun Tao , Ji Chunyan 
Published: November 2022

AbstractMethyltransferase-like protein 3 (METTL3) plays critical roles in acute myeloid leukemia (AML) progression, however, the mechanism of abnormal overexpression of METTL3 in AML remain elusive. In the current study, we uncovered that Yin Yang 1 (YY1) binds to the promoter region of METTL3 as a transcription factor and promotes its expression, which in turn enhances the proliferation of AML cells. Mechanistically, YY1 binds to HDAC1/3 and regulates METTL3 expression in a moderate liquid-liquid phase separation (LLPS) manner. After mutation of the HDAC-binding site of YY1 or HDAC inhibitor (HDACi) treatment, YY1 was separated from HDAC1/3, which resulted in an excessive LLPS state, thereby inhibiting the expression of METTL3 and the proliferation of AML cells. In conclusion, our study clarified the regulatory mechanism of the abnormal expression of METTL3 in AML, revealed the precise “Yin-Yang” regulatory mechanism of YY1 from the perspective of LLPS degree, and provided new ideas for the precise diagnosis and treatment of AML.
Kinetics of mRNA nuclear export regulate innate immune response gene expression
Authors: Lefaudeux Diane , Sen Supriya , Jiang Kevin , Hoffmann Alexander ,   the UCLA Ribonomics Group, Sanchez Arriola Jose Guillermo , Miller Nick , Cheng Zhang , Chen Emily Yi Hsin , Roy Sukanya , Spreafico Roberto , Johnson Tracy L. , Wissink Erin M. , Ghosh Shubhamoy , Black Douglas L. , Lin Chia-Ho , Xiao Xinshu , Bahn Jae Hoon , Cass Ashley A. , Hsiao Esther Y. H. , Smale Stephen T. , Lo Jerry Hung-Hao , Ernst Jason , Jaroszewicz Artur , Pellegrini Matteo , Morselli Marco , Xing Yi , Park Eddie , Kosuri Sri 
Published: November 2022

AbstractThe abundance and stimulus-responsiveness of mature mRNA is thought to be determined by nuclear synthesis, processing, and cytoplasmic decay. However, the rate and efficiency of moving mRNA to the cytoplasm almost certainly contributes, but has rarely been measured. Here, we investigated mRNA export rates for innate immune genes. We generated high spatio-temporal resolution RNA-seq data from endotoxin-stimulated macrophages and parameterized a mathematical model to infer kinetic parameters with confidence intervals. We find that the effective chromatin-to-cytoplasm export rate is gene-specific, varying 100-fold: for some genes, less than 5% of synthesized transcripts arrive in the cytoplasm as mature mRNAs, while others show high export efficiency. Interestingly, effective export rates do not determine temporal gene responsiveness, but complement the wide range of mRNA decay rates; this ensures similar abundances of short- and long-lived mRNAs, which form successive innate immune response expression waves.
Quantum transport evidence of isolated topological nodal-line fermions
Authors: Kim Hoil , Ok Jong Mok , Cha Seyeong , Jang Bo Gyu , Kwon Chang Il , Kohama Yoshimitsu , Kindo Koichi , Cho Won Joon , Choi Eun Sang , Jo Youn Jung , Kang Woun , Shim Ji Hoon , Kim Keun Su , Kim Jun Sung 
Published: November 2022

AbstractAnomalous transport responses, dictated by the nontrivial band topology, are the key for application of topological materials to advanced electronics and spintronics. One promising platform is topological nodal-line semimetals due to their rich topology and exotic physical properties. However, their transport signatures have often been masked by the complexity in band crossings or the coexisting topologically trivial states. Here we show that, in slightly hole-doped SrAs3, the single-loop nodal-line states are well-isolated from the trivial states and entirely determine the transport responses. The characteristic torus-shaped Fermi surface and the associated encircling Berry flux of nodal-line fermions are clearly manifested by quantum oscillations of the magnetotransport properties and the quantum interference effect resulting in the two-dimensional behaviors of weak antilocalization. These unique quantum transport signatures make the isolated nodal-line fermions in SrAs3 desirable for novel devices based on their topological charge and spin transport.
Spatially aware dimension reduction for spatial transcriptomics
Authors: Shang Lulu , Zhou Xiang 
Published: November 2022

AbstractSpatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from various spatial transcriptomic technologies are often noisy and display substantial spatial correlation across tissue locations. Here, we develop a spatially-aware dimension reduction method, SpatialPCA, that can extract a low dimensional representation of the spatial transcriptomics data with biological signal and preserved spatial correlation structure, thus unlocking many existing computational tools previously developed in single-cell RNAseq studies for tailored analysis of spatial transcriptomics. We illustrate the benefits of SpatialPCA for spatial domain detection and explores its utility for trajectory inference on the tissue and for high-resolution spatial map construction. In the real data applications, SpatialPCA identifies key molecular and immunological signatures in a detected tumor surrounding microenvironment, including a tertiary lymphoid structure that shapes the gradual transcriptomic transition during tumorigenesis and metastasis. In addition, SpatialPCA detects the past neuronal developmental history that underlies the current transcriptomic landscape across tissue locations in the cortex.
GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies
Authors: He Zihuai , Liu Linxi , Belloy Michael E. , Le Guen Yann , Sossin Aaron , Liu Xiaoxia , Qi Xinran , Ma Shiyang , Gyawali Prashnna K. , Wyss-Coray Tony , Tang Hua , Sabatti Chiara , Candès Emmanuel , Greicius Michael D. , Ionita-Laza Iuliana 
Published: November 2022

AbstractRecent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer’s disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.
Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae
Authors: Khan Md. Arif , Al Mamun Khan Md. Abdullah , Mahfuz A. M. U. B. , Sanjana Jannatul Maowa , Ahsan Asif , Gupta Dipali Rani , Hoque M. Nazmul , Islam Tofazzal 
Published: November 2022

AbstractMagnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cereals, and results in enormous loss of grain production. Many chemical fungicides are being used to control the pathogen but none of them are fully effective in controlling blast disease. Therefore, there is a demand for the discovery of a new natural biofungicide to manage the blast disease efficiently. A large number of new natural products showed inhibitory activities against M. oryzae in vitro. To find out effective biofungicides, we performed in silico molecular docking analysis of some of the potent natural compounds targeting four enzymes namely, scytalone dehydratase, SDH1 (PDB ID:1STD), trihydroxynaphthalene reductase, 3HNR (PDB ID:1YBV), trehalose-6-phosphate synthase, Tps1 (PDB ID:6JBI) and isocitrate lyase, ICL1 (PDB ID:5E9G) of M. oryzae fungus that regulate melanin biosynthesis and/or appresorium formation. Thirty-nine natural compounds that were previously reported to inhibit the growth of M. oryzae were subjected to rigid and flexible molecular docking against aforementioned enzymes followed by molecular dynamic simulation. The results of virtual screening showed that out of 39, eight compounds showed good binding energy with any one of the target enzymes as compared to reference commercial fungicides, azoxystrobin and strobilurin. Among the compounds, camptothecin, GKK1032A2 and chaetoviridin-A bind with more than one target enzymes of M. oryzae. All of the compounds except tricyclazole showed good bioactivity score. Taken together, our results suggest that all of the eight compounds have the potential to develop new fungicides, and remarkably, camptothecin, GKK1032A2 and chaetoviridin-A could act as multi-site mode of action fungicides against the blast fungus M. oryzae.
Deep neural network-based structural health monitoring technique for real-time crack detection and localization using strain gauge sensors
Authors: Yoon Jiyoung , Lee Junhyeong , Kim Giyoung , Ryu Seunghwa , Park Jinhyoung 
Published: November 2022

AbstractStructural health monitoring (SHM) techniques often require a large number of sensors to evaluate and monitor the structural health. In this paper, we propose a deep neural network (DNN)-based SHM method for accurate crack detection and localization in real time using a small number of strain gauge sensors and confirm its feasibility based on experimental data. The proposed method combines a DNN model with principal component analysis (PCA) to predict the strain field based on the local strains measured by strain gauge sensors located rather sparsely. We demonstrate the potential of the proposed technique via a cyclic 4-point bending test performed on a composite material specimen without cracks and seven specimens with different lengths of cracks. A dataset containing local strains measured with 12 strain gauge sensors and strain field measured with a digital image correlation (DIC) device was prepared. The strain field dataset from DIC is converted to a smaller dimension latent space with a few eigen basis via PCA, and a DNN model is trained to predict principal component values of each image with 12 strain gauge sensor measurements as input. The proposed method turns out to accurately predict the strain field for all specimens considered in the study.
Polysaccharides from Pseudostellaria heterophylla modulate gut microbiota and alleviate syndrome of spleen deficiency in rats
Authors: Xiao Qing , Zhao Li , Jiang Chang , Zhu Yanjin , Zhang Jizhou , Hu Juan , Wang Guozeng 
Published: November 2022

AbstractPseudostellaria heterophylla, also called Tai-zi-shen (TZS) in Traditional Chinese Medicine (TCM), is always used clinically to treat spleen deficiency symptoms. Polysaccharides in TZS have various pharmacological activities, including anti-diabetic, immune regulation, and myocardial protection. However, the relationship between the spleen-invigorating effects of TZS or its polysaccharides and intestinal flora are not clear. This study investigated the effects of TZS decoction (PHD) and polysaccharide (PHP) on immune function and intestinal flora in a rat model of spleen deficiency syndrome (SDS) induced by a decoction of raw rhubarb (RRD). PHD and PHP increased immune organ index, alleviated inflammatory cell filtration, and reduced the levels of pro-inflammatory cytokines in rats with spleen deficiency syndrome. In addition, the production of butyric acid was promoted in PHD and PHP groups. Moreover, 16S rRNA gene sequencing showed that PHD and PHP reduced the relative abundance of Firmicutes while increasing the one of Bacteroidetes; significantly increased the abundance of Lactobacillus and decreased the abundance of Rombutsia; and PHP significantly increased the abundance of Alloprevotella. And there was a significant positive correlation between the alleviation of SDS and short-chain fatty acids (SCFAs)-producing bacteria. These findings suggested PHD and PHP, especially PHP, has a potential to relieve spleen deficiency by reducing intestinal inflammation, modulating structure and composition of gut microbiota, and promoting the production of butyric acid.
Distributed cooperative formation of stochastic multi‐agent systems in finite horizon
Authors: Shi Jiantao , Chen Chuang , Shen Mouquan , Liu Dan 
Published: November 2022

AbstractThe paper addresses the distributed cooperative formation control problem for a class of general stochastic multi‐agent systems subject to time‐varying dynamics. A type of novel modified distributed state observer is constructed, whose estimation information is used to design the control scheme for guaranteeing the mean‐square formation maintenance in finite‐horizon. Furthermore, the observer and controller parameters are obtained iteratively through solving a set of constrained recursive matrix equations. Finally, the proposed scheme has been validated by a simulation study.
Two‐person games for uncertain random singular dynamic systems
Authors: Chen Xin , Zhu Yuanguo , Park Ju H. 
Published: November 2022

AbstractA complex system exhibiting uncertainty as well as randomness may be portrayed by an uncertain random singular difference equation. This paper investigates two‐person nonzero‐sum and zero‐sum games based on uncertain random singular difference equations. First, an approach is proposed to translate the two‐person nonzero‐sum game into an equivalent game for a standard uncertain random dynamic system. The relevant recursive equations are developed to search the Nash equilibrium for the converted game. Solving the related recursive equations yields the solution to such a game. Following that, a Max‐Min Theorem is provided for finding the saddle‐point equilibrium of an uncertain random two‐person zero‐sum game. Finally, a numerical example is offered to demonstrate the validity of the findings.
Semi‐supervised learning dehazing algorithm based on the OSV model
Authors: Zhu Lijun , Wei Weibo , Pan Zhenkuan , Ji Lianshun , Song Jintao , Li Jinhan 
Published: November 2022

AbstractDespite the great progress that has been made in the task of single image dehazing, the results of the existing models in restoring image edge and texture information are still challenging. Besides, most dehazing models are trained on synthetic data, resulting in poor generalization ability to real‐world images. To address the aforementioned problems, a semi‐supervised learning dehazing method based on the decomposition model of Osher, Solé, and Vese(The OSV model) is presented. Specifically, the OSV model is first applied to decompose the hazy image into the structure layer and texture layer, save the texture layer and dehaze for the structure layer to restore images with sharper texture and edge. Furthermore, the network adopts a semi‐supervised learning algorithm based on generative adversarial networks (GAN) to generalize better to real‐world images, which includes two branches: supervised learning and unsupervised learning. Extensive experiments indicate that the proposed method preserves the texture and edge information of images more accurately while dehazing better, and performs favourably against the advanced dehazing algorithms on both synthetic outdoor datasets and real‐world hazy images.
3D zebrafish tracking with topology association
Authors: Xu Yuan , Jin Yichao , Zhang Yang , Zhu Qunxiong , He Yanlin , Sheng Hao 
Published: November 2022

AbstractRecently, zebrafish has received more and more attention due to its wide range of applications such as regeneration promoting therapeutics and drug discovery. Therefore, vision‐based trackers are utilized to record the swimming trajectory of zebrafish. In this paper, a re‐association method is introduced in the 3D reconstruction process to generate missed targets caused by occlusion. Since the variation of the overall tracking targets has the property of continuity and stability, a topology association model (TAM) is proposed by point group similarity into the tracking framework. TAM describes the movement of zebrafish from the macroscopic level and utilizes the changes of the point group structure for tracking. Experimental results show that the tracking framework enhances the overall performance and promotes the trajectory integrity. On the latest 3D‐ZeF20 benchmark, state‐of‐the‐art results are achieved. In addition, TAM tracking framework is applied to 2D general tracking to prove that the method is useful and have great advantage in other scenarios with relatively stable amount of targets as well.
Osteoprotektion beim nichtmetastasierten hormonsensitiven Prostatakarzinom (nmHSPC) unter androgendeprivativer Therapie (ADT): Aktuelle Daten aus Deutschland, vorgelegt von d-uo
Authors: Klier Jörg , König Frank , Schönfelder Robert , Eichenauer Rolf , Johannsen Manfred , Beuke Maike , Binder Manfred , Brenneis Horst , Burkert-Scholz Marcus , Fieseler Claus , Jaeger Andreas , Nitz Christian , Reese Stephan , Romagnolo Allesandro , Schröder Jörg , Hempel Elke , Doehn Christian 
Published: November 2022

Zusammenfassung
Einleitung Patienten mit einem Prostatakarzinom haben oftmals bereits eine verminderte Knochendichte. Wir haben die Versorgungssituation im Hinblick auf die Osteoprotektion zur Vermeidung eines Knochendichtverlusts bis hin zur sekundären Osteoporose bei Patienten mit einem nichtmetastasierten hormonsensitiven Prostatakarzinom (nmHSPC) unter androgendeprivativer Therapie (ADT) in urologischen Praxen in Deutschland untersucht.
Material und Methoden Es handelte sich um eine fragebogenbasierte
Untersuchung unter Mitgliedern von d-uo. Eingeschlossen wurden alle Patienten mit einem
histologisch gesicherten Prostatakarzinom, die zwischen 7/2019 und 6/2020 mindestens einmal in
der beteiligten Praxis gesehen wurden. Für die weitere Analyse wurden alle Patienten unter
einer Langzeit-ADT (definiert als > 12 Monate) hinsichtlich des Beginns, der Art und Dauer
der osteoprotektiven Therapie sowie der zusätzlichen Gabe von Kalzium und Vitamin D
betrachtet.
Ergebnisse Im o.g. Zeitraum wurden in 15 Praxen insgesamt 3.692 Patienten mit einem Prostatakarzinom gesehen. Hiervon erhielten 844 Patienten mit einem nmHSPC (22,9%) eine ADT. Eine osteoprotektive Therapie wurde bei 183/844 Patienten (21,7%) mit einem nmHSPC vorgenommen. Denosumab erhielten 73,2% dieser Patienten und ein Bisphosphonat 26,8%. Die Osteoprotektion wurde bei 32,8% der Patienten zeitgleich mit der ADT und bei 67,2% später begonnen. Bei 84,7% der Patienten wurde zusätzlich zur osteoprotektiven Therapie Kalzium und Vitamin D supplementiert. In 54,2% der Fälle war der Beginn zeitgleich mit der osteoprotektiven Therapie und in 45,8% der Fälle später.
Schlussfolgerung Eine medikamentöse Osteoprotektion wurde nur bei jedem fünften Patienten mit einem nmHSPC und ADT vorgenommen und nur bei jedem dritten Patienten zeitgleich mit der ADT begonnen. Zusammenfassend lässt sich daher feststellen, dass die medikamentöse osteoprotektive Therapie bei Patienten mit einem nmHSPC unter ADT eher die Ausnahme darstellt.