bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of propagule type and burial depth on knotroot foxtail (Setaria parviflora) emergence and plant development, compared to other Setaria species
Authors: Dyer Logan M. , Henry Gerald M. , McCullough Patrick E. , Belcher Jason , Zaccaro-Gruener Maria Leticia , Basinger Nicholas T. 
Published: October 2024

Abstract
Knotroot foxtail [Setaria parviflora (Poir.) Kerguélen], a perennial Setaria species, is becoming more problematic in forage and grazing systems across the southeastern United States. Setaria parviflora reproduces through the production of rhizomes and seeds, further complicating management strategies. Significant knowledge gaps exist regarding the biology and control of this species. This research aimed to understand the influence of burial depth on S. parviflora propagules and the physiological differences between it and other Setaria spp. Experiments were conducted between October 2019 and February 2021 in Clarke County, GA, to investigate the influence of burial depth (1, 2, 4, 8, and 16 cm) on the emergence and growth of S. parviflora rhizomes and seeds. Zero emergence was estimated at 8.7, 10.8, and 11.2 cm for small rhizomes, large rhizomes, and seeds, respectively. Therefore, producers could implement tillage events to a depth of 11.2 cm or greater to control S. parviflora. A separate study compared S. parviflora, yellow foxtail [Setaria pumila (Poir.) Roem. & Schult.], green foxtail [Setaria viridis (L.) P. Beauv.], and giant foxtail (Setaria faberi Herrm.) plant morphology. Despite similar aboveground appearances, S. pumila and S. parviflora had different total and belowground biomass 2 to 5 mo after emergence, which suggests differences in root formation and perennialization of S. parviflora. The present research determined that burying propagules using tillage could be included in management recommendations concerning S. parviflora; however, it should be complemented with herbicide applications during the growing season to assist in controlling S. parviflora plants produced by seeds.
A Deep Learning Approach for Automatic Ionogram Parameters Recognition With Convolutional Neural Networks
Authors: Sherstyukov Ruslan , Moges Samson , Kozlovsky Alexander , Ulich Thomas 
Published: October 2024

AbstractTypical ionosondes operate with >5 min time intervals, which is enough to obtain regular parameters of the ionosphere, but insufficient to observe short‐term processes in the Earth's ionosphere. The key point for this study is to increase the ionosondes data time resolution by automatization of ionogram scaling routine. In this study we show the results of implementation of deep learning approach for ionogram parameters scaling. We trained the model on 13 years ionogram data set of Sodankyla ionosonde at high latitude region (67°N). We tested our autoscaling program tool on 2021 years data set and evaluate errors between operator and automatic parameters scaling. The root mean square errors for critical frequencies foF2, foF1, foE, foEs, fmin, fbEs and virtual heights h′F, h′E, h′Es are estimated as 0.12 MHz (2 pixels), 0.07 MHz (1.16 pixels), 0.15 MHz (2.5 pixels), 0.33 MHz (5.5 pixels), 0.15 MHz (2.5 pixels), 0.17 MHz (2.83 pixels), 7.7 km (1.34 pixels), 7.0 km (1.22 pixels), 7.1 km (1.24 pixels), respectively.
Shear Instability and Turbulent Mixing by Kuroshio Intrusion Into the Changjiang River Plume
Authors: Tu Junbiao , Wu Jiaxue , Fan Daidu , Liu Zhiyu , Zhang Qianjiang , Smyth William 
Published: October 2024

AbstractShear instability is a dominant mechanism for mixing in the stratified oceans and coastal seas. For the first time, we present fine‐scale, direct measurements of shear instabilities in the bottom front generated by the Kuroshio intrusion into the Changjiang (Yangtze) river plume. Shear instabilities were identified using a shipboard echo‐sounder and the resulting turbulent mixing was quantified using a turbulence microstructure profiler. The shear instabilities generate vigorous turbulent mixing with dissipation rate and vertical diffusivity up to O (10−4 m2 s−3) and O (10−1 m2 s−1), respectively, comparable to values associated with shear instabilities observed in river plumes and western boundary currents but several orders of magnitude larger than typical values in the open ocean. The enhanced turbulence may contribute significantly to mixing between the Kuroshio water and coastal water and thereby alter the coastal biogeochemistry cycles.
MRI and CT compatible asymmetric bilayer hydrogel electrodes for EEG-based brain activity monitoring
Authors: Ren Guoqiang , Zhang Mingxuan , Zhuang Liping , Li Lianhui , Zhao Shunying , Guo Jinxiu , Zhao Yinchao , Peng Zhaoxiang , Lian Jiangfan , Liu Botao , Ma Jingyun , Hu Xiaodong , Zhang Zhewei , Zhang Ting , Lu Qifeng , Hao Mingming 
Published: October 2024

AbstractThe exploration of multi-dimensional brain activity with high temporal and spatial resolution is of great significance in the diagnosis of neurological disease and the study of brain science. Although the integration of electroencephalogram (EEG) with magnetic resonance imaging (MRI) and computed tomography (CT) provides a potential solution to achieve a brain-functional image with high spatiotemporal resolution, the critical issues of interface stability and magnetic compatibility remain challenging. Therefore, in this research, we proposed a conductive hydrogel EEG electrode with an asymmetrical bilayer structure, which shows the potential to overcome the challenges. Benefiting from the bilayer structure with different moduli, the hydrogel electrode exhibits high biological and mechanical compatibility with the heterogeneous brain-electrode interface. As a result, the impedance can be reduced compared with conventional metal electrodes. In addition, the hydrogel-based ionic conductive electrodes, which are free from metal conductors, are compatible with MRI and CT. Therefore, they can obtain high spatiotemporal resolution multi-dimensional brain information in clinical settings. The research outcome provides a new approach for establishing a platform for early diagnosis of brain diseases and the study of brain science.
Integrity of the circadian clock determines regularity of high-frequency and diurnal LFP rhythms within and between brain areas
Authors: Volkmann Paul , Geiger Annika E. I. , Hühne-Landgraf Anisja , Miljanovic Nina , Bly Jessica , Engl Tobias , Potschka Heidrun , Rossner Moritz J. , Landgraf Dominic 
Published: October 2024

AbstractCircadian clocks control most physiological processes of many species. We specifically wanted to investigate the influence of environmental and endogenous rhythms and their interplay on electrophysiological dynamics of neuronal populations. Therefore, we measured local field potential (LFP) time series in wild-type and Cryptochrome 1 and 2 deficient (Cry1/2−/−) mice in the suprachiasmatic nucleus and the nucleus accumbens under regular light conditions and constant darkness. Using refined descriptive and statistical analyses, we systematically profiled LFP time series activity. We show that both environmental and endogenous rhythms strongly influence the rhythmicity of LFP signals and their frequency components, but also shape neuronal patterns on much smaller time scales, as neuronal activity in Cry1/2−/− mice is significantly less regular but at each time more synchronous within and between brain areas than in wild-type mice. These results show that functional circadian rhythms are integral for both circadian and non-circadian coordination of neuronal ensemble dynamics.
Ror2 signaling regulated by differential Wnt proteins determines pathological fate of muscle mesenchymal progenitors
Authors: Kamizaki Koki , Katsukawa Mitsuko , Yamamoto Ayano , Fukada So-ichiro , Uezumi Akiyoshi , Endo Mitsuharu , Minami Yasuhiro 
Published: October 2024

AbstractSkeletal muscle mesenchymal progenitors (MPs) play a critical role in supporting muscle regeneration. However, under pathological conditions, they contribute to intramuscular adipose tissue accumulation, involved in muscle diseases, including muscular dystrophy and sarcopenia, age-related muscular atrophy. How MP fate is determined in these different contexts remains unelucidated. Here, we report that Ror2, a non-canonical Wnt signaling receptor, is selectively expressed in MPs and regulates their pathological features in a differential ligand-dependent manner. We identified Wnt11 and Wnt5b as ligands of Ror2. In vitro, Wnt11 inhibited MP senescence, which is required for normal muscle regeneration, and Wnt5b promoted MP proliferation. We further found that both Wnts are abundant in degenerating muscle and synergistically stimulate Ror2, leading to unwanted MP proliferation and eventually intramuscular adipose tissue accumulation. These findings provide evidence that Ror2-mediated signaling elicited by differential Wnts plays a critical role in determining the pathological fate of MPs.
Nicotine-induced CHRNA5 activation modulates CES1 expression, impacting head and neck squamous cell carcinoma recurrence and metastasis via MEK/ERK pathway
Authors: Feng Chen , Mao Wei , Yuan Chenyang , Dong Pin , Liu Yuying 
Published: October 2024

Abstract
The mucosal epithelium of the head and neck region (including the oral cavity, nasal cavity, pharynx, nasopharynx, and larynx) is the primary site exposed to tobacco smoke, and its presence of nicotinic acetylcholine receptors (nAChRs) has been observed in the mucosal epithelial cells of this area. It remains unclear whether HNSC cells can migrate and invade through nAChR signaling. A model of HNSC cells exposed to nicotine is established. Cell proliferation following nicotine exposure is assessed using the CCK-8 assay, while migration and invasion are evaluated through wound healing and Transwell assays. The effects of CHRNA5 knockdown and overexpression are also investigated. Immunofluorescence staining is used to analyze CHRNA5 expression and localization, and clonogenic assays are performed to measure colony proliferation after CHRNA5 knockdown and overexpression. The interaction between CHRNA5 and CES1 is examined using molecular docking, co-immunoprecipitation, and immunofluorescence. Differentially expressed genes are subjected to pathway enrichment analysis, and MEK/ERK protein expression and phosphorylation are validated via western blot. Tumor formation assays are performed in nude mice using sh-CHRNA5 Cal27 cells, followed by western blot and immunohistochemical staining. Additionally, laryngeal and hypopharyngeal cancer tissues are analyzed through immunohistochemistry. Nicotine significantly enhanced the proliferation, migration, and invasion capabilities of head and neck tumor cells, including Cal27, Fadu, HN6, and Tu686 cells, through the expression of CHRNA5. Knockdown of CHRNA5 can reduce cell migration, invasion, and proliferation, whereas nicotine exposure can reverse this trend. Additionally, the mRNA and protein expression of CES1 decreases with the knockdown of CHRNA5, indicating a regulatory relationship between the two. Transcriptomics revealed that the knockdown of CHRNA5 is associated with the MEK/ERK signaling pathway. Further cellular- and tissue-level evidence confirmed that the levels of p-MEK/MEK, p-ERK/ERK, and CES1 decreased following knockdown of CHRNA5, a trend that nicotine can reverse. Nicotine promotes the proliferation, migration, and invasion of HNSC by upregulating CHRNA5 expression. Knockdown of CHRNA5 reduces these effects, which can be reversed by nicotine. Nicotine exposure activates CHRNA5, regulating CES1 expression via the MEK/ERK pathway, contributing to the recurrence and metastasis of head and neck squamous carcinoma.
Nr1d1 inhibition mitigates intermittent hypoxia-induced pulmonary hypertension via Dusp1-mediated Erk1/2 deactivation and mitochondrial fission attenuation
Authors: Pan Zhou , Yao Yan , Liu Xu , Wang Yixuan , Zhang Xinyue , Zha Shiqian , Hu Ke 
Published: October 2024

AbstractIntermittent hypoxia (IH) precipitates pulmonary vasoconstriction, culminating in the onset of pulmonary hypertension (PH) among individuals afflicted with sleep apnea. While Nuclear receptor subfamily 1 group D member 1 (Nr1d1) is progressively recognized as pivotal regulator of cellular physiology, the role in the pathogenesis of IH-induced PH remains largely uncharted. The expression of Nr1d1 was examined in IH-induced rodent PH and in IH-treated PASMCs. To elucidate the contribution of Nr1d1 to the development of IH-induced PH, we employed siRNA to modulate Nr1d1 expression in vitro and employed serotype 1 adeno-associated virus (AAV1) in vivo. Nr1d1 levels were elevated in IH-induced rodents PH lung tissues and IH-treated PASMCs. Knocking down Nr1d1 by AAV1 effectively inhibited PH progression in chronic IH-induced PH models. Mechanistic investigations identified dual specificity phosphatase 1 (Dusp1), as a direct target that Nr1d1 trans-repressed, mediating Nr1d1’s regulatory influence on Erk1/2/Drp1 signaling. Nr1d1 deficiency ameliorates mitochondrial dysfunction and fission by restoring Dusp1 dysregulation and Drp1 phosphorylation. Activation of Erk1/2 with PMA reversed the Dusp1-mediated regulation of Drp1 phosphorylation, indicating the involvement of the Erk1/2 pathway in Drp1 phosphorylation controlled by Dusp1. Meanwhile, intermittent hypoxia induced more severe PH in Dusp1 knockout mice compared with wild-type mice. Our data unveil a novel role for Nr1d1 in IH-induced PH pathogenesis and an undisclosed Nr1d1-Dusp1 axis in PASMCs mitochondrial fission regulation.
Targeting a chemo-induced adaptive signaling circuit confers therapeutic vulnerabilities in pancreatic cancer
Authors: Saito Yohei , Xiao Yi , Yao Jun , Li Yunhai , Liu Wendao , Yuzhalin Arseniy E. , Shyu Yueh-Ming , Li Hongzhong , Yuan Xiangliang , Li Ping , Zhang Qingling , Li Ziyi , Wei Yongkun , Yin Xuedong , Zhao Jun , Kariminia Seyed M. , Wu Yao-Chung , Wang Jinyang , Yang Jun , Xia Weiya , Sun Yutong , Jho Eek-hoon , Chiao Paul J. , Hwang Rosa F. , Ying Haoqiang , Wang Huamin , Zhao Zhongming , Maitra Anirban , Hung Mien-Chie , DePinho Ronald A. , Yu Dihua 
Published: October 2024

AbstractAdvanced pancreatic ductal adenocarcinomas (PDACs) respond poorly to all therapies, including the first-line treatment, chemotherapy, the latest immunotherapies, and KRAS-targeting therapies. Despite an enormous effort to improve therapeutic efficacy in late-stage PDAC patients, effective treatment modalities remain an unmet medical challenge. To change the status quo, we explored the key signaling networks underlying the universally poor response of PDAC to therapy. Here, we report a previously unknown chemo-induced symbiotic signaling circuit that adaptively confers chemoresistance in patients and mice with advanced PDAC. By integrating single-cell transcriptomic data from PDAC mouse models and clinical pathological information from PDAC patients, we identified Yap1 in cancer cells and Cox2 in stromal fibroblasts as two key nodes in this signaling circuit. Co-targeting Yap1 in cancer cells and Cox2 in stroma sensitized PDAC to Gemcitabine treatment and dramatically prolonged survival of mice bearing late-stage PDAC, whereas simultaneously inhibiting Yap1 and Cox2 only in cancer cells was ineffective. Mechanistically, chemotherapy triggers non-canonical Yap1 activation by nemo-like kinase in 14-3-3ζ-overexpressing PDAC cells and increases secretion of CXCL2/5, which bind to CXCR2 on fibroblasts to induce Cox2 and PGE2 expression, which reciprocally facilitate PDAC cell survival. Finally, analyses of PDAC patient data revealed that patients who received Statins, which inhibit Yap1 signaling, and Cox2 inhibitors (including Aspirin) while receiving Gemcitabine displayed markedly prolonged survival compared to others. The robust anti-tumor efficacy of Statins and Aspirin, which co-target the chemo-induced adaptive circuit in the tumor cells and stroma, signifies a unique therapeutic strategy for PDAC.
Characterization of anti-AAV2 neutralizing antibody levels in sheep prior to and following intravitreal AAV2.7m8 injection
Authors: Ross Maya , Sade Kareen , Obolensky Alexey , Averbukh Edward , Desrosiers Melissa , Rosov Alexander , Dvir Hay , Gootwine Elisha , Banin Eyal , Dalkara Deniz , Ofri Ron 
Published: October 2024

AbstractGene augmentation therapy is a promising treatment for incurable, blinding inherited retinal diseases, and intravitreal delivery is being studied as a safe alternative to subretinal injections. Adeno-Associated Viruses (AAV) are commonly-used vectors for ocular gene augmentation therapy. Naturally occurring pre-operative exposure and infection with AAV could result in presence of neutralizing antibodies (NAB’s) in patients’ serum, and may affect the safety and efficacy of treatment. Our aim was to characterize the humoral response against AAV pre- and post-intravitreal delivery of AAV2.7m8 vectors in a naturally-occurring sheep model of CNGA3 achromatopsia. Serial serum neutralization assays were performed to screen sheep for pre-exiting anti-AAV2 NAB’s, and to assess the effect of intravitreal AAV2.7m8 injection on post-operative NAB titers and intraocular inflammation in sheep. The effect of viral dose and transgene type were also assessed. Serological screening revealed pre-operative seropositivity in 21.4% of animals, with age being a risk factor for the presence of anti-AAV2 NAB’s. NAB titers increased following intravitreal AAV administration in the majority of sheep. There was no significant difference in the degree of post-operative serum neutralization between pre-operatively seronegative sheep and those with pre-existing antibodies. However, only sheep with pre-existing antibodies presented with signs of post-operative inflammation. We conclude that pre-existing anti-AAV2 NAB’s do not affect the level of post-operative NAB titers; however, they increase the risk of post-operative ocular inflammation. Our results could have implications for the management of AAV-mediated ocular gene therapies, a technology being increasingly studied and used in patients.
Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference
Authors: Čepaitė R. , Klein N. , Mikšys A. , Camara-Wilpert S. , Ragožius V. , Benz F. , Skorupskaitė A. , Becker H. , Žvejytė G. , Steube N. , Hochberg G.K.A , Randau L. , Pinilla-Redondo R. , Malinauskaitė L. , Pausch P. 
Published: October 2024

AbstractCRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.
From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan
Authors: Li Yao-Tsun , Ko Hui-Ying , Hughes Joseph , Liu Ming-Tsan , Lin Yi-Ling , Hampson Katie , Brunker Kirstyn 
Published: October 2024

AbstractA/goose/Guangdong/1/96-like (GsGd) highly pathogenic avian influenza (HPAI) H5 viruses cause severe outbreaks in poultry when introduced. Since emergence in 1996, control measures in most countries have suppressed local GsGd transmission following introductions, making persistent transmission in domestic birds rare. However, geographical expansion of clade 2.3.4.4 sublineages has raised concern about establishment of endemic circulation, while mechanistic drivers leading to endemicity remain unknown. We reconstructed the evolutionary history of GsGd sublineage, clade 2.3.4.4c, in Taiwan using a time-heterogeneous rate phylogeographic model. During Taiwan’s initial epidemic wave (January 2015 - August 2016), we inferred that localised outbreaks had multiple origins from rapid spread between counties/cities nationwide. Subsequently, outbreaks predominantly originated from a single county, Yunlin, where persistent transmission harbours the trunk viruses of the sublineage. Endemic hotspots determined by phylogeographic reconstruction largely predicted the locations of re-emerging outbreaks in Yunlin. The transition to endemicity involved a shift to chicken-dominant circulation, following the initial bidirectional spread between chicken and domestic waterfowl. Our results suggest that following their emergence in Taiwan, source-sink dynamics from a single county have maintained GsGd endemicity up until 2023, pointing to where control efforts should be targeted to eliminate the disease.
Diverse prehistoric cattle husbandry strategies in the forests of Central Europe
Authors: Gillis Rosalind E. , Kendall Iain P. , Roffet-Salque Mélanie , Zanon Marco , Anders Alexandra , Arbogast Rose-Marie , Bogucki Peter , Brychova Veronika , Casanova Emmanuelle , Classen Erich , Csengeri Piroska , Czerniak Lech , Domboróczki László , Fiorillo Denis , Gronenborn Detlef , Hachem Lamys , Jakucs János , Ilett Michael , Lyublyanovics Kyra , Lenneis Eva , Marciniak Arkadiusz , Marton Tibor , Oross Krisztián , Pavúk Juraj , Pechtl Joachim , Pyzel Joanna , Stadler Peter , Stäuble Harald , Vostrovská Ivana , van Wijk Ivo , Vigne Jean-Denis , Balasse Marie , Evershed Richard P. 
Published: October 2024

Abstract
During the sixth millennium bce, the first farmers of Central Europe rapidly expanded across a varied mosaic of forested environments. Such environments would have offered important sources of mineral-rich animal feed and shelter, prompting the question: to what extent did early farmers exploit forests to raise their herds? Here, to resolve this, we have assembled multi-regional datasets, comprising bulk and compound-specific stable isotope values from zooarchaeological remains and pottery, and conducted cross-correlation analyses within a palaeo-environmental framework. Our findings reveal a diversity of pasturing strategies for cattle employed by early farmers, with a notable emphasis on intensive utilization of forests for grazing and seasonal foddering in some regions. This experimentation with forest-based animal feeds by early farmers would have enhanced animal fertility and milk yields for human consumption, concurrently contributing to the expansion of prehistoric farming settlements and the transformation of forest ecosystems. Our study emphasizes the intricate relationship that existed between early farmers and forested landscapes, shedding light on the adaptive dynamics that shaped humans, animals and environments in the past.
A global dataset of salmonid biomass in streams
Authors: Foote Kyleisha J. , Grant James W. A. , Biron Pascale M. 
Published: October 2024

AbstractSalmonid fishes are arguably one of the most studied fish taxa on Earth, but little is known about their biomass range in many parts of the world. We created a dataset of estimated salmonid biomass using published material of over 1000 rivers, covering 27 countries and 11 species. The dataset, spanning 84 years of data, is the largest known compilation of published studies on salmonid biomass in streams, allowing detailed analyses of differences in biomass by species, region, period, and sampling techniques. Production is also recorded for 194 rivers, allowing further analyses and relationships between biomass and production to be explored. There is scope to expand the list of variables in the dataset, which would be useful to the scientific community as it would enable models to be developed to predict salmonid biomass and production, among many other analyses.