bluuebunny/crossref_metadata_2025_split huggingface dataset:
NFκB and NLRP3/NLRC4 inflammasomes regulate differentiation, activation and functional properties of monocytes in response to distinct SARS-CoV-2 proteins
Authors: Tsukalov Ilya , Sánchez-Cerrillo Ildefonso , Rajas Olga , Avalos Elena , Iturricastillo Gorane , Esparcia Laura , Buzón María José , Genescà Meritxell , Scagnetti Camila , Popova Olga , Martin-Cófreces Noa , Calvet-Mirabent Marta , Marcos-Jimenez Ana , Martínez-Fleta Pedro , Delgado-Arévalo Cristina , de los Santos Ignacio , Muñoz-Calleja Cecilia , Calzada María José , González Álvaro Isidoro , Palacios-Calvo José , Alfranca Arantzazu , Ancochea Julio , Sánchez-Madrid Francisco , Martin-Gayo Enrique 
Published: March 2024

AbstractIncreased recruitment of transitional and non-classical monocytes in the lung during SARS-CoV-2 infection is associated with COVID-19 severity. However, whether specific innate sensors mediate the activation or differentiation of monocytes in response to different SARS-CoV-2 proteins remain poorly characterized. Here, we show that SARS-CoV-2 Spike 1 but not nucleoprotein induce differentiation of monocytes into transitional or non-classical subsets from both peripheral blood and COVID-19 bronchoalveolar lavage samples in a NFκB-dependent manner, but this process does not require inflammasome activation. However, NLRP3 and NLRC4 differentially regulated CD86 expression in monocytes in response to Spike 1 and Nucleoprotein, respectively. Moreover, monocytes exposed to Spike 1 induce significantly higher proportions of Th1 and Th17 CD4 + T cells. In contrast, monocytes exposed to Nucleoprotein reduce the degranulation of CD8 + T cells from severe COVID-19 patients. Our study provides insights in the differential impact of innate sensors in regulating monocytes in response to different SARS-CoV-2 proteins, which might be useful to better understand COVID-19 immunopathology and identify therapeutic targets.
Effects of plant diversity on productivity strengthen over time due to trait-dependent shifts in species overyielding
Authors: Zheng Liting , Barry Kathryn E. , Guerrero-Ramírez Nathaly R. , Craven Dylan , Reich Peter B. , Verheyen Kris , Scherer-Lorenzen Michael , Eisenhauer Nico , Barsoum Nadia , Bauhus Jürgen , Bruelheide Helge , Cavender-Bares Jeannine , Dolezal Jiri , Auge Harald , Fagundes Marina V. , Ferlian Olga , Fiedler Sebastian , Forrester David I. , Ganade Gislene , Gebauer Tobias , Haase Josephine , Hajek Peter , Hector Andy , Hérault Bruno , Hölscher Dirk , Hulvey Kristin B. , Irawan Bambang , Jactel Hervé , Koricheva Julia , Kreft Holger , Lanta Vojtech , Leps Jan , Mereu Simone , Messier Christian , Montagnini Florencia , Mörsdorf Martin , Müller Sandra , Muys Bart , Nock Charles A. , Paquette Alain , Parker William C. , Parker John D. , Parrotta John A. , Paterno Gustavo B. , Perring Michael P. , Piotto Daniel , Wayne Polley H. , Ponette Quentin , Potvin Catherine , Quosh Julius , Rewald Boris , Godbold Douglas L. , van Ruijven Jasper , Standish Rachel J. , Stefanski Artur , Sundawati Leti , Urgoiti Jon , Williams Laura J. , Wilsey Brian J. , Yang Baiyu , Zhang Li , Zhao Zhao , Yang Yongchuan , Sandén Hans , Ebeling Anne , Schmid Bernhard , Fischer Markus , Kotowska Martyna M. , Palmborg Cecilia , Tilman David , Yan Enrong , Hautier Yann 
Published: March 2024

AbstractPlant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems.
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme
Authors: d’Oelsnitz Simon , Diaz Daniel J. , Kim Wantae , Acosta Daniel J. , Dangerfield Tyler L. , Schechter Mason W. , Minus Matthew B. , Howard James R. , Do Hannah , Loy James M. , Alper Hal S. , Zhang Y. Jessie , Ellington Andrew D. 
Published: March 2024

AbstractA major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are complex plant secondary metabolites with recognized therapeutic value. Due to their difficult synthesis they are regularly sourced by extraction and purification from the low-yielding daffodil Narcissus pseudonarcissus. Here, we propose an efficient biosensor-machine learning technology stack for biocatalyst development, which we apply to engineer an Amaryllidaceae enzyme in Escherichia coli. Directed evolution is used to develop a highly sensitive (EC50 = 20 μM) and specific biosensor for the key Amaryllidaceae alkaloid branchpoint 4’-O-methylnorbelladine. A structure-based residual neural network (MutComputeX) is subsequently developed and used to generate activity-enriched variants of a plant methyltransferase, which are rapidly screened with the biosensor. Functional enzyme variants are identified that yield a 60% improvement in product titer, 2-fold higher catalytic activity, and 3-fold lower off-product regioisomer formation. A solved crystal structure elucidates the mechanism behind key beneficial mutations.
Comprehensive multi-omics analysis reveals WEE1 as a synergistic lethal target with hyperthermia through CDK1 super-activation
Authors: Yang Xiaohang , Hu Xingyuan , Yin Jingjing , Li Wenting , Fu Yu , Yang Bin , Fan Junpeng , Lu Funian , Qin Tianyu , Kang Xiaoyan , Zhuang Xucui , Li Fuxia , Xiao Rourou , Shi Tingyan , Song Kun , Li Jing , Chen Gang , Sun Chaoyang 
Published: March 2024

AbstractHyperthermic intraperitoneal chemotherapy’s role in ovarian cancer remains controversial, hindered by limited understanding of hyperthermia-induced tumor cellular changes. This limits developing potent combinatory strategies anchored in hyperthermic intraperitoneal therapy (HIPET). Here, we perform a comprehensive multi-omics study on ovarian cancer cells under hyperthermia, unveiling a distinct molecular panorama, primarily characterized by rapid protein phosphorylation changes. Based on the phospho-signature, we pinpoint CDK1 kinase is hyperactivated during hyperthermia, influencing the global signaling landscape. We observe dynamic, reversible CDK1 activity, causing replication arrest and early mitotic entry post-hyperthermia. Subsequent drug screening shows WEE1 inhibition synergistically destroys cancer cells with hyperthermia. An in-house developed miniaturized device confirms hyperthermia and WEE1 inhibitor combination significantly reduces tumors in vivo. These findings offer additional insights into HIPET, detailing molecular mechanisms of hyperthermia and identifying precise drug combinations for targeted treatment. This research propels the concept of precise hyperthermic intraperitoneal therapy, highlighting its potential against ovarian cancer.
Natural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat
Authors: Cao Jie , Qin Zhen , Cui Guangxian , Chen Zhaoyan , Cheng Xuejiao , Peng Huiru , Yao Yingyin , Hu Zhaorong , Guo Weilong , Ni Zhongfu , Sun Qixin , Xin Mingming 
Published: March 2024

AbstractHeat stress threatens global wheat (Triticum aestivum) production, causing dramatic yield losses worldwide. Identifying heat tolerance genes and comprehending molecular mechanisms are essential. Here, we identify a heat tolerance gene, TaSG-D1E286K, in Indian dwarf wheat (Triticum sphaerococcum), which encodes an STKc_GSK3 kinase. TaSG-D1E286K improves heat tolerance compared to TaSG-D1 by enhancing phosphorylation and stability of downstream target TaPIF4 under heat stress condition. Additionally, we reveal evolutionary footprints of TaPIF4 during wheat selective breeding in China, that is, InDels predominantly occur in the TaPIF4 promoter of Chinese modern wheat cultivars and result in decreased expression level of TaPIF4 in response to heat stress. These sequence variations with negative effect on heat tolerance are mainly introduced from European germplasm. Our study provides insight into heat stress response mechanisms and proposes a potential strategy to improve wheat heat tolerance in future.
Ammonia marine engine design for enhanced efficiency and reduced greenhouse gas emissions
Authors: Zhou Xinyi , Li Tie , Chen Run , Wei Yijie , Wang Xinran , Wang Ning , Li Shiyan , Kuang Min , Yang Wenming 
Published: March 2024

AbstractPilot-diesel-ignition ammonia combustion engines have attracted widespread attentions from the maritime sector, but there are still bottleneck problems such as high unburned NH3 and N2O emissions as well as low thermal efficiency that need to be solved before further applications. In this study, a concept termed as in-cylinder reforming gas recirculation is initiated to simultaneously improve the thermal efficiency and reduce the unburned NH3, NOx, N2O and greenhouse gas emissions of pilot-diesel-ignition ammonia combustion engine. For this concept, one cylinder of the multi-cylinder engine operates rich of stoichiometric and the excess ammonia in the cylinder is partially decomposed into hydrogen, then the exhaust of this dedicated reforming cylinder is recirculated into the other cylinders and therefore the advantages of hydrogen-enriched combustion and exhaust gas recirculation can be combined. The results show that at 3% diesel energetic ratio and 1000 rpm, the engine can increase the indicated thermal efficiency by 15.8% and reduce the unburned NH3 by 89.3%, N2O by 91.2% compared to the base/traditional ammonia engine without the proposed method. At the same time, it is able to reduce carbon footprint by 97.0% and greenhouse gases by 94.0% compared to the traditional pure diesel mode.
Ultrastrong to nearly deep-strong magnon-magnon coupling with a high degree of freedom in synthetic antiferromagnets
Authors: Wang Yuqiang , Zhang Yu , Li Chaozhong , Wei Jinwu , He Bin , Xu Hongjun , Xia Jihao , Luo Xuming , Li Jiahui , Dong Jing , He Wenqing , Yan Zhengren , Yang Wenlong , Ma Fusheng , Chai Guozhi , Yan Peng , Wan Caihua , Han Xiufeng , Yu Guoqiang 
Published: March 2024

AbstractUltrastrong and deep-strong coupling are two coupling regimes rich in intriguing physical phenomena. Recently, hybrid magnonic systems have emerged as promising candidates for exploring these regimes, owing to their unique advantages in quantum engineering. However, because of the relatively weak coupling between magnons and other quasiparticles, ultrastrong coupling is predominantly realized at cryogenic temperatures, while deep-strong coupling remains to be explored. In our work, we achieve both theoretical and experimental realization of room-temperature ultrastrong magnon-magnon coupling in synthetic antiferromagnets with intrinsic asymmetry of magnetic anisotropy. Unlike most ultrastrong coupling systems, where the counter-rotating coupling strength g2 is strictly equal to the co-rotating coupling strength g1, our systems allow for highly tunable g1 and g2. This high degree of freedom also enables the realization of normalized g1 or g2 larger than 0.5. Particularly, our experimental findings reveal that the maximum observed g1 is nearly identical to the bare frequency, with g1/ω0 = 0.963, indicating a close realization of deep-strong coupling within our hybrid magnonic systems. Our results highlight synthetic antiferromagnets as platforms for exploring unconventional ultrastrong and even deep-strong coupling regimes, facilitating the further exploration of quantum phenomena.
Inherently integrated microfiber-based flexible proprioceptive sensor for feedback-controlled soft actuators
Authors: Kim Hwajoong , Na Hyunbin , Noh Seungbeom , Chang Shinwon , Kim Jinho , Kong Taejune , Shin Gyowook , Lee Chankyu , Lee Seonggyu , Park Yong-Lae , Oh Sehoon , Lee Jaehong 
Published: March 2024

AbstractFor the accurate and continuous control of soft actuators in dynamic environments, the movements of the soft actuators must be monitored in real-time. To this end, various soft actuators capable of self-monitoring have been developed by separately integrating sensing devices into actuators. However, integrating such heterogeneous sensing components into soft actuators results in structural complexity, high manufacturing costs, and poor interfacial stability. Here, we report on intelligent pneumatic fiber-reinforced soft actuators with an inherent flexible proprioceptive sensor that uses only the essential components of typical fiber-reinforced soft actuators. The inherent flexible proprioceptive sensor is achieved by leveraging two parallel conductive microfibers around an elastomeric chamber of the soft actuator, which simultaneously acts as both a capacitive bending sensor and radial expansion limiting fibers of typical fiber-reinforced soft actuators. The proprioceptive soft actuator exhibits excellent mechanical actuation up to 240° bending motion and proprioceptive sensing performance with high sensitivity of 1.2 pF rad−1. Mathematical analysis and simulations of the soft actuator can effectively predict the bending actuation and capacitive responses against input pressures. We demonstrate that proprioceptive soft actuators can be used to construct a soft gripping system and prosthetic hand which express various hand gestures and perform dexterous manipulation with real-time proprioceptive sensing capability.
Diffusion tensor imaging of white-matter structural features of maltreating mothers and their associations with intergenerational chain of childhood abuse
Authors: Kurata Sawa , Nishitani Shota , Kawata Natasha Y. S. , Yao Akiko , Fujisawa Takashi X. , Okazawa Hidehiko , Tomoda Akemi 
Published: March 2024

AbstractChild abuse causes lifelong adverse outcomes for both physical and mental health, although many are resilient. Efforts to prevent this issue from the parental side require an understanding of the neurobiological basis that leads abusive parents to perpetrate abuse and the influence of the intergenerational chain of childhood abuse. Therefore, this study was conducted to compare the brain white-matter fiber structures between 11 maltreating mothers who had been recognized as having conducted child abuse prior to the intervention and 40 age-matched control mothers using tract-based spatial statistics. There was a significantly reduced axial diffusivity (AD) and a similar trend in fractional anisotropy (FA) in the right corticospinal tract in maltreating mothers compared to control mothers. Therefore, maltreating mothers may have excessive control over the forcefulness of voluntary movements. These features also decreased as the number of childhood abuse experiences increased, suggesting that an intergenerational chain of child abuse may also be involved. Other aspects observed were that the higher the current depressive symptoms, the lower the AD and FA values; however, they were not related to parental practice or empathy. These results corroborate the neurobiological features that perpetrate behaviors in abusive mothers.
Quantitative analysis of mass mortality events in salmon aquaculture shows increasing scale of fish loss events around the world
Authors: Singh Gerald G. , Sajid Zaman , Mather Charles 
Published: March 2024

AbstractGlobally, salmon aquaculture promises to contribute to sustainable sources of animal protein for a growing human population. However, the growth of the industry also includes increased reports of mass mortality events—disaster events where large numbers of fish die in short periods of time. As salmon production increases in scale and more technology is used to grow salmon in contexts otherwise not suited for them, there is a possibility for more frequent and more severe mortality events. Despite investigations into specific cases of mass mortality events—no global study has been conducted to see if large scale mortality is increasing in frequency and scale. Using a global dataset of publicly available and government-collated data on salmon mortality events including nations responsible for the majority of salmon aquaculture, we document trends in mortality events, showing that in some of the major salmon producing nations of the world (in particular Norway, Canada, and the UK), mass mortality events have increased in frequency from 2012 to 2022. We also show that the scope of mass mortality events has increased over time—that is, the upper bound of how many fish were killed in a specific mortality event has increased over time. Finally, the expected maximum size of a mass mortality event differs from country to country, but is likely much larger than site and jurisdictional thresholds of concern for animal welfare, early warning thresholds, and capacity to respond to mortality events. The consequences of the increased scale and scope of mass mortality events extend past aquaculture production to include severe consequences to aquaculture companies and to coastal communities who depend on aquaculture. Our results agree with predictions of the concept of “manufactured risk”, which suggests that risk emerges from the aggressive use of technology to optimize production in variable environments, and we argue that there is a need for more fine-scale and standard data collection on salmon mortality events, and that future investigations into salmon aquaculture should increase focus on disaster potential and realization.
Genomic insights and anti-phytopathogenic potential of siderophore metabolome of endolithic Nocardia mangyaensis NH1
Authors: Khilyas Irina V. , Markelova Maria I. , Valeeva Liia R. , Ivoilova Tatiana M. , Shagimardanova Elena , Laikov Alexander V. , Elistratova Anna A. , Berkutova Ekaterina S. , Lochnit Guenter , Sharipova Margarita R. 
Published: March 2024

AbstractActinobacteria are one of the predominant groups that successfully colonize and survive in various aquatic, terrestrial and rhizhospheric ecosystems. Among actinobacteria, Nocardia is one of the most important agricultural and industrial bacteria. Screening and isolation of Nocardia related bacteria from extreme habitats such as endolithic environments are beneficial for practical applications in agricultural and environmental biotechnology. In this work, bioinformatics analysis revealed that a novel strain Nocardia mangyaensis NH1 has the capacity to produce structurally varied bioactive compounds, which encoded by non-ribosomal peptide synthases (NRPS), polyketide synthase (PKS), and post-translationally modified peptides (RiPPs). Among NRPS, five gene clusters have a sequence homology with clusters encoding for siderophore synthesis. We also show that N. mangyaensis NH1 accumulates both catechol- and hydroxamate-type siderophores simultaneously under iron-deficient conditions. Untargeted LC–MS/MS analysis revealed a variety of metabolites, including siderophores, lipopeptides, cyclic peptides, and indole-3-acetic acid (IAA) in the culture medium of N. mangyaensis NH1 grown under iron deficiency. We demonstrate that four CAS (chrome azurol S)-positive fractions display variable affinity to metals, with a high Fe3+ chelating capability. Additionally, three of these fractions exhibit antioxidant activity. A combination of iron scavenging metabolites produced by N. mangyaensis NH1 showed antifungal activity against several plant pathogenic fungi. We have shown that the pure culture of N. mangyaensis NH1 and its metabolites have no adverse impact on Arabidopsis seedlings. The ability of N. mangyaensis NH1 to produce siderophores with antifungal, metal-chelating, and antioxidant properties, when supplemented with phytohormones, has the potential to improve the release of macro- and micronutrients, increase soil fertility, promote plant growth and development, and enable the production of biofertilizers across diverse soil systems.
Genomic insights into Yak (Bos grunniens) adaptations for nutrient assimilation in high-altitudes
Authors: Ahmad Hafiz Ishfaq , Mahmood Sammina , Hassan Mubashar , Sajid Muhammad , Ahmed Irfan , Shokrollahi Borhan , Shahzad Abid Hussain , Abbas Shaista , Raza Sanan , Khan Komal , Muhammad Sayyed Aun , Fouad Dalia , Ataya Farid S. , Li Zhengtian 
Published: March 2024

AbstractHigh-altitude environments present formidable challenges for survival and reproduction, with organisms facing limited oxygen availability and scarce nutrient resources. The yak (Bos grunniens), indigenous to the Tibetan Plateau, has notably adapted to these extreme conditions. This study delves into the genomic basis of the yak’s adaptation, focusing on the positive selection acting on genes involved in nutrient assimilation pathways. Employing techniques in comparative genomics and molecular evolutionary analyses, we selected genes in the yak that show signs of positive selection associated with nutrient metabolism, absorption, and transport. Our findings reveal specific genetic adaptations related to nutrient metabolism in harsh climatic conditions. Notably, genes involved in energy metabolism, oxygen transport, and thermoregulation exhibited signs of positive selection, suggesting their crucial role in the yak’s successful colonization of high-altitude regions. The study also sheds light on the yak's immune system adaptations, emphasizing genes involved in response to various stresses prevalent at elevated altitudes. Insights into the yak’s genomic makeup provide valuable information for understanding the broader implications of high-altitude adaptations in mammalian evolution. They may contribute to efforts in enhancing livestock resilience to environmental challenges.