bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades
Authors: Dong Yang , Chen Ruirui , Graham Emily B. , Yu Bingqian , Bao Yuanyuan , Li Xin , You Xiangwei , Feng Youzhi 
Published: July 2024

AbstractWith the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.
Anterior cingulate cortex provides the neural substrates for feedback-driven iteration of decision and value representation
Authors: Chen Wenqi , Liang Jiejunyi , Wu Qiyun , Han Yunyun 
Published: July 2024

AbstractAdjusting decision-making under uncertain and dynamic situations is the hallmark of intelligence. It requires a system capable of converting feedback information to renew the internal value. The anterior cingulate cortex (ACC) involves in error and reward events that prompt switching or maintenance of current decision strategies. However, it is unclear whether and how the changes of stimulus-action mapping during behavioral adaptation are encoded, nor how such computation drives decision adaptation. Here, we tracked ACC activity in male mice performing go/no-go auditory discrimination tasks with manipulated stimulus-reward contingencies. Individual ACC neurons integrate the outcome information to the value representation in the next-run trials. Dynamic recruitment of them determines the learning rate of error-guided value iteration and decision adaptation, forming a non-linear feedback-driven updating system to secure the appropriate decision switch. Optogenetically suppressing ACC significantly slowed down feedback-driven decision switching without interfering with the execution of the established strategy.
A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis
Authors: Pérez-Burgos María , Herfurth Marco , Kaczmarczyk Andreas , Harms Andrea , Huber Katrin , Jenal Urs , Glatter Timo , Søgaard-Andersen Lotte 
Published: July 2024

AbstractPhenotypic heterogeneity in bacteria can result from stochastic processes or deterministic programs. The deterministic programs often involve the versatile second messenger c-di-GMP, and give rise to daughter cells with different c-di-GMP levels by deploying c-di-GMP metabolizing enzymes asymmetrically during cell division. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity is switched on during cytokinesis, resulting in a transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating phenotypically similar daughters with correct motility behaviours. Thus, our findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria can ensure the formation of dissimilar or similar daughter cells by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations.
Score-based denoising for atomic structure identification
Authors: Hsu Tim , Sadigh Babak , Bertin Nicolas , Park Cheol Woo , Chapman James , Bulatov Vasily , Zhou Fei 
Published: July 2024

AbstractWe propose an effective method for removing thermal vibrations that complicate the task of analyzing complex dynamics in atomistic simulation of condensed matter. Our method iteratively subtracts thermal noises or perturbations in atomic positions using a denoising score function trained on synthetically noised but otherwise perfect crystal lattices. The resulting denoised structures clearly reveal underlying crystal order while retaining disorder associated with crystal defects. Purely geometric, agnostic to interatomic potentials, and trained without inputs from explicit simulations, our denoiser can be applied to simulation data generated from vastly different interatomic interactions. The denoiser is shown to improve existing classification methods, such as common neighbor analysis and polyhedral template matching, reaching perfect classification accuracy on a recent benchmark dataset of thermally perturbed structures up to the melting point. Demonstrated here in a wide variety of atomistic simulation contexts, the denoiser is general, robust, and readily extendable to delineate order from disorder in structurally and chemically complex materials.
Clonal inactivation of TERT impairs stem cell competition
Authors: Hasegawa Kazuteru , Zhao Yang , Garbuzov Alina , Corces M. Ryan , Neuhöfer Patrick , Gillespie Victoria M. , Cheung Peggie , Belk Julia A. , Huang Yung-Hsin , Wei Yuning , Chen Lu , Chang Howard Y. , Artandi Steven E. 
Published: July 2024

AbstractTelomerase is intimately associated with stem cells and cancer, because it catalytically elongates telomeres—nucleoprotein caps that protect chromosome ends1. Overexpression of telomerase reverse transcriptase (TERT) enhances the proliferation of cells in a telomere-independent manner2–8, but so far, loss-of-function studies have provided no evidence that TERT has a direct role in stem cell function. In many tissues, homeostasis is shaped by stem cell competition, a process in which stem cells compete on the basis of inherent fitness. Here we show that conditional deletion of Tert in the spermatogonial stem cell (SSC)-containing population in mice markedly impairs competitive clone formation. Using lineage tracing from the Tert locus, we find that TERT-expressing SSCs yield long-lived clones, but that clonal inactivation of TERT promotes stem cell differentiation and a genome-wide reduction in open chromatin. This role for TERT in competitive clone formation occurs independently of both its reverse transcriptase activity and the canonical telomerase complex. Inactivation of TERT causes reduced activity of the MYC oncogene, and transgenic expression of MYC in the TERT-deleted pool of SSCs efficiently rescues clone formation. Together, these data reveal a catalytic-activity-independent requirement for TERT in enhancing stem cell competition, uncover a genetic connection between TERT and MYC and suggest that a selective advantage for stem cells with high levels of TERT contributes to telomere elongation in the male germline during homeostasis and ageing.
Inhibition of IL-11 signalling extends mammalian healthspan and lifespan
Authors: Widjaja Anissa A. , Lim Wei-Wen , Viswanathan Sivakumar , Chothani Sonia , Corden Ben , Dasan Cibi Mary , Goh Joyce Wei Ting , Lim Radiance , Singh Brijesh K. , Tan Jessie , Pua Chee Jian , Lim Sze Yun , Adami Eleonora , Schafer Sebastian , George Benjamin L. , Sweeney Mark , Xie Chen , Tripathi Madhulika , Sims Natalie A. , Hübner Norbert , Petretto Enrico , Withers Dominic J. , Ho Lena , Gil Jesus , Carling David , Cook Stuart A. 
Published: July 2024

AbstractFor healthspan and lifespan, ERK, AMPK and mTORC1 represent critical pathways and inflammation is a centrally important hallmark1–7. Here we examined whether IL-11, a pro-inflammatory cytokine of the IL-6 family, has a negative effect on age-associated disease and lifespan. As mice age, IL-11 is upregulated across cell types and tissues to regulate an ERK–AMPK–mTORC1 axis to modulate cellular, tissue- and organismal-level ageing pathologies. Deletion of Il11 or Il11ra1 protects against metabolic decline, multi-morbidity and frailty in old age. Administration of anti-IL-11 to 75-week-old mice for 25 weeks improves metabolism and muscle function, and reduces ageing biomarkers and frailty across sexes. In lifespan studies, genetic deletion of Il11 extended the lives of mice of both sexes, by 24.9% on average. Treatment with anti-IL-11 from 75 weeks of age until death extends the median lifespan of male mice by 22.5% and of female mice by 25%. Together, these results demonstrate a role for the pro-inflammatory factor IL-11 in mammalian healthspan and lifespan. We suggest that anti-IL-11 therapy, which is currently in early-stage clinical trials for fibrotic lung disease, may provide a translational opportunity to determine the effects of IL-11 inhibition on ageing pathologies in older people.
Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer
Authors: Zhao Shuang G. , Bootsma Matthew , Zhou Stanley , Shrestha Raunak , Moreno-Rodriguez Thaidy , Lundberg Arian , Pan Chu , Arlidge Christopher , Hawley James R. , Foye Adam , Weinstein Alana S. , Sjöström Martin , Zhang Meng , Li Haolong , Chesner Lisa N. , Rydzewski Nicholas R. , Helzer Kyle T. , Shi Yue ,   West Coast Dream Team Consortium, Bailey Adina M. , Zhang Li , Beer Tomasz M. , Thomas George , Chi Kim N. , Gleave Martin , Zoubeidi Amina , Reiter Robert E. , Rettig Matthew B. , Witte Owen , Bose Rohit , Huang Franklin W. , Fong Larry , Lara Primo N. , Evans Christopher P. , Huang Jiaoti , Lynch Molly , Dehm Scott M. , Lang Joshua M. , Alumkal Joshi J. , He Hansen H. , Wyatt Alexander W. , Aggarwal Rahul , Zwart Wilbert , Small Eric J. , Quigley David A. , Lupien Mathieu , Feng Felix Y. 
Published: July 2024

AbstractThe impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2–ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.
Streamflow in the United States: Characteristics, trends, regime shifts, and extremes
Authors: Wang Yiming , Zhang Xuesong , Zhao Kaiguang , Singh Debjani 
Published: July 2024

AbstractLong-term streamflow observations contain essential information for understanding hydrological changes and managing water resources. A continental-scale dataset or analysis of temporal streamflow change is still lacking across hydrologic gauges in the Conterminous United States (CONUS). Here, we compiled 70 years of streamflow records from 1951 to 2021 at ~ 8000 hydrologic stations across the CONUS and characterized temporal trends, regime shifts, and extreme events using a Bayesian time series analysis algorithm. We found that the occurrences of sudden streamflow changes (e.g., regime shifts and extreme events) have been increasing with time across the CONUS. In addition, we derived 181 streamflow indicators that are valuable for hydrological and biological applications, such as the duration and frequency of high or low streamflow events. The Mississippi River Basin, especially the middle and lower parts, was a hot spot of high-frequency high-flow events. Overall, we anticipate the dataset generated here offers valuable information for understanding and quantifying changes in water resources across the CONUS.
Optimizing decision-making with aggregation operators for generalized intuitionistic fuzzy sets and their applications in the tech industry
Authors: Wasim Muhammad , Yousaf Awais , Alolaiyan Hanan , Akbar Muhammad Azeem , Alburaikan Alhanouf , El-Wahed Khalifa Hamiden Abd 
Published: July 2024

AbstractIntuitionistic fuzzy sets (IFSs) represent a significant advancement in classical fuzzy set (FS) theory. This study advances IFS theory to generalized intuitionistic fuzzy sets (GIFSBs) and introduces novel operators GIFWAA, GIFWGA, GIFOWAA, and GIFOWGA, tailored for GIFSBs. The primary aim is to enhance decision-making capabilities by introducing aggregation operators within the GIFSB framework that align with preferences for optimal outcomes. The article introduces new operators for GIFSBs characterized by attributes like idempotency, boundedness, monotonicity and commutativity, resulting in aggregated values aligned with GIFNs. A comprehensive analysis of the relationships among these operations is conducted, offering a thorough understanding of their applicability. These operators are practically demonstrated in a multiple-criteria decision-making process for evaluating startup success in the Tech Industry.
Delivery of CDNF by AAV-mediated gene transfer protects dopamine neurons and regulates ER stress and inflammation in an acute MPTP mouse model of Parkinson’s disease
Authors: Nam Jinhan , Richie Christopher T. , Harvey Brandon K. , Voutilainen Merja H. 
Published: July 2024

AbstractCerebral dopamine neurotrophic factor (CDNF) and its close structural relative, mesencephalic astrocyte-derived neurotrophic factor (MANF), are proteins with neurotrophic properties. CDNF protects and restores the function of dopamine (DA) neurons in rodent and non-human primate (NHP) toxin models of Parkinson’s disease (PD) and therefore shows promise as a drug candidate for disease-modifying treatment of PD. Moreover, CDNF was found to be safe and to have some therapeutic effects on PD patients in phase 1/2 clinical trials. However, the mechanism underlying the neurotrophic activity of CDNF is unknown. In this study, we delivered human CDNF (hCDNF) to the brain using an adeno-associated viral (AAV) vector and demonstrated the neurotrophic effect of AAV-hCDNF in an acute 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. AAV-hCDNF resulted in the expression of hCDNF in the striatum (STR) and substantia nigra (SN), and no toxic effects on the nigrostriatal pathway were observed. Intrastriatal injection of AAV-hCDNF reduced motor impairment and partially alleviated gait dysfunction in the acute MPTP mouse model. In addition, gene therapy with AAV-hCDNF had significant neuroprotective effects on the nigrostriatal pathway and decreased the levels of interleukin 1beta (IL-1β) and complement 3 (C3) in glial cells in the acute MPTP mouse model. Moreover, AAV-hCDNF reduced C/EBP homologous protein (CHOP) and glucose regulatory protein 78 (GRP78) expression in astroglia. These results suggest that the neuroprotective effects of CDNF may be mediated at least in part through the regulation of neuroinflammation and the UPR pathway in a mouse MPTP model of PD in vivo.
Impact of the digital economy on carbon dioxide emissions in resource-based cities
Authors: Kuang Yiming , Fan Yaojun , Bin Jie , Fan Min 
Published: July 2024

AbstractWith the rapid development of the digital economy, its environmental impact, particularly on carbon dioxide emissions in resource-based cities, has emerged as a vital research topic. Resource-based cities, often central to traditional industries, are confronted with the dual challenges of environmental pollution and economic transformation. This study employs empirical analysis to examine the influence of the digital economy on carbon dioxide emissions in these cities. The findings reveal that the digital economy significantly reduces carbon dioxide emissions, with this impact being more pronounced in the early stages of digital economic development and gradually diminishing thereafter. In the mechanism analysis, we found that the digital economy can reduce carbon dioxide emissions in resource-based cities by raising public concern about the environment. Moreover, the study highlights significant variations in carbon reduction effects among different types of resource-based cities, noting that stronger environmental regulations further enhance these effects. These insights not only provide a new theoretical perspective but also offer practical guidance for policymakers in promoting sustainable development within the digital economy.
Kiwifruit-Agaricus blazei intercropping effectively improved yield productivity, nutrient uptake, and rhizospheric bacterial community
Authors: Shen Chuan , Li Xia , Qin Jianfeng 
Published: July 2024

AbstractIntercropping systems have garnered attention as a sustainable agricultural approach for efficient land use, increased ecological diversity in farmland, and enhanced crop yields. This study examined the effect of intercropping on the kiwifruit rhizosphere to gain a deeper understanding of the relationships between cover plants and kiwifruit in this sustainable agricultural system. Soil physicochemical properties and bacterial communities were analyzed using the Kiwifruit-Agaricus blazei intercropping System. Moreover, a combined analysis of 16S rRNA gene sequencing and metabolomic sequencing was used to identify differential microbes and metabolites in the rhizosphere. Intercropping led to an increase in soil physicochemical and enzyme activity, as well as re-shaping the bacterial community and increasing microbial diversity. Proteobacteria, Bacteroidota, Myxococcota, and Patescibacteria were the most abundant and diverse phyla in the intercropping system. Expression analysis further revealed that the bacterial genera BIrii41, Acidibacter, and Altererythrobacter were significantly upregulated in the intercropping system. Moreover, 358 differential metabolites (DMs) were identified between the monocropping and intercropping cultivation patterns, with fatty acyls, carboxylic acids and derivatives, and organooxygen compounds being significantly upregulated in the intercropping system. The KEGG metabolic pathways further revealed considerable enrichment of DMs in ABC transporters, histidine metabolism, and pyrimidine metabolism. This study identified a significant correlation between 95 bacterial genera and 79 soil metabolites, and an interactive network was constructed to explore the relationships between these differential microbes and metabolites in the rhizosphere. This study demonstrated that Kiwifruit-Agaricus blazei intercropping can be an effective, labor-saving, economic, and sustainable practice for reshaping bacterial communities and promoting the accumulation and metabolism of beneficial microorganisms in the rhizosphere.
Catalytic reduction of toxic dyes over nickel oxide nanoparticles supported on CMK-3 catalyst
Authors: Younus Mohammed M. , Sayed M. A. , El Saied Mohamed , El Naga Ahmed O. Abo 
Published: July 2024

AbstractIn the current paper, a NiO nanoparticles-loaded mesoporous carbon (CMK-3) catalyst, denoted as NiO/CMK-3, has been successfully synthesized using a facile strategy. The as-prepared material has been characterized through XRD, Raman spectroscopy, low-temperature N2 physisorption measurements, FTIR, FE-SEM, TEM, and XPS. The as-fabricated NiO/CMK-3 catalyst manifested a superior activity in the NaBH4-assisted reduction of methylene blue (MB) dye to its colorless leuco form. Remarkably, over 99% of 25 mg L−1 MB was reduced by 7.5 mM/L NaBH4 using 0.1 g L−1 NiO/CMK-3 within 3 min at room temperature. Furthermore, the kinetics study confirmed the appropriateness of the pseudo-first-order kinetic model for elucidating the kinetics of MB reduction by the catalyst. Importantly, the NiO/CMK-3 catalyst maintained almost constant catalytic activity even after 5 times of reuse in MB reduction, demonstrating its superior stability and reusable ability. So, NiO/CMK-5 appears as a promising heterogeneous catalyst for the effective remediation of dye-containing wastewater.
Boosting piezoelectric properties of PVDF nanofibers via embedded graphene oxide nanosheets
Authors: Salama Mahmoud , Hamed Aya , Noman Sara , Magdy Germein , Shehata Nader , Kandas Ishac 
Published: July 2024

AbstractTremendous research efforts have been directed toward developing polymer-based piezoelectric nanogenerators (PENG) in a promising step to investigate self-charging powered systems (SCPSs) and consequently, support the need for flexible, intelligent, and ultra-compact wearable electronic devices. In our work, electrospun polyvinylidene fluoride (PVDF) nanofiber mats were investigated while graphene oxide (GO) was added with different concentrations (from 0 to 3 wt.%). Sonication treatment was introduced for 5 min to GO nanosheets before combined PVDF solution. A comprehensive study was conducted to examine the GO incremental effect. Microstructural and mechanical properties were examined using a scanning electron microscope (SEM) and a texture analyzer. Moreover, piezoelectric properties were assessed via various tests including impulse response, frequency effect, d33 coefficient, charging and discharging analysis, and sawyer tower circuit. Experimental results indicate that incorporation of GO nanosheets enhances piezoelectric properties for all concentrations, which was linked to the increase in β phase inside the nanofibers, which has a significant potential of enhancing nanogenerator performance. PVDF-GO 1.5 wt.% shows a notably higher enhancing effect where the electroactive β-phase and γ-phase are recorded to be boosted to ~ 68.13%, as well as piezoelectric coefficient (d33 ~ 55.57 pC/N). Furthermore, increasing impact force encouraged the output voltage. Also noted that the delivered open circuit voltage is ~ 3671 V/g and the power density is ~ 150 µw/cm2. It was observed that GO of concentration 1.5 wt.% recorded a conversion efficiency of ~ 74.73%. All results are in line, showing better performance for PVDF-GO 1.5 wt.% for almost all concentrations.