bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes
Authors: Rönn Tina , Ofori Jones K. , Perfilyev Alexander , Hamilton Alexander , Pircs Karolina , Eichelmann Fabian , Garcia-Calzon Sonia , Karagiannopoulos Alexandros , Stenlund Hans , Wendt Anna , Volkov Petr , Schulze Matthias B. , Mulder Hindrik , Eliasson Lena , Ruhrmann Sabrina , Bacos Karl , Ling Charlotte 
Published: December 2023

AbstractEpigenetic dysregulation may influence disease progression. Here we explore whether epigenetic alterations in human pancreatic islets impact insulin secretion and type 2 diabetes (T2D). In islets, 5,584 DNA methylation sites exhibit alterations in T2D cases versus controls and are associated with HbA1c in individuals not diagnosed with T2D. T2D-associated methylation changes are found in enhancers and regions bound by β-cell-specific transcription factors and associated with reduced expression of e.g. CABLES1, FOXP1, GABRA2, GLR1A, RHOT1, and TBC1D4. We find RHOT1 (MIRO1) to be a key regulator of insulin secretion in human islets. Rhot1-deficiency in β-cells leads to reduced insulin secretion, ATP/ADP ratio, mitochondrial mass, Ca2+, and respiration. Regulators of mitochondrial dynamics and metabolites, including L-proline, glycine, GABA, and carnitines, are altered in Rhot1-deficient β-cells. Islets from diabetic GK rats present Rhot1-deficiency. Finally, RHOT1methylation in blood is associated with future T2D. Together, individuals with T2D exhibit epigenetic alterations linked to mitochondrial dysfunction in pancreatic islets.
A microscopic Kondo lattice model for the heavy fermion antiferromagnet CeIn3
Authors: Simeth W. , Wang Z. , Ghioldi E. A. , Fobes D. M. , Podlesnyak A. , Sung N. H. , Bauer E. D. , Lass J. , Flury S. , Vonka J. , Mazzone D. G. , Niedermayer C. , Nomura Yusuke , Arita Ryotaro , Batista C. D. , Ronning F. , Janoschek M. 
Published: December 2023

AbstractElectrons at the border of localization generate exotic states of matter across all classes of strongly correlated electron materials and many other quantum materials with emergent functionality. Heavy electron metals are a model example, in which magnetic interactions arise from the opposing limits of localized and itinerant electrons. This remarkable duality is intimately related to the emergence of a plethora of novel quantum matter states such as unconventional superconductivity, electronic-nematic states, hidden order and most recently topological states of matter such as topological Kondo insulators and Kondo semimetals and putative chiral superconductors. The outstanding challenge is that the archetypal Kondo lattice model that captures the underlying electronic dichotomy is notoriously difficult to solve for real materials. Here we show, using the prototypical strongly-correlated antiferromagnet CeIn3, that a multi-orbital periodic Anderson model embedded with input from ab initio bandstructure calculations can be reduced to a simple Kondo-Heisenberg model, which captures the magnetic interactions quantitatively. We validate this tractable Hamiltonian via high-resolution neutron spectroscopy that reproduces accurately the magnetic soft modes in CeIn3, which are believed to mediate unconventional superconductivity. Our study paves the way for a quantitative understanding of metallic quantum states such as unconventional superconductivity.
Single-photon microscopy to study biomolecular condensates
Authors: Perego Eleonora , Zappone Sabrina , Castagnetti Francesco , Mariani Davide , Vitiello Erika , Rupert Jakob , Zacco Elsa , Tartaglia Gian Gaetano , Bozzoni Irene , Slenders Eli , Vicidomini Giuseppe 
Published: December 2023

AbstractBiomolecular condensates serve as membrane-less compartments within cells, concentrating proteins and nucleic acids to facilitate precise spatial and temporal orchestration of various biological processes. The diversity of these processes and the substantial variability in condensate characteristics present a formidable challenge for quantifying their molecular dynamics, surpassing the capabilities of conventional microscopy. Here, we show that our single-photon microscope provides a comprehensive live-cell spectroscopy and imaging framework for investigating biomolecular condensation. Leveraging a single-photon detector array, single-photon microscopy enhances the potential of quantitative confocal microscopy by providing access to fluorescence signals at the single-photon level. Our platform incorporates photon spatiotemporal tagging, which allowed us to perform time-lapse super-resolved imaging for molecular sub-diffraction environment organization with simultaneous monitoring of molecular mobility, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. This integrated correlative study reveals the dynamics and interactions of RNA-binding proteins involved in forming stress granules, a specific type of biomolecular condensates, across a wide range of spatial and temporal scales. Our versatile framework opens up avenues for exploring a broad spectrum of biomolecular processes beyond the formation of membrane-less organelles.
Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
Authors: Zhang Hao , Jin Zhiyuan , Cui Fa , Zhao Long , Zhang Xiaoyu , Chen Jinchao , Zhang Jing , Li Yanyan , Li Yongpeng , Niu Yanxiao , Zhang Wenli , Gao Caixia , Fu Xiangdong , Tong Yiping , Wang Lei , Ling Hong-Qing , Li Junming , Xiao Jun 
Published: December 2023

AbstractThe breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Authors: Saghaï Aurélien , Pold Grace , Jones Christopher M. , Hallin Sara 
Published: December 2023

AbstractNitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes fornrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments ofnrfA, onrand denitrification nitrite reductase genes (nirK,nirS) in 1861 global terrestrial metagenomes.nrfAoutnumbers the nearly negligibleonrcounts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N onnrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.
Enhanced glacial lake activity threatens numerous communities and infrastructure in the Third Pole
Authors: Zhang Taigang , Wang Weicai , An Baosheng , Wei Lele 
Published: December 2023

AbstractGlacial lake outburst floods (GLOFs) are among the most severe cryospheric hazards in the Third Pole, encompassing the Tibetan Plateau and surrounding Himalayas, Hindu Kush, and Tianshan Mountains. Recent studies on glacial lake changes and GLOF characteristics and risks in this region have shown scattered and insufficiently detailed features. Here, we conduct an appraisal of the GLOF risks by combining high-resolution satellite images, case-by-case high-precision GLOF modeling, and detailed downstream exposure data. The glacial lake changes from 2018 to 2022 in the region were primarily driven by the accelerated expansion of proglacial lakes. The GLOF frequency has exhibited a significant increasing trend since 1980, with intensified activity in Southeastern Tibet and the China-Nepal border area over the past decade. Approximately 6,353 km2 of land could be at risk from potential GLOFs, posing threats to 55,808 buildings, 105 hydropower projects, 194 km2 of farmland, 5,005 km of roads, and 4,038 bridges. This study directly responds to the need for local disaster prevention and mitigation strategies, highlighting the urgent requirement of reducing GLOF threats in the Third Pole and the importance of regional cooperation.
Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies
Authors: Xu Xi-wen , Sun Pengchuan , Gao Chengbin , Zheng Weiwei , Chen Songlin 
Published: December 2023

AbstractThe assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a young sex chromosome and showed signs of expansion in repetitive sequences. The major component of the expansion was Ty3/Gypsy. The ancestral Osteichthyes karyotype consists of 24 protochromosomes. The sex chromosomes in four Pleuronectiformes species derived from a pair of homologous protochromosomes resulting from a whole-genome duplication event in teleost fish, yet with different sex-determination systems. V. variegatus and Cynoglossus semilaevis adhere to the ZZ/ZW system, while Hippoglossus stenolepis and H. hippoglossus follow the XX/XY system. Interestingly, V. variegatus and H. hippoglossus derived from one protochromosome, while C. semilaevis and H. stenolepis derived from another protochromosome. Our study provides valuable insights into the evolution of sex chromosomes in flatfish and sheds light on the important role of whole-genome duplication in shaping the evolution of sex chromosomes.
Sugar feeding by invasive mosquito species on ornamental and wild plants
Authors: Upshur Irving Forde , Fehlman Mikhyle , Parikh Vansh , Vinauger Clément , Lahondère Chloé 
Published: December 2023

AbstractFeeding on plant-derived sugars is an essential component of mosquito biology, affecting key aspects of their lives such as survival, metabolism, and reproduction. Among mosquitoes, Aedes aegypti and Aedes albopictus are two invasive mosquito species in the US, and are vectors of diseases such as dengue fever, chikungunya, and Zika. These species live in heavily populated, urban areas, where they have high accessibility to human hosts as well as to plants in backyards and public landscapes. However, the range of plants that are suitable sugar hosts for these species remains to be described, despite the importance of understanding what plants may attract or repel mosquitoes to inform citizens and municipal authorities accordingly. Here, we tested whether Ae. aegypti and Ae. albopictus would sugar-feed on eleven commonly planted ornamental plant species. We confirmed feeding activity using the anthrone method and identified the volatile composition of plant headspace using gas-chromatography mass-spectroscopy. These chemical analyses revealed that a broad range of olfactory cues are associated with plants that mosquitoes feed on. This prompted us to use plant DNA barcoding to identify plants that field-caught mosquitoes feed on. Altogether, results show that native and invasive mosquito species can exploit a broader range of plants than originally suspected, including wild and ornamental plants from different phyla throughout the Spring, Summer and Fall seasons.
Learning exceptions to category rules varies across the menstrual cycle
Authors: Perović Mateja , Heffernan Emily M. , Einstein Gillian , Mack Michael L. 
Published: December 2023

AbstractWays in which ovarian hormones affect cognition have been long overlooked despite strong evidence of their effects on the brain. To address this gap, we study performance on a rule-plus-exception category learning task, a complex task that requires careful coordination of core cognitive mechanisms, across the menstrual cycle (N = 171). Results show that the menstrual cycle distinctly affects exception learning in a manner that parallels the typical rise and fall of estradiol across the cycle. Participants in their high estradiol phase outperform participants in their low estradiol phase and demonstrate more rapid learning of exceptions than a male comparison group. A likely mechanism underlying this effect is estradiol’s impact on pattern separation and completion pathways in the hippocampus. These results provide novel evidence for the effects of the menstrual cycle on category learning, and underscore the importance of considering female sex-related variables in cognitive neuroscience research.
Multimodal photoacoustic microscopy, optical coherence tomography, and fluorescence imaging of USH2A knockout rabbits
Authors: Nguyen Van Phuc , Hu Justin , Zhe Josh , Chen Eugene Y. , Yang Dongshan , Paulus Yannis M. 
Published: December 2023

AbstractUsher syndrome type 2A (USH2A) is a genetic disorder characterized by retinal degeneration and hearing loss. To better understand the pathogenesis and progression of this syndrome, animal models such as USH2A knockout (USH2AKO) rabbits have been developed. In this study, we employed multimodal imaging techniques, including photoacoustic microscopy (PAM), optical coherence tomography (OCT), fundus autofluorescence (FAF), fluorescein angiography (FA), and indocyanine green angiography (ICGA) imaging to evaluate the retinal changes in the USH2AKO rabbit model. Twelve New Zealand White rabbits including USH2AKO and wild type (WT) were used for the experiments. Multimodal imaging was implemented at different time points over a period of 12 months to visualize the progression of retinal changes in USH2AKO rabbits. The results demonstrate that ellipsoid zone (EZ) disruption and degeneration, key features of Usher syndrome, began at the age of 4 months old and persisted up to 12 months. The EZ degeneration areas were clearly observed on the FAF and OCT images. The FAF images revealed retinal pigment epithelium (RPE) degeneration, confirming the presence of the disease phenotype in the USH2AKO rabbits. In addition, PAM images provided high-resolution and high image contrast of the optic nerve and the retinal microvasculature, including retinal vessels, choroidal vessels, and capillaries in three-dimensions. The quantification of EZ fluorescent intensity using FAF and EZ thickness using OCT provided comprehensive quantitative data on the progression of degenerative changes over time. This multimodal imaging approach allowed for a comprehensive and non-invasive assessment of retinal structure, microvasculature, and degenerative changes in the USH2AKO rabbit model. The combination of PAM, OCT, and fluorescent imaging facilitated longitudinal monitoring of disease progression and provided valuable insights into the pathophysiology of USH2A syndrome. These findings contribute to the understanding of USH2A syndrome and may have implications for the development of diagnostic and therapeutic strategies for affected individuals. The multimodal imaging techniques employed in this study offer a promising platform for preclinical evaluation of potential treatments and may pave the way for future clinical applications in patients with Usher syndrome.
Research on coordination of the NEV battery closed-loop supply chain considering CSR and fairness concerns in third-party recycling models
Authors: Zhang Zhenfang , Liang Huan 
Published: December 2023

AbstractDue to the pressure of the ecological environment and government, it is incumbent for enterprises to undertake corporate social responsibility (CSR). However, during the recycling process, awareness of equity concerns due to the distribution of benefits among members has intensified, and it is crucial to resolve channel conflicts and design a reasonable cooperation model to recycle used power batteries. Therefore, this paper constructs a closed-loop supply chain composed of power battery manufacturer, retailer and third-party collector based on the consideration of cascade utilization, in order to study the impact of the level of CSR and the degree of fairness concern on the decision-making of channel participants. Our research shows that: (1) Fairness concern behavior adversely affects the supply chain, which raises the sales price and reduces the collecting rate and the utility of the supply chain as a whole. (2) Undertaking CSR is beneficial to the development of the power battery market, and also helps to reduce the sense of unfairness among third-party recycling companies. (3) The cost-sharing contract effectively coordinates the distribution of supply chain benefits and improves the recycling rate. Finally, we further verify the correctness of the conclusions through numerical studies.
Sustainable oil palm trunk fibre based activated carbon for the adsorption of methylene blue
Authors: Gayathiri Muniandy , Pulingam Thiruchelvi , Lee K. T. , Mohd Din Azam Taufik , Kosugi Akihiko , Sudesh Kumar 
Published: December 2023

AbstractActivated carbon (AC) is becoming the limelight due to its widespread application as an adsorbent for wastewater treatment, gases, and catalysis. However, its high consumption and price have drawn more attention to the sustainable use of natural resources as precursor for AC production. This study focuses on synthesising AC from two types of oil palm trunk (OPT) fibres, a significant agricultural waste products produced by Malaysia's thriving palm oil industries. The BET surface area of about 2057.9 m2 g−1 was achieved by chemical activation with phosphoric acid (H3PO4). The efficiency of the synthesised AC was critically analysed based on the adsorption experiments with methylene blue (MB) by varying several parameters (dosage of adsorbent, pH, initial dye concentration, and temperature of the solution) to elucidate the adsorption mechanism(s). A maximum adsorption capacity of 320.4 mg g−1 at 50 °C was achieved, and the Temkin (r2 = 0.98, 0.95, 0.95) and Langmuir (r2 = 0.94, 0.93, 0.95) isotherm models fitted the adsorption process better than the Freundlich (r2 = 0.95, 0.90, 0.86) model. Besides, the pseudo-second-order model (r2 > 0.90) best described the adsorption process, favouring chemisorption over physisorption. Thermodynamics showed MB adsorption on AC was spontaneous except at the highest dye concentration. It was exothermic at lower dye concentrations (50 and 100 mg L−1) and endothermic at higher ones (300, 500, and 700 mg L−1). In a nutshell, this study reveals that OPT fibre is a promising precursor for synthesising highly porous AC for the adsorption of MB dye.
Predicting others’ actions from their social contexts
Authors: Azaad Shaheed , Sebanz Natalie 
Published: December 2023

AbstractContextual cues have been shown to inform our understanding and predictions of others’ actions. In this study, we tested whether observers’ predictions about unfolding actions depend upon the social context in which they occur. Across five experiments, we showed participants videos of an actor walking toward a piece of furniture either with (joint context) or without (solo context) a partner standing by it. We found greater predictive bias, indicative of stronger action expectations when videos contained a second actor (Experiment 1), even when the solo condition had a perceptually-matched control object in place of the actor (Experiment 2). Critically, belief manipulations about the actions the walking actor would perform suppressed the difference between social context conditions when the manipulation specified an action possible in both contexts (Experiment 5) but not when the action was one that would be difficult without a partner (Experiment 4). Interestingly, the social context effect persisted when the belief manipulation specified an unlikely action given the depicted scene (Experiment 3). These findings provide novel evidence that kinematically-identical actions can elicit different predictions depending on the social context in which they occur.
Smart home energy management and power trading optimization using an enhanced manta ray foraging optimization
Authors: Youssef Heba , Kamel Salah , Hassan Mohamed H. 
Published: December 2023

AbstractThis paper proposes a plan to manage energy consumption in residential areas using the demand response method, which allows electricity users to contribute to the reliability of the power system by controlling their usage. Due to the growing population, the residential sector consumes a significant amount of energy, and the objectives of this study are to lower electricity costs and the peak to average ratio, as well as reduce the amount of imported electricity from the grid. The study aims to maximize profit by properly utilizing renewable energy sources and addressing energy trading. The manta ray foraging optimization (MRFO) and long term memory MRFO (LMMRFO) algorithms are used to solve this problem. Firstly, the validation of the proposed LMMRFO technique is confirmed by seven benchmark functions and compared its results with the results of the well-known optimization algorithms including hunter prey optimization, gorilla troops optimizer, beluga whale optimization, and the original MRFO algorithm. Then, the performance of the LMMRFO is checked on the optimization of smart home energy management. In the suggested approach, a smart home decides whether to purchase or sell electricity from the commercial grid based on the cost, demand, and production of electricity from its own microgrid, which consists of a wind turbine and solar panels. Energy storage systems support the stable and dependable functioning of the power system since the solar panel and wind turbine only occasionally produce electricity. Through various case studies, the proposed plan is tested and found to be effective in reducing electricity costs and the peak to average ratio while maximizing profit. Furthermore, a comparative study is conducted to demonstrate the legality and effectiveness of LMMRFO and MRFO.