bluuebunny/crossref_metadata_2025_split huggingface dataset:
The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes
Authors: Ruppelt Dominik , Trollmann Marius F. W. , Dema Taulant , Wirtz Sebastian N. , Flegel Hendrik , Mönnikes Sophia , Grond Stephanie , Böckmann Rainer A. , Steinem Claudia 
Published: April 2024

AbstractRecently, a novel cyclo-heptapeptide composed of alternating d,l-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential. However, the precise mode of action of this new class of fibupeptides remains largely elusive. Here, we disclose the mechanism by which lugdunin rapidly destabilizes the bacterial membrane potential using an in vitro approach. The peptide strongly partitions into lipid compositions resembling Gram-positive bacterial membranes but less in those harboring the eukaryotic membrane component cholesterol. Upon insertion, lugdunin forms hydrogen-bonded antiparallel β-sheets by the formation of peptide nanotubes, as demonstrated by ATR-FTIR spectroscopy and molecular dynamics simulations. These hydrophilic nanotubes filled with a water wire facilitate not only the translocation of protons but also of monovalent cations as demonstrated by voltage-clamp experiments on black lipid membranes. Collectively, our results provide evidence that the natural fibupeptide lugdunin acts as a peptidic channel that is spontaneously formed by an intricate stacking mechanism, leading to the dissipation of a bacterial cell’s membrane potential.
Quantum annealing of a frustrated magnet
Authors: Zhao Yuqian , Ma Zhaohua , He Zhangzhen , Liao Haijun , Wang Yan-Cheng , Wang Junfeng , Li Yuesheng 
Published: April 2024

AbstractQuantum annealing, which involves quantum tunnelling among possible solutions, has state-of-the-art applications not only in quickly finding the lowest-energy configuration of a complex system, but also in quantum computing. Here we report a single-crystal study of the frustrated magnet α-CoV2O6, consisting of a triangular arrangement of ferromagnetic Ising spin chains without evident structural disorder. We observe quantum annealing phenomena resulting from time-reversal symmetry breaking in a tiny transverse field. Below ~ 1 K, the system exhibits no indication of approaching the lowest-energy state for at least 15 hours in zero transverse field, but quickly converges towards that configuration with a nearly temperature-independent relaxation time of ~ 10 seconds in a transverse field of ~ 3.5 mK. Our many-body simulations show qualitative agreement with the experimental results, and suggest that a tiny transverse field can profoundly enhance quantum spin fluctuations, triggering rapid quantum annealing process from topological metastable Kosterlitz-Thouless phases, at low temperatures.
BIN1 knockdown rescues systolic dysfunction in aging male mouse hearts
Authors: Westhoff Maartje , del Villar Silvia G. , Voelker Taylor L. , Thai Phung N. , Spooner Heather C. , Costa Alexandre D. , Sirish Padmini , Chiamvimonvat Nipavan , Dickson Eamonn J. , Dixon Rose E. 
Published: April 2024

AbstractCardiac dysfunction is a hallmark of aging in humans and mice. Here we report that a two-week treatment to restore youthful Bridging Integrator 1 (BIN1) levels in the hearts of 24-month-old mice rejuvenates cardiac function and substantially reverses the aging phenotype. Our data indicate that age-associated overexpression of BIN1 occurs alongside dysregulated endosomal recycling and disrupted trafficking of cardiac CaV1.2 and type 2 ryanodine receptors. These deficiencies affect channel function at rest and their upregulation during acute stress. In vivo echocardiography reveals reduced systolic function in old mice. BIN1 knockdown using an adeno-associated virus serotype 9 packaged shRNA-mBIN1 restores the nanoscale distribution and clustering plasticity of ryanodine receptors and recovers Ca2+ transient amplitudes and cardiac systolic function toward youthful levels. Enhanced systolic function correlates with increased phosphorylation of the myofilament protein cardiac myosin binding protein-C. These results reveal BIN1 knockdown as a novel therapeutic strategy to rejuvenate the aging myocardium.
Planar thermal Hall effect from phonons in a Kitaev candidate material
Authors: Chen Lu , Lefrançois Étienne , Vallipuram Ashvini , Barthélemy Quentin , Ataei Amirreza , Yao Weiliang , Li Yuan , Taillefer Louis 
Published: April 2024

AbstractThe thermal Hall effect has emerged as a potential probe of exotic excitations in spin liquids. In the Kitaev magnet $${{\alpha }}$$
α
-RuCl3, the thermal Hall conductivity $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

has been attributed to Majorana fermions, chiral magnons, or phonons. Theoretically, the former two types of heat carriers can generate a “planar” $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

, whereby the magnetic field is parallel to the heat current, but it is unknown whether phonons also could. Here we show that a planar $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

is present in another Kitaev candidate material, Na2Co2TeO6. Based on the striking similarity between $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

and the phonon-dominated thermal conductivity $${{{\kappa }}}_{{{xx}}}$$

κ

x
x

, we attribute the effect to phonons. We observe a large difference in $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

between different configurations of heat current and magnetic field, which reveals that the direction of heat current matters in determining the planar $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

. Our observation calls for a re-evaluation of the planar $${{{\kappa }}}_{{{xy}}}$$

κ

x
y

observed in$$\,{{\alpha }}$$

α
-RuCl3.
Ice sheet and precession controlled subarctic Pacific productivity and upwelling over the last 550,000 years
Authors: Yao Zhengquan , Shi Xuefa , Yin Qiuzhen , Jaccard Samuel , Liu Yanguang , Guo Zhengtang , Gorbarenko Sergey A. , Wang Kunshan , Chen Tianyu , Wu Zhipeng , Nan Qingyun , Zou Jianjun , Wang Hongmin , Cui Jingjing , Wang Anqi , Yang Gongxu , Zhu Aimei , Bosin Aleksandr , Vasilenko Yuriy , Yu Yonggui 
Published: April 2024

AbstractThe polar oceans play a vital role in regulating atmospheric CO2 concentrations (pCO2) during the Pleistocene glacial cycles. However, despite being the largest modern reservoir of respired carbon, the impact of the subarctic Pacific remains poorly understood due to limited records. Here, we present high-resolution, 230Th-normalized export productivity records from the subarctic northwestern Pacific covering the last five glacial cycles. Our records display pronounced, glacial-interglacial cyclicity superimposed with precessional-driven variability, with warm interglacial climate and high boreal summer insolation providing favorable conditions to sustain upwelling of nutrient-rich subsurface waters and hence increased export productivity. Our transient model simulations consistently show that ice sheets and to a lesser degree, precession are the main drivers that control the strength and latitudinal position of the westerlies. Enhanced upwelling of nutrient/carbon-rich water caused by the intensification and poleward migration of the northern westerlies during warmer climate intervals would have led to the release of previously sequestered CO2 from the subarctic Pacific to the atmosphere. Our results also highlight the significant role of the subarctic Pacific in modulating pCO2 changes during the Pleistocene climate cycles, especially on precession timescale ( ~ 20 kyr).
Sub-millisecond lithiothermal synthesis of graphitic meso–microporous carbon
Authors: Zhang Huimin , Qiu Jingyi , Pang Jie , Cao Gaoping , Zhang Bingsen , Wang Li , He Xiangming , Feng Xuning , Ma Shizhou , Zhang Xinggao , Ming Hai , Li Zhuangnan , Li Feng , Zhang Hao 
Published: April 2024

AbstractPorous carbons with concurrently high specific surface area and electronic conductivity are desirable by virtue of their desirable electron and ion transport ability, but conventional preparing methods suffer from either low yield or inferior quality carbons. Here we developed a lithiothermal approach to bottom–up synthesize highly meso–microporous graphitized carbon (MGC). The preparation can be finished in a few milliseconds by the self-propagating reaction between polytetrafluoroethylene powder and molten lithium (Li) metal, during which instant ultra-high temperature (>3000 K) was produced. This instantaneous carbon vaporization and condensation at ultra-high temperatures and in ultra-short duration enable the MGC to show a highly graphitized and continuously cross-coupled open pore structure. MGC displays superior electrochemical capacitor performance of exceptional power capability and ultralong-term cyclability. The processes used to make this carbon are readily scalable to industrial levels.
Control of polymers’ amorphous-crystalline transition enables miniaturization and multifunctional integration for hydrogel bioelectronics
Authors: Huang Sizhe , Liu Xinyue , Lin Shaoting , Glynn Christopher , Felix Kayla , Sahasrabudhe Atharva , Maley Collin , Xu Jingyi , Chen Weixuan , Hong Eunji , Crosby Alfred J. , Wang Qianbin , Rao Siyuan 
Published: April 2024

AbstractSoft bioelectronic devices exhibit motion-adaptive properties for neural interfaces to investigate complex neural circuits. Here, we develop a fabrication approach through the control of metamorphic polymers’ amorphous-crystalline transition to miniaturize and integrate multiple components into hydrogel bioelectronics. We attain an about 80% diameter reduction in chemically cross-linked polyvinyl alcohol hydrogel fibers in a fully hydrated state. This strategy allows regulation of hydrogel properties, including refractive index (1.37-1.40 at 480 nm), light transmission (>96%), stretchability (139-169%), bending stiffness (4.6 ± 1.4 N/m), and elastic modulus (2.8-9.3 MPa). To exploit the applications, we apply step-index hydrogel optical probes in the mouse ventral tegmental area, coupled with fiber photometry recordings and social behavioral assays. Additionally, we fabricate carbon nanotubes-PVA hydrogel microelectrodes by incorporating conductive nanomaterials in hydrogel for spontaneous neural activities recording. We enable simultaneous optogenetic stimulation and electrophysiological recordings of light-triggered neural activities in Channelrhodopsin-2 transgenic mice.
Extensive protein pyrophosphorylation revealed in human cell lines
Authors: Morgan Jeremy A. M. , Singh Arpita , Kurz Leonie , Nadler-Holly Michal , Ruwolt Max , Ganguli Shubhra , Sharma Sheenam , Penkert Martin , Krause Eberhard , Liu Fan , Bhandari Rashna , Fiedler Dorothea 
Published: April 2024

AbstractReversible protein phosphorylation is a central signaling mechanism in eukaryotes. Although mass-spectrometry-based phosphoproteomics has become routine, identification of non-canonical phosphorylation has remained a challenge. Here we report a tailored workflow to detect and reliably assign protein pyrophosphorylation in two human cell lines, providing, to our knowledge, the first direct evidence of endogenous protein pyrophosphorylation. We manually validated 148 pyrophosphosites across 71 human proteins, the most heavily pyrophosphorylated of which were the nucleolar proteins NOLC1 and TCOF1. Detection was consistent with previous biochemical evidence relating the installation of the modification to inositol pyrophosphates (PP-InsPs). When the biosynthesis of PP-InsPs was perturbed, proteins expressed in this background exhibited no signs of pyrophosphorylation. Disruption of PP-InsP biosynthesis also significantly reduced rDNA transcription, potentially by lowering pyrophosphorylation on regulatory proteins NOLC1, TCOF1 and UBF1. Overall, protein pyrophosphorylation emerges as an archetype of non-canonical phosphorylation and should be considered in future phosphoproteomic analyses.
Electrospray-assisted cryo-EM sample preparation to mitigate interfacial effects
Authors: Yang Zi , Fan Jingjin , Wang Jia , Fan Xiao , Ouyang Zheng , Wang Hong-Wei , Zhou Xiaoyu 
Published: April 2024

AbstractAddressing interfacial effects during specimen preparation in cryogenic electron microscopy remains challenging. Here we introduce ESI-cryoPrep, a specimen preparation method based on electrospray ionization in native mass spectrometry, designed to alleviate issues associated with protein denaturation or preferred orientation induced by macromolecule adsorption at interfaces. Through fine-tuning spraying parameters, we optimized protein integrity preservation and achieved the desired ice thickness for analyzing target macromolecules. With ESI-cryoPrep, we prepared high-quality cryo-specimens of five proteins and obtained three-dimensional reconstructions at near-atomic resolution. Our findings demonstrate that ESI-cryoPrep effectively confines macromolecules within the middle of the thin layer of amorphous ice, facilitating the preparation of blotting-free vitreous samples. The protective mechanism, characterized by the uneven distribution of charged biomolecules of varying sizes within charged droplets, prevents the adsorption of target biomolecules at air–water or graphene–water interfaces, thereby avoiding structural damage to the protein particles or the introduction of dominant orientation issues.
Potassium humate supplementation improves photosynthesis and agronomic and yield traits of foxtail millet
Authors: Shen Jie , Xiao Xiaolu , Zhong Dandan , Lian Huida 
Published: April 2024

AbstractFoxtail millet is a highly nutritious crop, which is widely cultivated in arid and semi-arid areas worldwide. Humic acid (HA), as a common plant growth regulator, is used as an organic fertilizer and feed additive in agricultural production. However, the impact of potassium humate KH on the photosynthetic rate and yield of foxtail millet has not yet been studied. We explored the effects of KH application on the morphology, photosynthetic ability, carbon and nitrogen metabolism, and yield of foxtail millet. A field experiment was performed using six concentrations of KH (0, 20, 40, 80, 160, and 320 kg ha−1) supplied foliarly at the booting stage in Zhangza 10 cultivar (a widely grown high-yield variety). The results showed that KH treatment increased growth, chlorophyll content (SPAD), photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs). In addition, soluble protein content, sugar content, and nitrate reductase activity increased in KH-treated plants. With increased KH concentration, the effects became more evident and the peak values of each factor were achieved at 80 kg ha−1. Photosynthetic rate showed significant correlation with SPAD, Tr, Gs, and soluble protein content, but was negatively correlated with intercellular CO2 concentration. Compared to that of the control, the yield of foxtail millet under the T2, T3, T4, and T5 (40, 80, 160, and 320 kg ha−1 of KH) treatments significantly increased by 6.0%, 12.7%, 10.5%, and 8.6%, respectively. Yield exhibited a significant positive correlation with Tr, Pn, and Gs. Overall, KH enhances photosynthetic rate and yield of foxtail millet, therefore it may be conducive to stable millet production. These findings may provide a theoretical basis for the green and efficient production of millet fields.
Tire mode shape categorization using Zernike annular moment and machine learning classification
Authors: Parthasarathy Sudharsan , Seo Junhyeon , Kapania Rakesh K. 
Published: April 2024

AbstractThis research proposes a framework for categorizing the radial tire mode shapes using machine learning (ML) based classification and feature recognition algorithms, advancing the development of a digital twin for tire performance analysis. Tire mode shape categorization is required to identify modal features in a specific frequency range to maximize driving performance and secure safety. However, the mode categorization work requires a lot of manual effort to interpret modes. Therefore, this study suggests an ML-based classification tool to replace the conventional categorization process with two primary objectives: (1) create a database by categorizing the tire mode shapes based on the identified features and (2) develop an ML-based surrogate model to classify the tire mode shapes without manual effort. The feature map of the tire mode shape is built with the Zernike annular moment descriptor (ZAMD). The mode shapes are categorized using the correlation value derived by the modal assurance criteria (MAC) with all ZAMD values for each tire mode shape and subsequently creating the appropriate labels. The decision tree, random forests, and XGBoost, the representative supervised-learning algorithms for classification, are implemented for surrogate model development. The best-performed classifier can categorize the mode shapes without any manual effort with a high accuracy of 99.5%.
Automatic brain-tumor diagnosis using cascaded deep convolutional neural networks with symmetric U-Net and asymmetric residual-blocks
Authors: Abd-Ellah Mahmoud Khaled , Awad Ali Ismail , Khalaf Ashraf A. M. , Ibraheem Amira Mofreh 
Published: April 2024

AbstractThe use of various kinds of magnetic resonance imaging (MRI) techniques for examining brain tissue has increased significantly in recent years, and manual investigation of each of the resulting images can be a time-consuming task. This paper presents an automatic brain-tumor diagnosis system that uses a CNN for detection, classification, and segmentation of glioblastomas; the latter stage seeks to segment tumors inside glioma MRI images. The structure of the developed multi-unit system consists of two stages. The first stage is responsible for tumor detection and classification by categorizing brain MRI images into normal, high-grade glioma (glioblastoma), and low-grade glioma. The uniqueness of the proposed network lies in its use of different levels of features, including local and global paths. The second stage is responsible for tumor segmentation, and skip connections and residual units are used during this step. Using 1800 images extracted from the BraTS 2017 dataset, the detection and classification stage was found to achieve a maximum accuracy of 99%. The segmentation stage was then evaluated using the Dice score, specificity, and sensitivity. The results showed that the suggested deep-learning-based system ranks highest among a variety of different strategies reported in the literature.
Changes in bacterial community composition in the uterus of Holstein cow with endometritis before and after treatment with oxytetracycline
Authors: Cai Xiao-Shi , Jiang Hao , Xiao Jie , Yan Xiangmin , Xie Penggui , Yu Wenjie , Lv Wen-fa , Wang Jun , Meng Xiangyu , Chen Cheng-zhen , Zhang Mingjun , Zhang Yang , Yuan Bao , Zhang Jia-Bao 
Published: April 2024

AbstractIt is important to study the bacteria that cause endometritis to identify effective therapeutic drugs for dairy cows. In this study, 20% oxytetracycline was used to treat Holstein cows (n = 6) with severe endometritis. Additional 10 Holstein cows (5 for healthy cows, 5 for cows with mild endometritis) were also selected. At the same time, changes in bacterial communities were monitored by high-throughput sequencing. The results show that Escherichia coli, Staphylococcus aureus and other common pathogenic bacteria could be detected by traditional methods in cows both with and without endometritis. However, 16S sequencing results show that changes in the abundance of these bacteria were not significant. Endometritis is often caused by mixed infections in the uterus. Oxytetracycline did not completely remove existing bacteria. However, oxytetracycline could effectively inhibit endometritis and had a significant inhibitory effect on the genera Bacteroides, Trueperella, Peptoniphilus, Parvimonas, Porphyromonas, and Fusobacterium but had no significant inhibitory effect on the bacterial genera Marinospirillum, Erysipelothrix, and Enteractinococcus. During oxytetracycline treatment, the cell motility, endocrine system, exogenous system, glycan biosynthesis and metabolism, lipid metabolism, metabolism of terpenoids, polyketides, cofactors and vitamins, signal transduction, and transport and catabolism pathways were affected.
Response of Sorghum bicolor genotypes for yield and yield components and organic carbon storage in the shoot and root systems
Authors: Ngidi Asande , Shimelis Hussein , Abady Seltene , Figlan Sandiswa , Chaplot Vincent 
Published: April 2024

AbstractSorghum is a vital food and feed crop in the world’s dry regions. Developing sorghum cultivars with high biomass production and carbon sequestration can contribute to soil health and crop productivity. The objective of this study was to assess agronomic performance, biomass production and carbon accumulation in selected sorghum genotypes for production and breeding. Fifty sorghum genotypes were evaluated at three locations (Silverton, Ukulinga, and Bethlehem) in South Africa during 2022 and 2023 growing seasons. Significant genotype × location (p < 0.05) interactions were detected for days to 50% heading (DTH), days to 50% maturity (DTM), plant height (PH), total plant biomass (PB), shoot biomass (SB), root biomass (RB), root-to-shoot biomass ratio (RS), and grain yield (GY). The highest GY was recorded for genotypes AS115 (25.08 g plant−1), AS251 (21.83 g plant−1), and AS134 (21.42 g plant−1). Genotypes AS122 and AS27 ranked first and second, respectively, for all the carbon stock parameters except for root carbon stock (RCs), whereas genotype AS108 had the highest RCs of 8.87 g plant−1. The principal component analysis identified GY, DTH, PH, PB, SB, RB, RCs, RCs/SCs, total plant carbon stock (PCs), shoot carbon stock (SCs), and grain carbon stock (GCs) as the most discriminated traits among the test genotypes. The cluster analysis using agronomic and carbon-related parameters delineated the test genotypes into three genetic groups, indicating marked genetic diversity for cultivar development and enhanced C storage and sustainable sorghum production. The selected sorghum genotypes are recommended for further breeding and variety release adapted to various agroecologies in South Africa.
Development and testing of a sedation protocol for Neocaridina davidi
Authors: Rodríguez Diego , Moscoso Miguel , Desco Manuel , Ripoll Jorge , Fernández Roberto 
Published: April 2024

AbstractNeocaridina davidi, a small freshwater shrimp native to Asia, specifically China, Japan, Korea, and Vietnam, possesses remarkable resistance to poor water quality and offers various advantages over other invertebrate species to examine crucial issues in neuroscience and other related areas. These advantages include robustness, ease of maintenance, and transparency, making them useful for in vivo studies with optical imaging techniques. Despite its suitability for research purposes, particularly in the fields of imaging and fluorescent techniques, the lack of attention given to this species has resulted in the absence of a robust and replicable sedation protocol for immobilization and safe manipulation. Consequently, researchers face challenges in performing experimental procedures while minimizing harm to this specimen. In this study, we have developed and evaluated a simple sedation protocol specifically designed for Neocaridina davidi, assessing its effectiveness using light microscopy and image processing.