bluuebunny/crossref_metadata_2025 huggingface dataset:
CHCHD2 up-regulation in Huntington disease mediates a compensatory protective response against oxidative stress
Authors: Liu Xuanzhuo , Wang Fang , Fan Xinman , Chen Mingyi , Xu Xiaoxin , Xu Qiuhong , Zhu Huili , Xu Anding , Pouladi Mahmoud A. , Xu Xiaohong
Published: February 2024

Huntington disease (HD) is a neurodegenerative disease caused by the abnormal expansion of a polyglutamine tract resulting from a mutation in the HTT gene. Oxidative stress has been identified as a significant contributing factor to the development of HD and other neurodegenerative diseases, and targeting anti-oxidative stress has emerged as a potential therapeutic approach. CHCHD2 is a mitochondria-related protein involved in regulating cell migration, anti-oxidative stress, and anti-apoptosis. Although CHCHD2 is highly expressed in HD cells, its specific role in the pathogenesis of HD remains uncertain. We postulate that the up-regulation of CHCHD2 in HD models represents a compensatory protective response against mitochondrial dysfunction and oxidative stress associated with HD. To investigate this hypothesis, we employed HD mouse striatal cells and human induced pluripotent stem cells (hiPSCs) as models to examine the effects of CHCHD2 overexpression (CHCHD2-OE) or knockdown (CHCHD2-KD) on the HD phenotype. Our findings demonstrate that CHCHD2 is crucial for maintaining cell survival in both HD mouse striatal cells and hiPSCs-derived neurons. Our study demonstrates that CHCHD2 up-regulation in HD serves as a compensatory protective response against oxidative stress, suggesting a potential anti-oxidative strategy for the treatment of HD.
Hsa_circ_0021205 enhances lipolysis via regulating miR-195-5p/HSL axis and drives malignant progression of glioblastoma
Authors: Li Suwen , Yuan Jiaqi , Cheng Zhe , Li Yongdong , Cheng Shan , Liu Xinglei , Huang Shilu , Xu Zhipeng , Wu Anyi , Liu Liang , Dong Jun
Published: February 2024

Abnormal lipid metabolism is an essential hallmark of glioblastoma. Hormone sensitive lipase (HSL), an important rate-limiting enzyme contributed to lipolysis, which was involved in aberrant lipolysis of glioblastoma, however, its definite roles and the relevant regulatory pathway have not been fully elucidated. Our investigations disclosed high expression of HSL in glioblastoma. Knock-down of HSL restrained proliferation, migration, and invasion of glioblastoma cells while adding to FAs could significantly rescue the inhibitory effect of si-HSL on tumor cells. Overexpression of HSL further promoted tumor cell proliferation and invasion. Bioinformatics analysis and dual-luciferase reporter assay were performed to predict and verify the regulatory role of ncRNAs on HSL. Mechanistically, hsa_circ_0021205 regulated HSL expression by sponging miR-195-5p, which further promoted lipolysis and drove the malignant progression of glioblastoma. Besides, hsa_circ_0021205/miR-195-5p/HSL axis activated the epithelial-mesenchymal transition (EMT) signaling pathway. These findings suggested that hsa_circ_0021205 promoted tumorigenesis of glioblastoma through regulation of HSL, and targeting hsa_circ_0021205/miR-195-5p/HSL axis can serve as a promising new strategy against glioblastoma.
Mitochondrial metabolism and targeted treatment strategies in ischemic-induced acute kidney injury
Authors: Chen Yongming , Li Zixian , Zhang Hongyong , Chen Huixia , Hao Junfeng , Liu Huafeng , Li Xiaoyu
Published: February 2024

Ischemia-reperfusion injury (IRI) is a common cause of acute kidney injury (AKI). The kidney is susceptible to IRI under several clinical conditions, including hypotension, sepsis, and surgical procedures, such as partial nephrectomy and kidney transplantation. Extensive research has been conducted on the mechanism and intervention strategies of renal IRI in past decades; however, the complex pathophysiology of IRI-induced AKI (IRI-AKI) is not fully understood, and there remains a lack of effective treatments for AKI. Renal IRI involves several processes, including reactive oxygen species (ROS) production, inflammation, and apoptosis. Mitochondria, the centers of energy metabolism, are increasingly recognized as substantial contributors to the early phases of IRI. Multiple mitochondrial lesions have been observed in the renal tubular epithelial cells (TECs) of IRI-AKI mice, and damaged or dysfunctional mitochondria are toxic to the cells because they produce ROS and release cell death factors, resulting in TEC apoptosis. In this review, we summarize the recent advances in the mitochondrial pathology in ischemic AKI and highlight promising therapeutic approaches targeting mitochondrial dysfunction to prevent or treat human ischemic AKI.
Solvation-property relationship of lithium-sulphur battery electrolytes
Authors: Kim Sang Cheol , Gao Xin , Liao Sheng-Lun , Su Hance , Chen Yuelang , Zhang Wenbo , Greenburg Louisa C. , Pan Jou-An , Zheng Xueli , Ye Yusheng , Kim Mun Sek , Sayavong Philaphon , Brest Aaron , Qin Jian , Bao Zhenan , Cui Yi
Published: February 2024

The Li-S battery is a promising next-generation battery chemistry that offers high energy density and low cost. The Li-S battery has a unique chemistry with intermediate sulphur species readily solvated in electrolytes, and understanding their implications is important from both practical and fundamental perspectives. In this study, we utilise the solvation free energy of electrolytes as a metric to formulate solvation-property relationships in various electrolytes and investigate their impact on the solvated lithium polysulphides. We find that solvation free energy influences Li-S battery voltage profile, lithium polysulphide solubility, Li-S battery cyclability and the Li metal anode; weaker solvation leads to lower 1st plateau voltage, higher 2nd plateau voltage, lower lithium polysulphide solubility, and superior cyclability of Li-S full cells and Li metal anodes. We believe that relationships delineated in this study can guide the design of high-performance electrolytes for Li-S batteries.
A slow-fast trait continuum at the whole community level in relation to land-use intensification
Authors: Neyret Margot , Le Provost Gaëtane , Boesing Andrea Larissa , Schneider Florian D. , Baulechner Dennis , Bergmann Joana , de Vries Franciska T. , Fiore-Donno Anna Maria , Geisen Stefan , Goldmann Kezia , Merges Anna , Saifutdinov Ruslan A. , Simons Nadja K. , Tobias Joseph A. , Zaitsev Andrey S. , Gossner Martin M. , Jung Kirsten , Kandeler Ellen , Krauss Jochen , Penone Caterina , Schloter Michael , Schulz Stefanie , Staab Michael , Wolters Volkmar , Apostolakis Antonios , Birkhofer Klaus , Boch Steffen , Boeddinghaus Runa S. , Bolliger Ralph , Bonkowski Michael , Buscot François , Dumack Kenneth , Fischer Markus , Gan Huei Ying , Heinze Johannes , Hölzel Norbert , John Katharina , Klaus Valentin H. , Kleinebecker Till , Marhan Sven , Müller Jörg , Renner Swen C. , Rillig Matthias C. , Schenk Noëlle V. , Schöning Ingo , Schrumpf Marion , Seibold Sebastian , Socher Stephanie A. , Solly Emily F. , Teuscher Miriam , van Kleunen Mark , Wubet Tesfaye , Manning Peter
Published: February 2024

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a ‘slow-fast’ axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that ‘slow’ and ‘fast’ strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
Human-triggered magnification of erosion rates in European Alps since the Bronze Age
Authors: Rapuc William , Giguet-Covex Charline , Bouchez Julien , Sabatier Pierre , Gaillardet Jérôme , Jacq Kévin , Genuite Kim , Poulenard Jérôme , Messager Erwan , Arnaud Fabien
Published: February 2024

A major feature of the Anthropocene is the drastic increase in global soil erosion. Soil erosion is threatening Earth habitability not only as soils are an essential component of the Earth system but also because societies depend on soils. However, proper quantification of the impact of human activities on erosion over thousands of years is still lacking. This is particularly crucial in mountainous areas, where the highest erosion rates are recorded. Here we use the Lake Bourget catchment, one of the largest in the European Alps, to estimate quantitatively the impact of human activities on erosion. Based on a multi-proxy, source-to-sink approach relying on isotopic geochemistry, we discriminate the effects of climate fluctuations from those of human activities on erosion over the last 10,000 years. We demonstrate that until 3800 years ago, climate is the only driver of erosion. From that time on, climate alone cannot explain the measured rates of erosion. Thanks to an unprecedented regional paleoenvironmental reconstruction, we highlight that the development of pastoralism at high altitudes from the Bronze Age onwards and the extension of agriculture starting in the Middle Ages were key factors in the drastic increase in erosion observed in the Alps.
Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions
Authors: Liu Tianxin , Zhu Qian , Kai Yan , Bingham Trevor , Wang Stacy , Cha Hye Ji , Mehta Stuti , Schlaeger Thorsten M. , Yuan Guo-Cheng , Orkin Stuart H.
Published: February 2024

Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Changes in chromatin occupancy by Matr3 also correlated with these alterations. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.
Mesoscopic calcium imaging in a head-unrestrained male non-human primate using a lensless microscope
Authors: Wu Jimin , Chen Yuzhi , Veeraraghavan Ashok , Seidemann Eyal , Robinson Jacob T.
Published: February 2024

Mesoscopic calcium imaging enables studies of cell-type specific neural activity over large areas. A growing body of literature suggests that neural activity can be different when animals are free to move compared to when they are restrained. Unfortunately, existing systems for imaging calcium dynamics over large areas in non-human primates (NHPs) are table-top devices that require restraint of the animal’s head. Here, we demonstrate an imaging device capable of imaging mesoscale calcium activity in a head-unrestrained male non-human primate. We successfully miniaturize our system by replacing lenses with an optical mask and computational algorithms. The resulting lensless microscope can fit comfortably on an NHP, allowing its head to move freely while imaging. We are able to measure orientation columns maps over a 20 mm2 field-of-view in a head-unrestrained macaque. Our work establishes mesoscopic imaging using a lensless microscope as a powerful approach for studying neural activity under more naturalistic conditions.
Optimizing multi-user indoor sound communications with acoustic reconfigurable metasurfaces
Authors: Zhang Hongkuan , Wang Qiyuan , Fink Mathias , Ma Guancong
Published: February 2024

Sound in indoor spaces forms a complex wavefield due to multiple scattering encountered by the sound. Indoor acoustic communication involving multiple sources and receivers thus inevitably suffers from cross-talks. Here, we demonstrate the isolation of acoustic communication channels in a room by wavefield shaping using acoustic reconfigurable metasurfaces (ARMs) controlled by optimization protocols based on communication theories. The ARMs have 200 electrically switchable units, each selectively offering 0 or π phase shifts in the reflected waves. The sound field is reshaped for maximal Shannon capacity and minimal cross-talk simultaneously. We demonstrate diverse acoustic functionalities over a spectrum much larger than the coherence bandwidth of the room, including multi-channel, multi-spectral channel isolations, and frequency-multiplexed acoustic communication. Our work shows that wavefield shaping in complex media can offer new strategies for future acoustic engineering.
Dynamic nucleolar phase separation influenced by non-canonical function of LIN28A instructs pluripotent stem cell fate decisions
Authors: Tan Tianyu , Gao Bo , Yu Hua , Pan Hongru , Sun Zhen , Lei Anhua , Zhang Li , Lu Hengxing , Wu Hao , Daley George Q. , Feng Yu , Zhang Jin
Published: February 2024

LIN28A is important in somatic reprogramming and pluripotency regulation. Although previous studies addressed that LIN28A can repress let-7 microRNA maturation in the cytoplasm, few focused on its role within the nucleus. Here, we show that the nucleolus-localized LIN28A protein undergoes liquid-liquid phase separation (LLPS) in mouse embryonic stem cells (mESCs) and in vitro. The RNA binding domains (RBD) and intrinsically disordered regions (IDR) of LIN28A contribute to LIN28A and the other nucleolar proteins’ phase-separated condensate establishment. S120A, S200A and R192G mutations in the IDR result in subcellular mislocalization of LIN28A and abnormal nucleolar phase separation. Moreover, we find that the naive-to-primed pluripotency state conversion and the reprogramming are associated with dynamic nucleolar remodeling, which depends on LIN28A’s phase separation capacity, because the LIN28A IDR point mutations abolish its role in regulating nucleolus and in these cell fate decision processes, and an exogenous IDR rescues it. These findings shed light on the nucleolar function in pluripotent stem cell states and on a non-canonical RNA-independent role of LIN28A in phase separation and cell fate decisions.
Real-time monitoring polymerization degree of organic photovoltaic materials toward no batch-to-batch variations in device performance
Authors: Xu Lin-Yong , Wang Wei , Yang Xinrong , Wang Shanshan , Shao Yiming , Chen Mingxia , Sun Rui , Min Jie
Published: February 2024

Polymerization degree plays a vital role in material properties. Previous methodologies of molecular weight control generally cannot suppress or alleviate batch-to-batch variations in device performance, especially in polymer solar cells. Herein, we develop an in-situ photoluminescence system in tandem with a set of analysis and processing procedures to track and estimate the polymerization degree of organic photovoltaic materials. To support the development of this protocol, we introduce polymer acceptor PYT constructed by near-infrared Y-series small molecule acceptors via Stille polymerization, and shed light on the correlations between molecular weight, spectral parameters, and device efficiencies that enable the design of the optical setup and confirm its feasibility. The universality is verified in PYT derivatives with stereoregularity and fluoro-substitution as well as benzo[1,2-b:4,5-b’]dithiophene-based polymers. Overall, our result provides a tool to tailor suitable conjugated oligomers applied to polymer solar cells and other organic electronics for industrial scalability and desired cost reduction.
Effect of sub-bandgap defects on radiative and non-radiative open-circuit voltage losses in perovskite solar cells
Authors: Aalbers Guus J. W. , van der Pol Tom P. A. , Datta Kunal , Remmerswaal Willemijn H. M. , Wienk Martijn M. , Janssen René A. J.
Published: February 2024

The efficiency of perovskite solar cells is affected by open-circuit voltage losses due to radiative and non-radiative charge recombination. When estimated using sensitive photocurrent measurements that cover the above- and sub-bandgap regions, the radiative open-circuit voltage is often unphysically low. Here we report sensitive photocurrent and electroluminescence spectroscopy to probe radiative recombination at sub-bandgap defects in wide-bandgap mixed-halide lead perovskite solar cells. The radiative ideality factor associated with the optical transitions increases from 1, above and near the bandgap edge, to ~2 at mid-bandgap. Such photon energy-dependent ideality factor corresponds to a many-diode model. The radiative open-circuit voltage limit derived from this many-diode model enables differentiating between radiative and non-radiative voltage losses. The latter are deconvoluted into contributions from the bulk and interfaces via determining the quasi-Fermi level splitting. The experiments show that while sub-bandgap defects do not contribute to radiative voltage loss, they do affect non-radiative voltage losses.
Transient targeting of hypothalamic orexin neurons alleviates seizures in a mouse model of epilepsy
Authors: Li Han-Tao , Viskaitis Paulius , Bracey Eva , Peleg-Raibstein Daria , Burdakov Denis
Published: February 2024

Lateral hypothalamic (LH) hypocretin/orexin neurons (HONs) control brain-wide electrical excitation. Abnormally high excitation produces epileptic seizures, which affect millions of people and need better treatments. HON population activity spikes from minute to minute, but the role of this in seizures is unknown. Here, we describe correlative and causal links between HON activity spikes and seizures. Applying temporally-targeted HON recordings and optogenetic silencing to a male mouse model of acute epilepsy, we found that pre-seizure HON activity predicts and controls the electrophysiology and behavioral pathology of subsequent seizures. No such links were detected for HON activity during seizures. Having thus defined the time window where HONs influence seizures, we targeted it with LH deep brain stimulation (DBS), which inhibited HON population activity, and produced seizure protection. Collectively, these results uncover a feature of brain activity linked to seizures, and demonstrate a proof-of-concept treatment that controls this feature and alleviates epilepsy.
A nonmetallic plasmonic catalyst for photothermal CO2 flow conversion with high activity, selectivity and durability
Authors: Wan Xueying , Li Yifan , Chen Yihong , Ma Jun , Liu Ying-Ao , Zhao En-Dian , Gu Yadi , Zhao Yilin , Cui Yi , Li Rongtan , Liu Dong , Long Ran , Liew Kim Meow , Xiong Yujie
Published: February 2024

The meticulous design of active sites and light absorbers holds the key to the development of high-performance photothermal catalysts for CO2 hydrogenation. Here, we report a nonmetallic plasmonic catalyst of Mo2N/MoO2-x nanosheets by integrating a localized surface plasmon resonance effect with two distinct types of active sites for CO2 hydrogenation. Leveraging the synergism of dual active sites, H2 and CO2 molecules can be simultaneously adsorbed and activated on N atom and O vacancy, respectively. Meanwhile, the plasmonic effect of this noble-metal-free catalyst signifies its promising ability to convert photon energy into localized heat. Consequently, Mo2N/MoO2-x nanosheets exhibit remarkable photothermal catalytic performance in reverse water-gas shift reaction. Under continuous full-spectrum light irradiation (3 W·cm−2) for a duration of 168 h, the nanosheets achieve a CO yield rate of 355 mmol·gcat−1·h−1 in a flow reactor with a selectivity exceeding 99%. This work offers valuable insights into the precise design of noble-metal-free active sites and the development of plasmonic catalysts for reducing carbon footprints.
Ultralight crystalline hybrid composite material for highly efficient sequestration of radioiodine
Authors: Fajal Sahel , Mandal Writakshi , Torris Arun , Majumder Dipanjan , Let Sumanta , Sen Arunabha , Kanheerampockil Fayis , Shirolkar Mandar M. , Ghosh Sujit K.
Published: February 2024

Considering the importance of sustainable nuclear energy, effective management of radioactive nuclear waste, such as sequestration of radioiodine has inflicted a significant research attention in recent years. Despite the fact that materials have been reported for the adsorption of iodine, development of effective adsorbent with significantly improved segregation properties for widespread practical applications still remain exceedingly difficult due to lack of proper design strategies. Herein, utilizing unique hybridization synthetic strategy, a composite crystalline aerogel material has been fabricated by covalent stepping of an amino-functionalized stable cationic discrete metal-organic polyhedra with dual-pore containing imine-functionalized covalent organic framework. The ultralight hybrid composite exhibits large surface area with hierarchical macro-micro porosity and multifunctional binding sites, which collectively interact with iodine. The developed nano-adsorbent demonstrate ultrahigh vapor and aqueous-phase iodine adsorption capacities of 9.98 g.g−1 and 4.74 g.g−1, respectively, in static conditions with fast adsorption kinetics, high retention efficiency, reusability and recovery.
Separation of benzene and toluene associated with vapochromic behaviors by hybrid[4]arene-based co-crystals
Authors: Chen Jingyu , Zhang Wenjie , Yang Wenzhi , Xi Fengcheng , He Hongyi , Liang Minghao , Dong Qian , Hou Jiawang , Wang Mengbin , Yu Guocan , Zhou Jiong
Published: February 2024

The combination of macrocyclic chemistry with co-crystal engineering has promoted the development of materials with vapochromic behaviors in supramolecular science. Herein, we develop a macrocycle co-crystal based on hybrid[4]arene and 1,2,4,5-tetracyanobenzene that is able to construct vapochromic materials. After the capture of benzene and toluene vapors, activated hybrid[4]arene-based co-crystal forms new structures, accompanied by color changes from brown to yellow. However, when hybrid[4]arene-based co-crystal captures cyclohexane and pyridine, neither structures nor colors change. Interestingly, hybrid[4]arene-based co-crystal can separate benzene from a benzene/cyclohexane equal-volume mixture and allow toluene to be removed from a toluene/ pyridine equal-volume mixture with purities reaching 100%. In addition, the process of adsorptive separation can be visually monitored. The selectivity of benzene from a benzene/cyclohexane equal-volume mixture and toluene from a toluene/ pyridine equal-volume mixture is attributed to the different changes in the charge-transfer interaction between hybrid[4]arene and 1,2,4,5-tetracyanobenzene when hybrid[4]arene-based co-crystal captures different vapors. Moreover, hybrid[4]arene-based co-crystal can be reused without losing selectivity and performance. This work constructs a vapochromic material for hydrocarbon separation.
Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase
Authors: Nguyen Nguyet A. , Vidya F. N. U. , Yennawar Neela H. , Wu Hongwei , McShan Andrew C. , Agarwal Vinayak
Published: February 2024

To biosynthesize ribosomally synthesized and post-translationally modified peptides (RiPPs), enzymes recognize and bind to the N-terminal leader region of substrate peptides which enables catalytic modification of the C-terminal core. Our current understanding of RiPP leaders is that they are short and largely unstructured. Proteusins are RiPP precursor peptides that defy this characterization as they possess unusually long leaders. Proteusin peptides have not been structurally characterized, and we possess scant understanding of how these atypical leaders engage with modifying enzymes. Here, we determine the structure of a proteusin peptide which shows that unlike other RiPP leaders, proteusin leaders are preorganized into a rigidly structured region and a smaller intrinsically disordered region. With residue level resolution gained from NMR titration experiments, the intermolecular peptide-protein interactions between proteusin leaders and a flavin-dependent brominase are mapped onto the disordered region, leaving the rigidly structured region of the proteusin leader to be functionally dispensable. Spectroscopic observations are biochemically validated to identify a binding motif in proteusin peptides that is conserved among other RiPP leaders as well. This study provides a structural characterization of the proteusin peptides and extends the paradigm of RiPP modification enzymes using not only unstructured peptides, but also structured proteins as substrates.
A hepatic network of dendritic cells mediates CD4 T cell help outside lymphoid organs
Authors: English Kieran , Kwan Rain , Holz Lauren E. , McGuffog Claire , Krol Jelte M. M. , Kempe Daryan , Kaisho Tsuneyasu , Heath William R. , Lisowski Leszek , Biro Maté , McCaughan Geoffrey W. , Bowen David G. , Bertolino Patrick
Published: February 2024

While CD4+ T cells are a prerequisite for CD8+ T cell-mediated protection against intracellular hepatotropic pathogens, the mechanisms facilitating the transfer of CD4-help to intrahepatic CD8+ T cells are unknown. Here, we developed an experimental system to investigate cognate CD4+ and CD8+ T cell responses to a model-antigen expressed de novo in hepatocytes and reveal that after initial priming, effector CD4+ and CD8+ T cells migrate into portal tracts and peri-central vein regions of the liver where they cluster with type-1 conventional dendritic cells. These dendritic cells are locally licensed by CD4+ T cells and expand the number of CD8+ T cells in situ, resulting in larger effector and memory CD8+ T cell pools. These findings reveal that CD4+ T cells promote intrahepatic immunity by amplifying the CD8+ T cell response via peripheral licensing of hepatic type-1 conventional dendritic cells and identify intrahepatic perivascular compartments specialized in facilitating effector T cell-dendritic cell interactions.
Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1
Authors: Wu Xiangwei , Du Yunxiang , Liang Lu-Jun , Ding Ruichao , Zhang Tianyi , Cai Hongyi , Tian Xiaolin , Pan Man , Liu Lei
Published: February 2024

Ubiquitination, catalyzed usually by a three-enzyme cascade (E1, E2, E3), regulates various eukaryotic cellular processes. E3 ligases are the most critical components of this catalytic cascade, determining both substrate specificity and polyubiquitination linkage specificity. Here, we reveal the mechanism of a naturally occurring E3-independent ubiquitination reaction of a unique human E2 enzyme UBE2E1 by solving the structure of UBE2E1 in complex with substrate SETDB1-derived peptide. Guided by this peptide sequence-dependent ubiquitination mechanism, we developed an E3-free enzymatic strategy SUE1 (sequence-dependent ubiquitination using UBE2E1) to efficiently generate ubiquitinated proteins with customized ubiquitinated sites, ubiquitin chain linkages and lengths. Notably, this strategy can also be used to generate site-specific branched ubiquitin chains or even NEDD8-modified proteins. Our work not only deepens the understanding of how an E3-free substrate ubiquitination reaction occurs in human cells, but also provides a practical approach for obtaining ubiquitinated proteins to dissect the biochemical functions of ubiquitination.
Observation of giant room-temperature anisotropic magnetoresistance in the topological insulator β-Ag2Te
Authors: Ai Wei , Chen Fuyang , Liu Zhaochao , Yuan Xixi , Zhang Lei , He Yuyu , Dong Xinyue , Fu Huixia , Luo Feng , Deng Mingxun , Wang Ruiqiang , Wu Jinxiong
Published: February 2024

Achieving room-temperature high anisotropic magnetoresistance ratios is highly desirable for magnetic sensors with scaled supply voltages and high sensitivities. However, the ratios in heterojunction-free thin films are currently limited to only a few percent at room temperature. Here, we observe a high anisotropic magnetoresistance ratio of −39% and a giant planar Hall effect (520 μΩ⋅cm) at room temperature under 9 T in β-Ag2Te crystals grown by chemical vapor deposition. We propose a theoretical model of anisotropic scattering — induced by a Dirac cone tilt and modulated by intrinsic properties of effective mass and sound velocity — as a possible origin. Moreover, small-size angle sensors with a Wheatstone bridge configuration were fabricated using the synthesized β-Ag2Te crystals. The sensors exhibited high output response (240 mV/V), high angle sensitivity (4.2 mV/V/°) and small angle error (<1°). Our work translates the developments in topological insulators to a broader impact on practical applications such as high-field magnetic and angle sensors.
Phonon thermal transport shaped by strong spin-phonon scattering in a Kitaev material Na2Co2TeO6
Authors: Hong Xiaochen , Gillig Matthias , Yao Weiliang , Janssen Lukas , Kocsis Vilmos , Gass Sebastian , Li Yuan , Wolter Anja U. B. , Büchner Bernd , Hess Christian
Published: February 2024

The report of a half-quantized thermal Hall effect and oscillatory structures in the magnetothermal conductivity in the Kitaev material α-RuCl3 have sparked a strong debate on whether it is generated by Majorana fermion edge currents, spinon Fermi surface, or whether other more conventional mechanisms are at its origin. Here, we report low temperature thermal conductivity (κ) of another candidate Kitaev material, Na2Co2TeO6. The application of a magnetic field (B) along different principal axes of the crystal reveals a strong directional-dependent B impact on κ, while no evidence for mobile quasiparticles except phonons can be concluded at any field. Instead, severely scattered phonon transport prevails across the B−T phase diagram, revealing cascades of phase transitions for all B directions. Our results thus cast doubt on recent proposals for significant itinerant magnetic excitations in Na2Co2TeO6, and emphasize the importance of discriminating true spin liquid transport properties from scattered phonons in candidate materials.
Fluorescent Neuronal Cells v2: multi-task, multi-format annotations for deep learning in microscopy
Authors: Clissa Luca , Macaluso Antonio , Morelli Roberto , Occhinegro Alessandra , Piscitiello Emiliana , Taddei Ludovico , Luppi Marco , Amici Roberto , Cerri Matteo , Hitrec Timna , Rinaldi Lorenzo , Zoccoli Antonio
Published: February 2024

Fluorescent Neuronal Cells v2 is a collection of fluorescence microscopy images and the corresponding ground-truth annotations, designed to foster innovative research in the domains of Life Sciences and Deep Learning. This dataset encompasses three image collections wherein rodent neuronal cell nuclei and cytoplasm are stained with diverse markers to highlight their anatomical or functional characteristics. Specifically, we release 1874 high-resolution images alongside 750 corresponding ground-truth annotations for several learning tasks, including semantic segmentation, object detection and counting. The contribution is two-fold. First, thanks to the variety of annotations and their accessible formats, we anticipate our work will facilitate methodological advancements in computer vision approaches for segmentation, detection, feature extraction, unsupervised and self-supervised learning, transfer learning, and related areas. Second, by enabling extensive exploration and benchmarking, we hope Fluorescent Neuronal Cells v2 will catalyze breakthroughs in fluorescence microscopy analysis and promote cutting-edge discoveries in life sciences.
A 10-m annual grazing intensity dataset in 2015–2021 for the largest temperate meadow steppe in China
Authors: Chang Chuchen , Wang Jie , Zhao Yanbo , Cai Tianyu , Yang Jilin , Zhang Geli , Wu Xiaocui , Otgonbayar Munkhdulam , Xiao Xiangming , Xin Xiaoping , Zhang Yingjun
Published: February 2024

Mapping grazing intensity (GI) using satellites is crucial for developing adaptive utilization strategies according to grassland conditions. Here we developed a monitoring framework based on a paired sampling strategy and the classification probability of random forest algorithm to produce annual grazing probability (GP) and GI maps at 10-m spatial resolution from 2015 to 2021 for the largest temperate meadow in China (Hulun Buir grasslands), by harmonized Landsat 7/8 and Sentinel-2 images. The GP maps used values of 0–1 to present detailed grazing gradient information. To match widely used grazing gradients, annual GI maps with ungrazed, moderately grazed, and heavily grazed levels were generated from the GP dataset with a decision tree. The GI maps for 2015–2021 had an overall accuracy of more than 0.97 having significant correlations with the statistical data at city (r = 0.51) and county (r = 0.75) scales. They also effectively captured the GI gradients at site scale (r = 0.94). Our study proposed a monitoring approach and presented annual 10-m grazing information maps for sustainable grassland management.
Chromosome-scale genome assembly of Lepus oiostolus (Lepus, Leporidae)
Authors: Feng Shuo , Zhang Yaying , He Zhaotong , Xi Erning , Ru Dafu , Liang Jian , Yang Yongzhi
Published: February 2024

Lepus oiostolus (L. oiostolus) is a species endemic to the Qinghai-Tibet Plateau. However, the absence of a reference genome limits genetic studies. Here, we reported a high-quality L. oiostolus genome assembly, with scaffolds anchored to 24 chromosomes and a total assembled length of 2.80 Gb (contig N50 = 64.25 Mb). Genomic annotation uncovered 22,295 protein-coding genes and identified 49.84% of the sequences as transposable elements. Long interspersed nuclear elements (LINEs) constitute a high proportion of the genome. Our study is at the first time to report the chromosome-scale genome for the species of the L. oiostolus. It provides a valuable genomic resource for future research on the evolution of the Leporidae.
Bayesian network approach for reliability analysis of mining trucks
Authors: Rahimdel Mohammad Javad
Published: February 2024

Having a safe and efficient system for mineral transportation is a top priority for all mining operations. Trucks are the most widely used material transportation systems that are applied in both surface and underground mines. Any truck failure disrupts the mineral transportation process and consequently decreases the overall output. Therefore, the reliability analysis of such equipment plays a critical role in increasing the efficiency and productivity of a mining operation. This paper proposes a novel method for analyzing the reliability of a fleet of mining trucks based on the Bayesian Network modeling. Considering the reliability block diagram, the fault tree of trucks was developed according to the logical relationship between the units. Then, a dynamic Bayesian network was constructed according to the conditional probability analysis. Moreover, the relative contributions of each truck’s component to the occurrence of the fleet failure were studied by using critical analysis. The results of this paper show that the successful operation of the fleet of trucks is most sensitive to truck no. 5, which has the highest reliability level in all time intervals. The reliability of the fleet of trucks reaches 0.881 at 20 h, and the fuel injection system of the truck’s engine is the main leading cause of the trucks failure. A proper preventive maintenance strategy should be paid more attention to improve the reliability and availability of the engine system.
Effect of apricot kernel seed extract on biophysical properties of chitosan film for packaging applications
Authors: Saied Mona , Ward Azza , Hamieda Shimaa Farag
Published: February 2024

Chitosan is a natural biodegradable biopolymer that has drawbacks in mechanical and antibacterial properties, limiting its usage in biological and medicinal fields. Chitosan is combined with other naturally occurring substances possessing biological antibacterial qualities in order to broaden its application. Ethanolic apricot kernel seed extract was prepared, analyzed, and incorporated into chitosan film with different concentrations (0.25, 0.5, and 0.75 wt%). Furthermore, the effect of AKSE and γ-radiation (20 Gy and 20 kGy) on the physical properties of the film was studied. The prepared films were characterized by Fourier transform infrared spectroscopy (FTIR), which revealed that AKSE did not cause any change in the molecular structure, whereas the γ-irradiation dose caused a decrease in the peak intensity of all concentrations except 0.75 wt%, which was the most resistant. In addition, their dielectric, optical, and antimicrobial properties were studied. Also, AKSE-enhanced optical qualities, allowed them to fully block light transmission at wavelengths of 450–600 nm. The dielectric properties, i.e., permittivity (ε′), dielectric loss (ε′′), and electrical conductivity (σ), increased with increasing AKSE concentration and film irradiation. The antimicrobial studies revealed that the antimicrobial activity against Escherichia coli and Canodida albicans increased with AKSE incorporation.
Customized three-dimensional printed ceramic bone grafts for osseous defects: a prospective randomized study
Authors: Kim Na-hyun , Yang Byoung-Eun , On Sung-Woon , Kwon Ik-Jae , Ahn Kang-Min , Lee Jong-Ho , Byun Soo-Hwan
Published: February 2024

Ridge resorption can result in insufficient bone volume for implant surgery, necessitating bone substitutes to restore the resorption area. Recent advances in computer-aided design and manufacturing enable the use of alloplastic bone graft materials with customizable compositions or shapes. This randomized study evaluated the clinical effectiveness of a customized three-dimensional (3D) printed alloplastic bone material. Sixty patients requiring guided bone regeneration for implant installation following tooth extraction due to alveolar bone resorption were recruited at two institutions. The participants were randomly allocated to either a group that received 3D-printed patient-customized bone graft material or a group that received conventional block bone graft material. Implant installation with bone harvesting was performed approximately 5 months after bone grafting. Histological and radiological assessments of the harvested bone area were performed. The experimental group had a significantly higher percent bone volume and a smaller tissue surface than the control group. Bone volume, bone surface, bone surface/volume ratio, bone surface density (bone surface/total volume), and bone mineral density did not differ significantly between groups. Patient-customized bone graft materials offer convenience and reduce patient discomfort. The findings suggest 3D-printed patient-customized bone graft materials could be used as an alternative for simpler bone grafting procedures.
Exploring the various effects of Cu doping in hydroxyapatite nanoparticle
Authors: Noori Alireza , Hoseinpour Mahdieh , Kolivand Sedighe , Lotfibakhshaiesh Nasrin , Ebrahimi‐Barough Somayeh , Ai Jafar , Azami Mahmoud
Published: February 2024

Adding foreign ions to hydroxyapatite (HAp) is a popular approach for improving its properties. This study focuses on the effects of calcium substitution with copper in HAp. Instead of calcium, copper ions were doped into the structure of hydroxyapatite nanoparticles at 1%, 3%, and 5% concentrations. XRD analysis showed that the amount of substituted copper was less than needed to generate a distinct phase, yet its lattice parameters and crystallinity slightly decreased. Further, the results of degradation tests revealed that copper doping in hydroxyapatite doubled calcium ion release in water. The incorporation of copper into the apatite structure also boosted the HAp zeta potential and FBS protein adsorption onto powders. According to antibacterial investigations, a concentration of 200 mg/ml of hydroxyapatite containing 5% copper was sufficient to effectively eradicate E. coli and S. aureus bacteria. Furthermore, copper improved hydroxyapatite biocompatibility. Alkaline phosphatase activity and alizarin red tests showed that copper in hydroxyapatite did not inhibit stem cell differentiation into osteoblasts. Also, the scratch test demonstrated that copper-containing hydroxyapatite extract increased HUVEC cell migration. Overall, our findings demonstrated the utility of incorporating copper into the structure of hydroxyapatite from several perspectives, including the induction of antibacterial characteristics, biocompatibility, and angiogenesis.
Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs
Authors: Balewski Jan , Amankwah Mercy G. , Van Beeumen Roel , Bethel E. Wes , Perciano Talita , Camps Daan
Published: February 2024

Compact data representations in quantum systems are crucial for the development of quantum algorithms for data analysis. In this study, we present two innovative data encoding techniques, known as QCrank and QBArt, which exhibit significant quantum parallelism via uniformly controlled rotation gates. The QCrank method encodes a series of real-valued data as rotations on data qubits, resulting in increased storage capacity. On the other hand, QBArt directly incorporates a binary representation of the data within the computational basis, requiring fewer quantum measurements and enabling well-established arithmetic operations on binary data. We showcase various applications of the proposed encoding methods for various data types. Notably, we demonstrate quantum algorithms for tasks such as DNA pattern matching, Hamming weight computation, complex value conjugation, and the retrieval of a binary image with 384 pixels, all executed on the Quantinuum trapped-ion QPU. Furthermore, we employ several cloud-accessible QPUs, including those from IBMQ and IonQ, to conduct supplementary benchmarking experiments.
Toward an application of automatic evaluation system for central facial palsy using two simple evaluation indices in emergency medicine
Authors: Ikezawa Naoki , Okamoto Takayuki , Yoshida Yoichi , Kurihara Satoru , Takahashi Nozomi , Nakada Taka-aki , Haneishi Hideaki
Published: February 2024

A stroke is a medical emergency and thus requires immediate treatment. Paramedics should accurately assess suspected stroke patients and promptly transport them to a hospital with stroke care facilities; however, current assessment procedures rely on subjective visual assessment. We aim to develop an automatic evaluation system for central facial palsy (CFP) that uses RGB cameras installed in an ambulance. This paper presents two evaluation indices, namely the symmetry of mouth movement and the difference in mouth shape, respectively, extracted from video frames. These evaluation indices allow us to quantitatively evaluate the degree of facial palsy. A classification model based on these indices can discriminate patients with CFP. The results of experiments using our dataset show that the values of the two evaluation indices are significantly different between healthy subjects and CFP patients. Furthermore, our classification model achieved an area under the curve of 0.847. This study demonstrates that the proposed automatic evaluation system has great potential for quantitatively assessing CFP patients based on two evaluation indices.
Full-length 16S rDNA sequencing based on Oxford Nanopore Technologies revealed the association between gut-pharyngeal microbiota and tuberculosis in cynomolgus macaques
Authors: Sawaswong Vorthon , Chanchaem Prangwalai , Klomkliew Pavit , Rotcheewaphan Suwatchareeporn , Meesawat Suthirote , Kemthong Taratorn , Kaewparuehaschai Mutchamon , Noradechanon Kirana , Ekatat Monya , Kanitpun Reka , Srilohasin Prapaporn , Warit Saradee , Chaiprasert Angkana , Malaivijitnond Suchinda , Payungporn Sunchai
Published: February 2024

Tuberculosis (TB) is an infectious disease caused by the Mycobacterium tuberculosis complex (Mtbc), which develops from asymptomatic latent TB to active stages. The microbiome was purposed as a potential factor affecting TB pathogenesis, but the study was limited. The present study explored the association between gut-pharyngeal microbiome and TB stages in cynomolgus macaques using the full-length 16S rDNA amplicon sequencing based on Oxford Nanopore Technologies. The total of 71 macaques was divided into TB (−) control, TB (+) latent and TB (+) active groups. The differential abundance analysis showed that Haemophilus hemolyticus was decreased, while Prevotella species were increased in the pharyngeal microbiome of TB (+) macaques. In addition, Eubacterium coprostanoligenes in the gut was enriched in TB (+) macaques. Alteration of these bacteria might affect immune regulation and TB severity, but details of mechanisms should be further explored and validated. In summary, microbiota may be associated with host immune regulation and affect TB progression. The findings suggested the potential mechanisms of host-microbes interaction, which may improve the understanding of the role of microbiota and help develop therapeutics for TB in the future.
WHOOPH: whale optimization-based optimal placement of hub node within a WBAN
Authors: Shukla Shubham , Sachan Vibhav Kumar , Sinha Anurag , Pandey Saroj Kumar , Rao G. Madhukar , Shah Mohd Asif , Choudhary Amit , Tamrakar Balram
Published: February 2024

Biosensor nodes of a wireless body area network (WBAN) transmit physiological parameter data to a central hub node, spending a substantial portion of their energy. Therefore, it is crucial to determine an optimal location for hub placement to minimize node energy consumption in data transmission. Existing methods determine the optimal hub location by sequentially placing the hub at multiple random locations within the WBAN. Performance measures like link reliability or overall node energy consumption in data transmission are estimated for each hub location. The best-performing location is finally selected for hub placement. Such methods are time-consuming. Moreover, the involvement of other nodes in the process of hub placement results in an undesirable loss of network energy. This paper shows the whale optimization algorithm (WOA)-based hub placement scheme. This scheme directly gives the best location for the hub in the least amount of time and with the least amount of help from other nodes. The presented scheme incorporates a population of candidate solutions called "whale search agents". These agents carry out the iterative steps of encircling the prey (identifying the best candidate solution), bubble-net feeding (exploitation phase), and random prey search (exploration phase). The WOA-based model eventually converges into an optimized solution that determines the optimal location for hub placement. The resultant hub location minimizes the overall amount of energy consumed by the WBAN nodes for data transmission, which ultimately results in an elongated lifespan of WBAN operation. The results show that the proposed WOA-based hub placement scheme outperforms various state-of-the-art related WBAN protocols by achieving a network lifetime of 8937 data transmission rounds with 93.8% network throughput and 9.74 ms network latency.