bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell cycle arrest induces lipid droplet formation and confers ferroptosis resistance
Authors: Lee Hyemin , Horbath Amber , Kondiparthi Lavanya , Meena Jitendra Kumar , Lei Guang , Dasgupta Shayani , Liu Xiaoguang , Zhuang Li , Koppula Pranavi , Li Mi , Mahmud Iqbal , Wei Bo , Lorenzi Philip L. , Keyomarsi Khandan , Poyurovsky Masha V. , Olszewski Kellen , Gan Boyi
Published: January 2024

How cells coordinate cell cycling with cell survival and death remains incompletely understood. Here, we show that cell cycle arrest has a potent suppressive effect on ferroptosis, a form of regulated cell death induced by overwhelming lipid peroxidation at cellular membranes. Mechanistically, cell cycle arrest induces diacylglycerol acyltransferase (DGAT)–dependent lipid droplet formation to sequester excessive polyunsaturated fatty acids (PUFAs) that accumulate in arrested cells in triacylglycerols (TAGs), resulting in ferroptosis suppression. Consequently, DGAT inhibition orchestrates a reshuffling of PUFAs from TAGs to phospholipids and re-sensitizes arrested cells to ferroptosis. We show that some slow-cycling antimitotic drug–resistant cancer cells, such as 5-fluorouracil–resistant cells, have accumulation of lipid droplets and that combined treatment with ferroptosis inducers and DGAT inhibitors effectively suppresses the growth of 5-fluorouracil–resistant tumors by inducing ferroptosis. Together, these results reveal a role for cell cycle arrest in driving ferroptosis resistance and suggest a ferroptosis-inducing therapeutic strategy to target slow-cycling therapy-resistant cancers.
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif
Authors: Pérez-Jover Isabel , Rochon Kristy , Hu Di , Mahajan Mukesh , Madan Mohan Pooja , Santos-Pérez Isaac , Ormaetxea Gisasola Julene , Martinez Galvez Juan Manuel , Agirre Jon , Qi Xin , Mears Jason A. , Shnyrova Anna V. , Ramachandran Rajesh
Published: January 2024

The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
A nanoemulsion targeting adipose hypertrophy and hyperplasia shows anti-obesity efficiency in female mice
Authors: Lu Yichao , Luo Zhenyu , Zhou Huanli , Shi Yingying , Zhu Ying , Guo Xuemeng , Huang Jiaxin , Zhang Junlei , Liu Xu , Wang Sijie , Shan Xinyu , Yin Hang , Du Yongzhong , Li Qingpo , You Jian , Luo Lihua
Published: January 2024

Obesity often leads to severe medical complications. However, existing FDA-approved medications to combat obesity have limited effectiveness in reducing adiposity and often cause side effects. These medications primarily act on the central nervous system or disrupt fat absorption through the gastrointestinal tract. Adipose tissue enlargement involves adipose hyperplasia and hypertrophy, both of which correlate with increased reactive oxygen species (ROS) and hyperactivated X-box binding protein 1 (XBP1) in (pre)adipocytes. In this study, we demonstrate that KT-NE, a nanoemulsion loaded with the XBP1 inhibitor KIRA6 and α-Tocopherol, simultaneously alleviates aberrant endoplasmic reticulum stress and oxidative stress in (pre)adipocytes. As a result, KT-NE significantly inhibits abnormal adipogenic differentiation, reduces lipid droplet accumulation, restricts lipid droplet transfer, impedes obesity progression, and lowers the risk of obesity-associated non-alcoholic fatty liver disease in female mice with obesity. Furthermore, diverse administration routes of KT-NE impact its in vivo biodistribution and contribute to localized and/or systemic anti-obesity effectiveness.
Injectable hydrogel electrodes as conduction highways to restore native pacing
Authors: Rodriguez-Rivera Gabriel J. , Post Allison , John Mathews , Buchan Skylar , Bernard Drew , Razavi Mehdi , Cosgriff-Hernandez Elizabeth
Published: January 2024

There is an urgent clinical need for a treatment regimen that addresses the underlying pathophysiology of ventricular arrhythmias, the leading cause of sudden cardiac death. The current report describes the design of an injectable hydrogel electrode and successful deployment in a pig model with access far more refined than any current pacing modalities allow. In addition to successful cardiac capture and pacing, analysis of surface ECG tracings and three-dimensional electroanatomic mapping revealed a QRS morphology comparable to native sinus rhythm, strongly suggesting the hydrogel electrode captures the deep septal bundle branches and Purkinje fibers. In an ablation model, electroanatomic mapping data demonstrated that the activation wavefront from the hydrogel reaches the mid-myocardium and endocardium much earlier than current single-point pacing modalities. Such uniform activation of broad swaths of tissue enables an opportunity to minimize the delayed myocardial conduction of heterogeneous tissue that underpins re-entry. Collectively, these studies demonstrate the feasibility of a new pacing modality that most closely resembles native conduction with the potential to eliminate lethal re-entrant arrhythmias and provide painless defibrillation.
A light-activatable theranostic combination for ratiometric hypoxia imaging and oxygen-deprived drug activity enhancement
Authors: Ge Lei , Tang Yikai , Wang Chongzhi , Chen Jian , Mao Hui , Jiang Xiqun
Published: January 2024

While performing oxygen-related tumour treatments such as chemotherapy and photodynamic therapy, real-time monitoring hypoxia of tumour is of great value and significance. Here, we design a theranostic combination for light-activated ratiometric hypoxia imaging, hypoxia modulating and prodrug activation. This combination consisted of an oxygen-sensitive near-infrared-emitting ratiometric phosphorescence probe and a hypoxia-activated prodrug-loaded covalent organic framework. In this combination, the probe plays two roles, including quantitative monitoring of oxygen concentration by ratiometric imaging and consuming the oxygen of tumour under light excitation by photodynamic therapy. Meanwhile, the enhanced hypoxia microenvironment of tumour can raise the cytotoxicity of prodrug loaded in covalent organic framework, resulting in boosting antitumour therapeutic effects in vivo. This theranostic combination can precisely provide therapeutic regime and screen hypoxia-activated prodrugs based on real-time tumour hypoxia level, offering a strategy to develop hypoxia mediated tumour theranostics with hypoxia targeted prodrugs.
Inferring language dispersal patterns with velocity field estimation
Authors: Yang Sizhe , Sun Xiaoru , Jin Li , Zhang Menghan
Published: January 2024

Reconstructing the spatial evolution of languages can deepen our understanding of the demic diffusion and cultural spread. However, the phylogeographic approach that is frequently used to infer language dispersal patterns has limitations, primarily because the phylogenetic tree cannot fully explain the language evolution induced by the horizontal contact among languages, such as borrowing and areal diffusion. Here, we introduce the language velocity field estimation, which does not rely on the phylogenetic tree, to infer language dispersal trajectories and centre. Its effectiveness and robustness are verified through both simulated and empirical validations. Using language velocity field estimation, we infer the dispersal patterns of four agricultural language families and groups, encompassing approximately 700 language samples. Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. Our findings highlight that the agricultural languages dispersed alongside the demic diffusions and cultural spreads during the past 10,000 years. We expect that language velocity field estimation could aid the spatial analysis of language evolution and further branch out into the studies of demographic and cultural dynamics.
Universal microbial reworking of dissolved organic matter along environmental gradients
Authors: Freeman Erika C. , Emilson Erik J. S. , Dittmar Thorsten , Braga Lucas P. P. , Emilson Caroline E. , Goldhammer Tobias , Martineau Christine , Singer Gabriel , Tanentzap Andrew J.
Published: January 2024

Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can offset their carbon sink capacity. However, the processes underlying DOM degradation across environments are poorly understood. Here we show DOM changes similarly along soil-aquatic gradients irrespective of environmental differences. Using ultrahigh-resolution mass spectrometry, we track DOM along soil depths and hillslope positions in forest catchments and relate its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, we find carbohydrate-like and unsaturated hydrocarbon-like compounds increase in abundance-weighted mass, and the expression of genes essential for degrading plant-derived carbohydrates explains >50% of the variation in abundance of these compounds. These results suggest that microbes transform plant-derived compounds, leaving DOM to become increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. By synthesising data from the land-to-ocean continuum, we suggest these processes generalise across ecosystems and spatiotemporal scales. Such general degradation patterns can help predict DOM composition and reactivity along environmental gradients to inform management of soil-to-stream carbon losses.
Projected soil carbon loss with warming in constrained Earth system models
Authors: Ren Shuai , Wang Tao , Guenet Bertrand , Liu Dan , Cao Yingfang , Ding Jinzhi , Smith Pete , Piao Shilong
Published: January 2024

The soil carbon-climate feedback is currently the least constrained component of global warming projections, and the major source of uncertainties stems from a poor understanding of soil carbon turnover processes. Here, we assemble data from long-term temperature-controlled soil incubation studies to show that the arctic and boreal region has the shortest intrinsic soil carbon turnover time while tropical forests have the longest one, and current Earth system models overestimate intrinsic turnover time by 30 percent across active, slow and passive carbon pools. Our constraint suggests that the global soils will switch from carbon sink to source, with a loss of 0.22–0.53 petagrams of carbon per year until the end of this century from strong mitigation to worst emission scenarios, suggesting that global soils will provide a strong positive carbon feedback on warming. Such a reversal of global soil carbon balance would lead to a reduction of 66% and 15% in the current estimated remaining carbon budget for limiting global warming well below 1.5 °C and 2 °C, respectively, rendering climate mitigation much more difficult.
CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei
Authors: Kijner Sivan , Ennis Dena , Shmorak Shimrit , Florentin Anat , Yassour Moran
Published: January 2024

The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
Terminal modifications independent cell-free RNA sequencing enables sensitive early cancer detection and classification
Authors: Wang Jun , Huang Jinyong , Hu Yunlong , Guo Qianwen , Zhang Shasha , Tian Jinglin , Niu Yanqin , Ji Ling , Xu Yuzhong , Tang Peijun , He Yaqin , Wang Yuna , Zhang Shuya , Yang Hao , Kang Kang , Chen Xinchun , Li Xinying , Yang Ming , Gou Deming
Published: January 2024

Cell-free RNAs (cfRNAs) offer an opportunity to detect diseases from a transcriptomic perspective, however, existing techniques have fallen short in generating a comprehensive cell-free transcriptome profile. We develop a sensitive library preparation method that is robust down to 100 µl input plasma to analyze cfRNAs independent of their 5’-end modifications. We show that it outperforms adapter ligation-based method in detecting a greater number of cfRNA species. We perform transcriptome-wide characterizations in 165 lung cancer, 30 breast cancer, 37 colorectal cancer, 55 gastric cancer, 15 liver cancer, and 133 cancer-free participants and demonstrate its ability to identify transcriptomic changes occurring in early-stage tumors. We also leverage machine learning analyses on the differentially expressed cfRNA signatures and reveal their robust performance in cancer detection and classification. Our work sets the stage for in-depth study of the cfRNA repertoire and highlights the value of cfRNAs as cancer biomarkers in clinical applications.
Molecular mechanism of antihistamines recognition and regulation of the histamine H1 receptor
Authors: Wang Dandan , Guo Qiong , Wu Zhangsong , Li Ming , He Binbin , Du Yang , Zhang Kaiming , Tao Yuyong
Published: January 2024

Histamine receptors are a group of G protein-coupled receptors (GPCRs) that play important roles in various physiological and pathophysiological conditions. Antihistamines that target the histamine H1 receptor (H1R) have been widely used to relieve the symptoms of allergy and inflammation. Here, to uncover the details of the regulation of H1R by the known second-generation antihistamines, thereby providing clues for the rational design of newer antihistamines, we determine the cryo-EM structure of H1R in the apo form and bound to different antihistamines. In addition to the deep hydrophobic cavity, we identify a secondary ligand-binding site in H1R, which potentially may support the introduction of new derivative groups to generate newer antihistamines. Furthermore, these structures show that antihistamines exert inverse regulation by utilizing a shared phenyl group that inserts into the deep cavity and block the movement of the toggle switch residue W4286.48. Together, these results enrich our understanding of GPCR modulation and facilitate the structure-based design of novel antihistamines.
Bioinspired structural hydrogels with highly ordered hierarchical orientations by flow-induced alignment of nanofibrils
Authors: Zhu Shuihong , Wang Sen , Huang Yifan , Tang Qiyun , Fu Tianqi , Su Riyan , Fan Chaoyu , Xia Shuang , Lee Pooi See , Lin Youhui
Published: January 2024

Natural structural materials often possess unique combinations of strength and toughness resulting from their complex hierarchical assembly across multiple length scales. However, engineering such well-ordered structures in synthetic materials via a universal and scalable manner still poses a grand challenge. Herein, a simple yet versatile approach is proposed to design hierarchically structured hydrogels by flow-induced alignment of nanofibrils, without high time/energy consumption or cumbersome postprocessing. Highly aligned fibrous configuration and structural densification are successfully achieved in anisotropic hydrogels under ambient conditions, resulting in desired mechanical properties and damage-tolerant architectures, for example, strength of 14 ± 1 MPa, toughness of 154 ± 13 MJ m−3, and fracture energy of 153 ± 8 kJ m−2. Moreover, a hydrogel mesoporous framework can deliver ultra-fast and unidirectional water transport (maximum speed at 65.75 mm s−1), highlighting its potential for water purification. This scalable fabrication explores a promising strategy for developing bioinspired structural hydrogels, facilitating their practical applications in biomedical and engineering fields.
Photogating-assisted tunneling boosts the responsivity and speed of heterogeneous WSe2/Ta2NiSe5 photodetectors
Authors: Liu Mingxiu , Wei Jingxuan , Qi Liujian , An Junru , Liu Xingsi , Li Yahui , Shi Zhiming , Li Dabing , Novoselov Kostya S. , Qiu Cheng-Wei , Li Shaojuan
Published: January 2024

Photogating effect is the dominant mechanism of most high-responsivity two-dimensional (2D) material photodetectors. However, the ultrahigh responsivities in those devices are intrinsically at the cost of very slow response speed. In this work, we report a WSe2/Ta2NiSe5 heterostructure detector whose photodetection gain and response speed can be enhanced simultaneously, overcoming the trade-off between responsivity and speed. We reveal that photogating-assisted tunneling synergistically allows photocarrier multiplication and carrier acceleration through tunneling under an electrical field. The photogating effect in our device features low-power consumption (in the order of nW) and shows a dependence on the polarization states of incident light, which can be further tuned by source-drain voltages, allowing for wavelength discrimination with just a two-electrode planar structure. Our findings offer more opportunities for the long-sought next-generation photodetectors with high responsivity, fast speed, polarization detection, and multi-color sensing, simultaneously.
Human apical-out nasal organoids reveal an essential role of matrix metalloproteinases in airway epithelial differentiation
Authors: Li Liyue , Jiao Linyi , Feng Danni , Yuan Yizhang , Yang Xiaoqian , Li Jian , Jiang Dong , Chen Hexin , Meng Qingxiang , Chen Ruchong , Fang Bixing , Zou Xuenong , Luo Zhenhua , Ye Xiaoyan , Hong Yue , Liu Chun , Li Chunwei
Published: January 2024

Extracellular matrix (ECM) assembly/disassembly is a critical regulator for airway epithelial development and remodeling. Airway organoid is widely used in respiratory research, yet there is limited study to indicate the roles and mechanisms of ECM organization in epithelial growth and differentiation by using in vitro organoid system. Moreover, most of current Matrigel-based airway organoids are in basal-out orientation where accessing the apical surface is challenging. We present a human apical-out airway organoid using a biochemically defined hybrid hydrogel system. During human nasal epithelial progenitor cells (hNEPCs) differentiation, the gel gradually degrade, leading to the organoid apical surfaces facing outward. The expression and activity of ECM-degrading enzymes, matrix metalloproteinases (MMP7, MMP9, MMP10 and MMP13) increases during organoid differentiation, where inhibition of MMPs significantly suppresses the normal ciliation, resulting in increased goblet cell proportion. Moreover, a decrease of MMPs is found in goblet cell hyperplastic epithelium in inflammatory mucosa. This system reveals essential roles of epithelial-derived MMPs on epithelial cell fate determination, and provides an applicable platform enabling further study for ECM in regulating airway development in health and diseases.
Isotope engineering for spin defects in van der Waals materials
Authors: Gong Ruotian , Du Xinyi , Janzen Eli , Liu Vincent , Liu Zhongyuan , He Guanghui , Ye Bingtian , Li Tongcang , Yao Norman Y. , Edgar James H. , Henriksen Erik A. , Zu Chong
Published: January 2024

Spin defects in van der Waals materials offer a promising platform for advancing quantum technologies. Here, we propose and demonstrate a powerful technique based on isotope engineering of host materials to significantly enhance the coherence properties of embedded spin defects. Focusing on the recently-discovered negatively charged boron vacancy center ($${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

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) in hexagonal boron nitride (hBN), we grow isotopically purified h10B15N crystals. Compared to $${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

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in hBN with the natural distribution of isotopes, we observe substantially narrower and less crowded $${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

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spin transitions as well as extended coherence time T2 and relaxation time T1. For quantum sensing, $${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

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centers in our h10B15N samples exhibit a factor of 4 (2) enhancement in DC (AC) magnetic field sensitivity. For additional quantum resources, the individual addressability of the $${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

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hyperfine levels enables the dynamical polarization and coherent control of the three nearest-neighbor 15N nuclear spins. Our results demonstrate the power of isotope engineering for enhancing the properties of quantum spin defects in hBN, and can be readily extended to improving spin qubits in a broad family of van der Waals materials.
Spontaneous emergence of rudimentary music detectors in deep neural networks
Authors: Kim Gwangsu , Kim Dong-Kyum , Jeong Hawoong
Published: January 2024

Music exists in almost every society, has universal acoustic features, and is processed by distinct neural circuits in humans even with no experience of musical training. However, it remains unclear how these innate characteristics emerge and what functions they serve. Here, using an artificial deep neural network that models the auditory information processing of the brain, we show that units tuned to music can spontaneously emerge by learning natural sound detection, even without learning music. The music-selective units encoded the temporal structure of music in multiple timescales, following the population-level response characteristics observed in the brain. We found that the process of generalization is critical for the emergence of music-selectivity and that music-selectivity can work as a functional basis for the generalization of natural sound, thereby elucidating its origin. These findings suggest that evolutionary adaptation to process natural sounds can provide an initial blueprint for our sense of music.
Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions
Authors: Tam Phoebe Lut Fei , Cheung Ming Fung , Chan Lu Yan , Leung Danny
Published: January 2024

SETDB1 is an essential histone methyltransferase that deposits histone H3 lysine 9 trimethylation (H3K9me3) to transcriptionally repress genes and repetitive elements. The function of differential H3K9me3 enrichment between cell-types remains unclear. Here, we demonstrate mutual exclusivity of H3K9me3 and CTCF across mouse tissues from different developmental timepoints. We analyze SETDB1 depleted cells and discover that H3K9me3 prevents aberrant CTCF binding independently of DNA methylation and H3K9me2. Such sites are enriched with SINE B2 retrotransposons. Moreover, analysis of higher-order genome architecture reveals that large chromatin structures including topologically associated domains and subnuclear compartments, remain intact in SETDB1 depleted cells. However, chromatin loops and local 3D interactions are disrupted, leading to transcriptional changes by modifying pre-existing chromatin landscapes. Specific genes with altered expression show differential interactions with dysregulated cis-regulatory elements. Collectively, we find that cell-type specific targets of SETDB1 maintain cellular identities by modulating CTCF binding, which shape nuclear architecture and transcriptomic networks.
Constructing sulfur and oxygen super-coordinated main-group electrocatalysts for selective and cumulative H2O2 production
Authors: Zhou Xiao , Min Yuan , Zhao Changming , Chen Cai , Ke Ming-Kun , Xu Shi-Lin , Chen Jie-Jie , Wu Yuen , Yu Han-Qing
Published: January 2024

Direct electrosynthesis of hydrogen peroxide (H2O2) via the two-electron oxygen reduction reaction presents a burgeoning alternative to the conventional energy-intensive anthraquinone process for on-site applications. Nevertheless, its adoption is currently hindered by inferior H2O2selectivity and diminished H2O2yield induced by consecutive H2O2reduction or Fenton reactions. Herein, guided by theoretical calculations, we endeavor to overcome this challenge by activating a main-group Pb single-atom catalyst via a local micro-environment engineering strategy employing a sulfur and oxygen super-coordinated structure. The main-group catalyst, synthesized using a carbon dot-assisted pyrolysis technique, displays an industrial current density reaching 400 mA cm−2and elevated accumulated H2O2concentrations (1358 mM) with remarkable Faradaic efficiencies. Both experimental results and theoretical simulations elucidate that S and O super-coordination directs a fraction of electrons from the main-group Pb sites to the coordinated oxygen atoms, consequently optimizing the *OOH binding energy and augmenting the 2e−oxygen reduction activity. This work unveils novel avenues for mitigating the production-depletion challenge in H2O2electrosynthesis through the rational design of main-group catalysts.
Nanowire-assisted electrochemical perforation of graphene oxide nanosheets for molecular separation
Authors: Liu Hai , Huang Xinxi , Wang Yang , Kuang Baian , Li Wanbin
Published: January 2024

Two-dimensional nanosheets, e.g., graphene oxide (GO), have been widely used to fabricate efficient membranes for molecular separation. However, because of poor transport across nanosheets and high width-to-thickness ratio, the permeation pathway length and tortuosity of these membranes are extremely large, which limit their separation performance. Here we report a facile, scalable, and controllable nanowire electrochemical concept for perforating and modifying nanosheets to shorten permeation pathway and adjust transport property. It is found that confinement effects with locally enhanced charge density, electric field, and hydroxyl radical generation over nanowire tips on anode can be executed under low voltage, thereby inducing confined direct electron loss and indirect oxidation to reform configuration and composition of GO nanosheets. We demonstrate that the porous GO nanosheets with a lot of holes are suitable for assembling separation membranes with tuned accessibility, tortuosity, interlayer space, electronegativity, and hydrophilicity. For molecular separation, the prepared membranes exhibit quadruple water permeance and higher rejections for salts (>91%) and small molecules (>96%) as/than original ones. This nanowire electrochemical perforation concept offers a feasible strategy to reconstruct two-dimensional materials and tune their transport property for separation.
Full-landscape selection rules of electrons and phonons and temperature-induced effects in 2D silicon and germanium allotropes
Authors: Shu Le , Xia Yujie , Li Ben , Peng Lei , Shao Hezhu , Wang Zengxu , Cen Yan , Zhu Heyuan , Zhang Hao
Published: January 2024

The electron-phonon (el-ph) and phonon-phonon interactions play crucial roles in determining the electronic and thermal transport properties of materials. Using the group theory and ab-initio calculations, we have derived the full-landscape selection rules for intravalley and intervalley scattering for carriers in 2D silicon and germanium allotropes with low buckled (LB) and large honeycomb dumbbell (LHD) structures, showing dominant role of optical modes in total el-ph coupling in LHD Si/Ge due to most el-ph scattering channels via acoustic modes blocked by symmetries. Remarkably, we show that due to the relatively large optical phonon bandwidth and “bunching effect" of acoustic phonon bands, the selection rules of three-phonon interactions reveal the dominant ooo and aoo channels in LHD and LB Si/Ge, respectively, and the temprature-induced effects significantly increase the ratio between mode-resolved four-phonon interactions and three-phonon interactions in most of the phonon-frequency region, finally leading to the low thermal conductivities in both LB and LHD Si/Ge. Furthermore, we observe the anomalous temperature-dependent thermal conductivities in LHD Ge, resulted from the vanishing quasi-acoustic-optical phonon gap under the temperature-induced effects. By considering full el-ph coupling and higher-order anharmonic phonon-phonon interactions, the maximal thermoelectric figures of merits in LHD Si and LB Ge are found to reach 1.06 and 0.66 at 700 K, respectively, significantly surpassing their bulk counterparts. Our work is poised to stimulate wide-ranging exploration into phonon transport across diverse materials, and benefits both fundamental knowledge and advanced technologies of 2D Si/Ge allotropes.
Structure-aware graph neural network based deep transfer learning framework for enhanced predictive analytics on diverse materials datasets
Authors: Gupta Vishu , Choudhary Kamal , DeCost Brian , Tavazza Francesca , Campbell Carelyn , Liao Wei-keng , Choudhary Alok , Agrawal Ankit
Published: January 2024

Modern data mining methods have demonstrated effectiveness in comprehending and predicting materials properties. An essential component in the process of materials discovery is to know which material(s) will possess desirable properties. For many materials properties, performing experiments and density functional theory computations are costly and time-consuming. Hence, it is challenging to build accurate predictive models for such properties using conventional data mining methods due to the small amount of available data. Here we present a framework for materials property prediction tasks using structure information that leverages graph neural network-based architecture along with deep-transfer-learning techniques to drastically improve the model’s predictive ability on diverse materials (3D/2D, inorganic/organic, computational/experimental) data. We evaluated the proposed framework in cross-property and cross-materials class scenarios using 115 datasets to find that transfer learning models outperform the models trained from scratch in 104 cases, i.e., ≈90%, with additional benefits in performance for extrapolation problems. We believe the proposed framework can be widely useful in accelerating materials discovery in materials science.
Aggregate-prone brain regions in Parkinson’s disease are rich in unique N-terminus α-synuclein conformers with high proteolysis susceptibility
Authors: Wiseman James A. , Murray Helen C. , Faull Richard L. M. F. , Dragunow Michael , Turner Clinton P. , Dieriks Birger Victor , Curtis Maurice A.
Published: January 2024

In Parkinson’s disease (PD), and other α-synucleinopathies, α-synuclein (α-Syn) aggregates form a myriad of conformational and truncational variants. Most antibodies used to detect and quantify α-Syn in the human brain target epitopes within the C-terminus (residues 96–140) of the 140 amino acid protein and may fail to capture the diversity of α-Syn variants present in PD. We sought to investigate the heterogeneity of α-Syn conformations and aggregation states in the PD human brain by labelling with multiple antibodies that detect epitopes along the entire length of α-Syn. We used multiplex immunohistochemistry to simultaneously immunolabel tissue sections with antibodies mapping the three structural domains of α-Syn. Discrete epitope-specific immunoreactivities were visualised and quantified in the olfactory bulb, medulla, substantia nigra, hippocampus, entorhinal cortex, middle temporal gyrus, and middle frontal gyrus of ten PD cases, and the middle temporal gyrus of 23 PD, and 24 neurologically normal cases. Distinct Lewy neurite and Lewy body aggregate morphologies were detected across all interrogated regions/cases. Lewy neurites were the most prominent in the olfactory bulb and hippocampus, while the substantia nigra, medulla and cortical regions showed a mixture of Lewy neurites and Lewy bodies. Importantly, unique N-terminus immunoreactivity revealed previously uncharacterised populations of (1) perinuclear, (2) glial (microglial and astrocytic), and (3) neuronal lysosomal α-Syn aggregates. These epitope-specific N-terminus immunoreactive aggregate populations were susceptible to proteolysis via time-dependent proteinase K digestion, suggesting a less stable oligomeric aggregation state. Our identification of unique N-terminus immunoreactive α-Syn aggregates adds to the emerging paradigm that α-Syn pathology is more abundant and complex in human brains with PD than previously realised. Our findings highlight that labelling multiple regions of the α-Syn protein is necessary to investigate the full spectrum of α-Syn pathology and prompt further investigation into the functional role of these N-terminus polymorphs.
Oral nanotherapeutic formulation of insulin with reduced episodes of hypoglycaemia
Authors: Hunt Nicholas J. , Lockwood Glen P. , Heffernan Scott J. , Daymond Jarryd , Ngu Meng , Narayanan Ramesh K. , Westwood Lara J. , Mohanty Biswaranjan , Esser Lars , Williams Charlotte C. , Kuncic Zdenka , McCourt Peter A. G. , Le Couteur David G. , Cogger Victoria C.
Published: January 2024

Injectable insulin is an extensively used medication with potential life-threatening hypoglycaemic events. Here we report on insulin-conjugated silver sulfide quantum dots coated with a chitosan/glucose polymer to produce a responsive oral insulin nanoformulation. This formulation is pH responsive, is insoluble in acidic environments and shows increased absorption in human duodenum explants and Caenorhabditis elegans at neutral pH. The formulation is sensitive to glucosidase enzymes to trigger insulin release. It is found that the formulation distributes to the liver in mice and rats after oral administration and promotes a dose-dependent reduction in blood glucose without promoting hypoglycaemia or weight gain in diabetic rodents. Non-diabetic baboons also show a dose-dependent reduction in blood glucose. No biochemical or haematological toxicity or adverse events were observed in mice, rats and non-human primates. The formulation demonstrates the potential to orally control blood glucose without hypoglycaemic episodes.
Short-range translocation by a restriction enzyme motor triggers diffusion along DNA
Authors: Göse Martin , Magill Emma E. , Hughes-Games Alex , Shaw Steven J. , Diffin Fiona M. , Rawson Tara , Nagy Zsofia , Seidel Ralf , Szczelkun Mark D.
Published: January 2024

Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion (‘DNA sliding’) initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8–15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.
A type 1 immunity-restricted promoter of the IL−33 receptor gene directs antiviral T-cell responses
Authors: Brunner Tobias M. , Serve Sebastian , Marx Anna-Friederike , Fadejeva Jelizaveta , Saikali Philippe , Dzamukova Maria , Durán-Hernández Nayar , Kommer Christoph , Heinrich Frederik , Durek Pawel , Heinz Gitta A. , Höfer Thomas , Mashreghi Mir-Farzin , Kühn Ralf , Pinschewer Daniel D. , Löhning Max
Published: January 2024

The pleiotropic alarmin interleukin-33 (IL-33) drives type 1, type 2 and regulatory T-cell responses via its receptor ST2. Subset-specific differences in ST2 expression intensity and dynamics suggest that transcriptional regulation is key in orchestrating the context-dependent activity of IL-33–ST2 signaling in T-cell immunity. Here, we identify a previously unrecognized alternative promoter in mice and humans that is located far upstream of the curated ST2-coding gene and drives ST2 expression in type 1 immunity. Mice lacking this promoter exhibit a selective loss of ST2 expression in type 1- but not type 2-biased T cells, resulting in impaired expansion of cytotoxic T cells (CTLs) and T-helper 1 cells upon viral infection. T-cell-intrinsic IL-33 signaling via type 1 promoter-driven ST2 is critical to generate a clonally diverse population of antiviral short-lived effector CTLs. Thus, lineage-specific alternative promoter usage directs alarmin responsiveness in T-cell subsets and offers opportunities for immune cell-specific targeting of the IL-33–ST2 axis in infections and inflammatory diseases.
Drone-Person Tracking in Uniform Appearance Crowd: A New Dataset
Authors: Alansari Mohamad , Abdul Hay Oussama , Alansari Sara , Javed Sajid , Shoufan Abdulhadi , Zweiri Yahya , Werghi Naoufel
Published: January 2024

Drone-person tracking in uniform appearance crowds poses unique challenges due to the difficulty in distinguishing individuals with similar attire and multi-scale variations. To address this issue and facilitate the development of effective tracking algorithms, we present a novel dataset named D-PTUAC (Drone-Person Tracking in Uniform Appearance Crowd). The dataset comprises 138 sequences comprising over 121 K frames, each manually annotated with bounding boxes and attributes. During dataset creation, we carefully consider 18 challenging attributes encompassing a wide range of viewpoints and scene complexities. These attributes are annotated to facilitate the analysis of performance based on specific attributes. Extensive experiments are conducted using 44 state-of-the-art (SOTA) trackers, and the performance gap between the visual object trackers on existing benchmarks compared to our proposed dataset demonstrate the need for a dedicated end-to-end aerial visual object tracker that accounts the inherent properties of aerial environment.
A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea
Authors: Latz Meike A. C. , Andersson Agneta , Brugel Sonia , Hedblom Mikael , Jurdzinski Krzysztof T. , Karlson Bengt , Lindh Markus , Lycken Jenny , Torstensson Anders , Andersson Anders F.
Published: January 2024

The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.
A global dataset of experimental intercropping and agroforestry studies in horticulture
Authors: Paut Raphaël , Garreau Léa , Ollivier Guillaume , Sabatier Rodolphe , Tchamitchian Marc
Published: January 2024

Intercropping and agroforestry systems have been increasingly well studied and documented. Yet, so far, no dataset has provided a systematic synthesis of existing data on intercropping experiments in the specific field of horticulture. A systematic literature search was carried using search terms and applied to Web of Science. The resulting dataset includes data from field experiments published in 191 articles covering experiments worldwide, between 1982 and 2022. The selected experiments cover five continents and involved 118 different crop species. Through manual extraction of information from publications, the dataset includes (i) general information on the articles; (ii) experimental site soil and climate conditions; (iii) descriptions of intercropping designs; (iv) crop management practices; (v) measurements of sole crop and intercrop yields and (v) Land Equivalent Ratios. The dataset is arranged in an easily reusable spreadsheet with columns as variables (n = 45) and rows as treatment (n = 1544). The dataset is freely reusable and updateable. We expect that it will provide valuable information for statistical analysis, modeling and innovative farming system design based on intercropping.
CAS Landslide Dataset: A Large-Scale and Multisensor Dataset for Deep Learning-Based Landslide Detection
Authors: Xu Yulin , Ouyang Chaojun , Xu Qingsong , Wang Dongpo , Zhao Bo , Luo Yutao
Published: January 2024

In this work, we present the CAS Landslide Dataset, a large-scale and multisensor dataset for deep learning-based landslide detection, developed by the Artificial Intelligence Group at the Institute of Mountain Hazards and Environment, Chinese Academy of Sciences (CAS). The dataset aims to address the challenges encountered in landslide recognition. With the increase in landslide occurrences due to climate change and earthquakes, there is a growing need for a precise and comprehensive dataset to support fast and efficient landslide recognition. In contrast to existing datasets with dataset size, coverage, sensor type and resolution limitations, the CAS Landslide Dataset comprises 20,865 images, integrating satellite and unmanned aerial vehicle data from nine regions. To ensure reliability and applicability, we establish a robust methodology to evaluate the dataset quality. We propose the use of the Landslide Dataset as a benchmark for the construction of landslide identification models and to facilitate the development of deep learning techniques. Researchers can leverage this dataset to obtain enhanced prediction, monitoring, and analysis capabilities, thereby advancing automated landslide detection.
Drought Atlas of India, 1901–2020
Authors: Chuphal Dipesh Singh , Kushwaha Anuj Prakash , Aadhar Saran , Mishra Vimal
Published: January 2024

India has been considerably affected by droughts in the recent past. Despite the considerable impacts of droughts on agriculture and water resources, long-term datasets to examine droughts and their consequences at appropriate spatial and temporal scales have been lacking in India. Datasets that provide drought information are mostly available for a short period and at coarser resolutions, therefore, these do not comprehend the information regarding the major droughts that occurred in the distant past at administrative scales of decision-making. To fill this critical gap, we developed the high-resolution (0.05°) and long-term monthly precipitation and temperature datasets for the 1901–2021 period. We used long-term high-resolution precipitation and temperature to estimate droughts using standardized precipitation and evapotranspiration index (SPEI). As SPEI considers the role of air temperature in drought estimation, it can be used to examine meteorological, agricultural, and hydrological droughts. Using high-resolution SPEI, we developed drought atlas for India (1901–2020) that can provide comprehensive information on drought occurrence, impacts, and risks in India.
Dynamical behavior of solitons of the (2+1)-dimensional Konopelchenko Dubrovsky system
Authors: Hussain A. , Parveen T. , Younis B. A. , Ahamd Huda U. M. , Ibrahim T. F. , Sallah Mohammed
Published: January 2024

Utilizing nonlinear evolution equations (NEEs) is common practice to establish the fundamental assumptions underlying natural phenomena. This paper examines the weakly dispersed non-linear waves in mathematical physics represented by the Konopelchenko-Dubrovsky (KD) equations. The $$(G^\prime /G^2)$$

(

G
′

/

G
2

)

-expansion method is used to analyze the model under consideration. Using symbolic computations, the $$(G^\prime /G^2)$$

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G
′

/

G
2

)

-expansion method is used to produce solitary waves and soliton solutions to the $$(2+1)$$

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2
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)

-dimensional KD model in terms of trigonometric, hyperbolic, and rational functions. Mathematica simulations are displayed using two, three, and density plots to demonstrate the obtained solitary wave solutions’ behavior. These proposed solutions have not been documented in the existing literature.
Home-based monitoring of persons with advanced Parkinson’s disease using smartwatch-smartphone technology
Authors: Fay-Karmon Tsviya , Galor Noam , Heimler Benedetta , Zilka Asaf , Bartsch Ronny P. , Plotnik Meir , Hassin-Baer Sharon
Published: January 2024

Movement deterioration is the hallmark of Parkinson’s disease (PD), characterized by levodopa-induced motor-fluctuations (i.e., symptoms’ variability related to the medication cycle) in advanced stages. However, motor symptoms are typically too sporadically and/or subjectively assessed, ultimately preventing the effective monitoring of their progression, and thus leading to suboptimal treatment/therapeutic choices. Smartwatches (SW) enable a quantitative-oriented approach to motor-symptoms evaluation, namely home-based monitoring (HBM) using an embedded inertial measurement unit. Studies validated such approach against in-clinic evaluations. In this work, we aimed at delineating personalized motor-fluctuations’ profiles, thus capturing individual differences. 21 advanced PD patients with motor fluctuations were monitored for 2 weeks using a SW and a smartphone-dedicated app (Intel Pharma Analytics Platform). The SW continuously collected passive data (tremor, dyskinesia, level of activity using dedicated algorithms) and active data, i.e., time-up-and-go, finger tapping, hand tremor and hand rotation carried out daily, once in OFF and once in ON levodopa periods. We observed overall high compliance with the protocol. Furthermore, we observed striking differences among the individual patterns of symptoms’ levodopa-related variations across the HBM, allowing to divide our participants among four data-driven, motor-fluctuations’ profiles. This highlights the potential of HBM using SW technology for revolutionizing clinical practices.