bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on signal characteristics of burst tendency coal under different loading rates
Authors: Zhou Chao , He Xueqiu , Song Dazhao , Li Zhenlei , Yang Huakang , Liu Yang , Guo Lei
Published: August 2024

In order to study the mechanics, acoustic emission (AE) and electromagnetic emission (EME) response law of bursting liability coal at different loading rates, uniaxial compression tests were carried out on coal mass from Konggu Coal Mine. The corresponding relations among mechanical properties, AE and EME signals in the process of coal failure under loading were analyzed, and the energy evolution law of coal failure with bursting liability under loading rate was discussed. The results show that within a certain range of loading rate, the higher the loading rate, the higher the compressive strength and peak load of bursting liability coal, and the shorter the time for coal to reach the peak load. Under different loading rates, the mechanics, AE and EME signals of coal samples can be well corresponded. When the loading rate is low, the number of blocks destroyed of coal sample is large and the block size is relatively small, and the blocks are mainly scattered around the test platform. When the loading rate is high, the number of damaged blocks is relatively small and the block size is relatively large, and the blocks are far away from the test bench. When loading at a low rate, the internal cracks in coal can be fully developed and connected, and the energy release rate is relatively uniform in the process of loading and failure of coal sample. In the case of high loading rate, the energy release rate of coal sample in the loading process is much smaller than that in the moment of failure. Combining the above test results with the actual situation of the working face, it can be concluded that the total energy stored in the coal of fast mining increases and the threshold of impact decreases compared with that of slow mining. Therefore, under the disturbance of external dynamic load, rapid mining is more likely to induce rock burst.
Effect of Spheroidization and Inoculation on the Early Solidification Steps of Hypereutectic Cast Irons
Authors: Popelar Patrik , Lacaze Jacques
Published: August 2024

Compacted and spheroidal graphite silicon cast irons generally have slightly hypereutectic compositions when referred to the equilibrium phase diagram. Previous studies have shown that the thermal analysis of these melts often exhibits misleading characteristics that could prevent proper process control. It was the aim of the present work to provide new results, taking into account the carbon equivalent as well as spheroidization and inoculation levels. Overall, the features of slightly and highly hypereutectic melts deduced from previous studies were confirmed, while additional information was obtained concerning the effect of spheroidization and inoculation levels.
The Association Between IQ and Its Components and Anxiety in Autistic Girls
Authors: Bitsika Vicki , Sharpley Christopher F.
Published: August 2024

Objectives

To explore the effects of specific components of IQ on various forms of anxiety in autistic girls.

Methods

Full-Scale IQ, Block Design, Vocabulary, Matrix Reasoning and Similarities subtests of IQ, and Generalised Anxiety Disorder, Social Anxiety, and Separation Anxiety were assessed in a sample of 53 autistic girls aged 6 to 17 years old. The sample was dichotomised for age and menarche.

Results

Matrix Reasoning was found to be the only meaningful correlate of Social Anxiety for the entire sample, although inversely. Exploratory analyses suggested the possible effect of a developmentally based interaction between aspects of IQ and anxiety in autistic girls.

Conclusions

The role of developmentally linked sex hormone influences upon the social brain and prefrontal cortex function may underlie the associations between Matrix Reasoning and Social Anxiety in autistic girls.
Unveiling the epilepsy enigma: an agile and optimal machine learning approach for detecting inter-ictal state from electroencephalogram signals
Authors: Kaushik Shoibolina , Balachandra Mamatha , Olivia Diana , Khan Zaid
Published: August 2024

Epilepsy is a chronic neurological disorder characterized by the occurrence of paroxysmal recurrent seizures, which are caused by abnormal electrical activity in the brain. Seizures vary widely in their presentation, depending on the specific region of the brain involved and the extent of the abnormal electrical discharges. The disease can affect cognitive function posing a serious threat to the patients’ lives. Epilepsy causes emotional and behavioral changes, along with sleep disorders and migraines, leading to social isolation and discrimination. Timely administration of medication can cure most cases of epilepsy. However, identifying epileptic patients requires reviewing multiple EEG signal sheets, which can delay disease prediction. Therefore, the aim of our study is to apply simplistic machine learning algorithms that can study the EEG signal data swiftly to identify individuals in seizure, inter-ictal, and normal states, thereby aiding in medical diagnosis. The novelty of this study lies in the utilization of pre-built methods and develop a fast and efficient model that is lightweight and easy to integrate in healthcare to provide relief to epileptic patients. While previous studies have achieved high accuracy, the discussion involving time complexity of their models has been scarce. Given the importance of timely medication in managing epilepsy, it is crucial to consider the runtime of the model rather than solely focusing on accuracy. Therefore, a model that balances both a short runtime (2.9 min) and a satisfactory accuracy (97.46%) has been developed in this project. Integration of this project's findings will catalyze transformative changes within the healthcare industry, enabling healthcare professionals to detect epilepsy at earlier stages and provide timely interventions, ultimately fostering a system that prioritizes precision, innovation, and improved patient outcomes.
Momentary Associations Between Emotional Responses to Social Media and Affect: Consistency Across Global Affect and Specific Emotional States
Authors: Boyd Simone Imani , Dreier Melissa J. , Jorgensen Saskia L. , Moghaddas Serena L. , Kleiman Evan , Hamilton Jessica L.
Published: August 2024

Social media (SM) is widely used among adolescents, making the relationship between SM and affect in this population important to understand. However, previous research has largely used methods that do not capture the dynamic and variable nature of SM or measure the consistency of effects across global affect and specific emotions. The current study examined the momentary relationship between positive and negative SM experiences and global positive affect (PA) and negative affect (NA), as well as specific affective states of PA and NA. Adolescents (N = 62; 14–17 years old) were recruited from SM platforms to participate in an eight-week ecological momentary assessment study. Participants reported three times per day on PA and NA and positive and negative SM experiences. Random intercept and random slope models were used to examine within-person associations between momentary positive and negative SM experiences and affect after controlling for between-person differences. At prompts when participants reported greater-than-usual positive SM experiences, they reported higher global PA and lower global NA. At prompts when participants reported greater than their average negative SM experiences, they endorsed lower global PA and higher global NA. These results were consistent across same-valence specific affective states. The current study highlights proximal associations between SM experiences and affect, highlighting potential avenues of short-term risk and protection.
Multi-gene-based investigation on the molecular phylogeny of the hypotrichous family Strongylidiidae (Protista, Ciliophora), with notes on the ontogeny of a new genus and new species
Authors: Song Wenya , Zhang Shijing , Li Yuqing , Ma Honggang , Li Qiyu , Luo Xiaotian , Al-Rasheid Khaled A. S. , Hines Hunter N. , Lu Xiaoteng
Published: August 2024

Ciliates in the subclass Hypotrichia have long been difficult to classify as they are one of the most polymorphic and highly differentiated groups, leading to their systematics remaining unresolved. Phylogenetic relationships within the hypotrich family Strongylidiidae have been ambiguous due to discordance between the morphological and genetic data. In this study, a new strongylidiid genus Heterouroleptus is established, mainly based on the novel mode of origin of the ventral cirral rows: left ventral cirral row (LVR) originates from frontal–ventral–transverse cirral anlagen (FVTA) III (anterior portion), IV (middle portion), and V (rear portion); right ventral cirral row comes from the entire FVTA VI. A new species, Heterouroleptus weishanensis gen. nov., sp. nov., is investigated along with the morphometric and molecular data from a population of Strongylidium wuhanense. Eight new sequences and nuclear gene markers (single-gene and multi-gene) are provided to analyze the phylogenetic relationships of strongylidiids, with the COI gene utilized to uncover further genetic information at species level and below. The results reveal that: (1) Strongylidiidae is monophyletic and has a close relationship with Dorsomarginalia; (2) Heterouroleptus gen. nov. forms a clade that is sister to all the other strongylidiids; (3) Hemiamphisiella Foissner, 1988 and Pseudouroleptus Hemberger, 1985 should not be synonyms, and both genera should be subdivided due to their variable morphological characteristics; (4) LVR originating from three anlagen is a plesiomorphy of Strongylidiidae. The discovery of the origin of the LVR not only contributes to the establishment of the genus Heterouroleptus, but also helps to improve the diagnosis of the family Strongylidiidae.
Formation Mechanisms of Large‐Scale Folding in Greenland's Ice Sheet
Authors: Zhang Yu , Sachau Till , Franke Steven , Yang Haibin , Li Dian , Weikusat Ilka , Bons Paul D.
Published: August 2024

Radio‐echo sounding (RES) shows large‐scale englacial stratigraphic folds are ubiquitous in Greenland's ice sheet. However, there is no consensus yet on how these folds form. Here, we use the full‐Stokes code Underworld2 to simulate ice movements in three‐dimensional convergent flow, mainly considering ice anisotropy due to a crystallographic preferred orientation, vertical viscosity and density gradients in ice layers, and bedrock topography. Our simulated folds show complex patterns and are classified into: large‐scale folds (>100 m amplitude), small‐scale folds (<<100 m) and basal‐shear folds. The amplitudes of large‐scale folds tend to be at their maximum in the middle of the ice column or just below, in accordance with observations in RES data. We conclude that ice anisotropy amplifies the perturbations in ice layers (mainly due to bedrock topography) into large‐scale folds during flow. Density differences between the warm deep ice and cold ice above may enhance fold amplification.
Characteristics of Thin Magnetotail Current Sheet Plasmas at Lunar Distances
Authors: Kamaletdinov S. R. , Artemyev A. V. , Runov A. , Angelopoulos V.
Published: August 2024

The magnetotail current sheet plays a key role in the dynamics of Earth's magnetosphere. Specifically, the formation and subsequent reconnection of thin (ion‐gyroscale) current sheets are critical components of magnetospheric substorms. However, the precise mechanisms governing the configuration and distribution of current density in these thin current sheets remain elusive. By analyzing a data set consisting of 453 thin current sheet crossings observed by the Acceleration, Reconnection, Turbulence and Electrodynamics of Moon's Interaction with the Sun (ARTEMIS) mission, we explore the statistical properties of the ion and electron pressures and current densities, Ji and Je, in the spacecraft rest frame. Using magnetotail flapping and magnetic field measurements to estimate the total current density, J0, we find that it agrees well with the sum of those from direct ion and electron measurements, Ji + Je, respectively. In 65% of thin current sheets, electrons were found to dominate the contribution to the total current density in the spacecraft frame, with a typical dawnward drift velocity of ≳100 km/s. Diamagnetic drifts of electrons and ions estimated from their respective vertical pressure profiles (along the current sheet normal) reveal that the gradient of electron pressure alone cannot fully account for the observed high values of Je/Ji. Counter‐intuitively, for most (52% of) thin current sheets the electron vertical pressure profile is wider than the ion pressure profile, again suggesting that electron diamagnetism is an insufficient contributor to the current density at such sheets. These findings suggest the presence of a significant E × B dawnward drift that the electrons can fully acquire but ions cannot, being partially unmagnetized. We compare our results with those previously reported for the near‐Earth magnetotail and discuss them in the context of magnetotail current sheet modeling.
The Abundance and Sources of Ice Nucleating Particles Within Alaskan Ice Fog
Authors: Lill Emily , Costa Emily J. , Barry Kevin , Mirrielees Jessica A. , Mashkevich Monica , Wu Judy , Holen Andrew L. , Cesler‐Maloney Meeta , DeMott Paul J. , Perkins Russell , Hill Thomas , Sullivan Amy , Levin Ezra , Simpson William R. , Mao Jingqiu , Temime‐Roussel Brice , D'Anna Barbara , Law Kathy S. , Ault Andrew P. , Schmitt Carl , Pratt Kerri A. , Fischer Emily V. , Creamean Jessie
Published: August 2024

The Alaskan Layered Pollution and Chemical Analysis (ALPACA) field campaign included deployment of a suite of atmospheric measurements in January–February 2022 with the goal of better understanding atmospheric processes and pollution under cold and dark conditions in Fairbanks, Alaska. We report on measurements of particle composition, particle size, ice nucleating particle (INP) composition, and INP size during an ice fog period (29 January–3 February). During this period, coarse particulate matter (PM10) concentrations increased by 150% in association with a decrease in air temperature, a stronger temperature inversion, and relatively stagnant conditions. Results also show a 18%–78% decrease in INPs during the ice fog period, indicating that particles had activated into the ice fog via nucleation. Peroxide and heat treatments performed on INPs indicated that, on average, the largest contributions to the INP population were heat‐labile (potentially biological, 63%), organic (31%), then inorganic (likely dust, 6%). Measurements of levoglucosan and bulk and single‐particle composition corroborate the presence of dust and aerosols from combustion sources. Heat‐labile and organic INPs decreased during the peak period of the ice fog, indicating those were preferentially activated, while inorganic INPs increased, suggesting they remained as interstitial INPs. In general, INP concentrations were unexpectedly high in Fairbanks compared to other locations in the Arctic during winter. The fact that these INPs likely facilitated ice fog formation in Fairbanks has implications for other high latitude locations subject to the hazards associated with ice fog.
The North Pacific Meridional Mode and Its Impact on ENSO in the Second Version of the Chinese Academy of Sciences Earth System Model
Authors: Chen Shaowen , Chen Shangfeng , Jin Jiangbo , Zheng Yuqiong , Chen Wen , Zheng Tao , Feng Tao
Published: August 2024

The North Pacific Meridional Mode (PMM) is the strongest interannual air‐sea coupled system in the subtropical northeastern Pacific, which can significantly impact the development of El Niño and Southern Oscillation (ENSO). This study examines performance of the second version of the Chinese Academy of Sciences Earth System Model (CAS‐ESM2), developed primarily at the Institute of Atmospheric Physics, Chinese Academy of Sciences (IAP/CAS), in simulating the PMM, ENSO, and their relationship. It reveals that CAS‐ESM2 can well reproduce the tropical climate mean states, including sea surface temperature (SST), surface winds, and precipitation. Furthermore, the model shows a good ability in reproducing the seasonal evolutions of the PMM and ENSO. Moreover, CAS‐ESM2 effectively simulates the influence of the PMM on subsequent ENSO and the underlying physical mechanisms, including the wind‐evaporation‐SST feedback process, the trade wind charging mechanism and summer deep convection mechanism. However, some improvements are still needed, particularly in representing the periodicity of the PMM, an overestimation of the ENSO intensity and westward extension of ENSO‐related SST anomalies in the tropical Pacific. The results obtained from the CAS‐ESM2 showcase significant progress in understanding the interaction between air‐sea interaction systems over the tropics and subtropics.
Advancing from scalar to vectorial liquid crystal holography: a paradigm shift
Authors: Li Yan , Wu Shin-Tson
Published: August 2024

A versatile and tunable vectorial holography is demonstrated based on single-layer single-material liquid crystal superstructures. This novel approach advances the process from scalar to vectorial holography, opening new opportunities for advanced cryptography, super‑resolution imaging, and many other tunable photonic applications.
Giant ultrafast dichroism and birefringence with active nonlocal metasurfaces
Authors: Crotti Giulia , Akturk Mert , Schirato Andrea , Vinel Vincent , Trifonov Anton A. , Buchvarov Ivan C. , Neshev Dragomir N. , Proietti Zaccaria Remo , Laporta Paolo , Lemaître Aristide , Leo Giuseppe , Cerullo Giulio , Maiuri Margherita , Della Valle Giuseppe
Published: August 2024

Switching of light polarization on the sub-picosecond timescale is a crucial functionality for applications in a variety of contexts, including telecommunications, biology and chemistry. The ability to control polarization at ultrafast speed would pave the way for the development of unprecedented free-space optical links and of novel techniques for probing dynamical processes in complex systems, as chiral molecules. Such high switching speeds can only be reached with an all-optical paradigm, i.e., engineering active platforms capable of controlling light polarization via ultrashort laser pulses. Here we demonstrate giant modulation of dichroism and birefringence in an all-dielectric metasurface, achieved at low fluences of the optical control beam. This performance, which leverages the many degrees of freedom offered by all-dielectric active metasurfaces, is obtained by combining a high-quality factor nonlocal resonance with the giant third-order optical nonlinearity dictated by photogenerated hot carriers at the semiconductor band edge.
Annexin A1 binds PDZ and LIM domain 7 to inhibit adipogenesis and prevent obesity
Authors: Fang Lu , Liu Changjie , Jiang Zong-zhe , Wang Mengxiao , Geng Kang , Xu Yangkai , Zhu Yujie , Fu Yiwen , Xue Jing , Shan Wenxin , Zhang Qi , Chen Jie , Chen Jiahong , Zhao Mingming , Guo Yuxuan , Siu K. W. Michael , Chen Y. Eugene , Xu Yong , Liu Donghui , Zheng Lemin
Published: August 2024

Obesity is a global issue that warrants the identification of more effective therapeutic targets and a better understanding of the pivotal molecular pathogenesis. Annexin A1 (ANXA1) is known to inhibit phospholipase A2, exhibiting anti-inflammatory activity. However, the specific effects of ANXA1 in obesity and the underlying mechanisms of action remain unclear. Our study reveals that ANXA1 levels are elevated in the adipose tissue of individuals with obesity. Whole-body or adipocyte-specific ANXA1 deletion aggravates obesity and metabolic disorders. ANXA1 levels are higher in stromal vascular fractions (SVFs) than in mature adipocytes. Further investigation into the role of ANXA1 in SVFs reveals that ANXA1 overexpression induces lower numbers of mature adipocytes, while ANXA1-knockout SVFs exhibit the opposite effect. This suggests that ANXA1 plays an important role in adipogenesis. Mechanistically, ANXA1 competes with MYC binding protein 2 (MYCBP2) for interaction with PDZ and LIM domain 7 (PDLIM7). This exposes the MYCBP2-binding site, allowing it to bind more readily to the SMAD family member 4 (SMAD4) and promoting its ubiquitination and degradation. SMAD4 degradation downregulates peroxisome proliferator-activated receptor gamma (PPARγ) transcription and reduces adipogenesis. Treatment with Ac2-26, an active peptide derived from ANXA1, inhibits both adipogenesis and obesity through the mechanism. In conclusion, the molecular mechanism of ANXA1 inhibiting adipogenesis was first uncovered in our study, which is a potential target for obesity prevention and treatment.
Childhood maltreatment is linked to larger preferred interpersonal distances towards friends and strangers across the globe
Authors: Haim-Nachum Shilat , Sopp Marie R. , Lüönd Antonia M. , Afzal Nimrah , Åhs Fredrik , Allgaier Antje-Kathrin , Arévalo Adrián , Asongwe Christian , Bachem Rahel , Balle Stefanie R. , Belete Habte , Belete Mossie Tilahun , Berzengi Azi , Capraz Necip , Ceylan Deniz , Dukes Daniel , Essadek Aziz , Fares-Otero Natalia E. , Halligan Sarah L. , Hemi Alla , Iqbal Naved , Jobson Laura , Levy-Gigi Einat , Martin-Soelch Chantal , Michael Tanja , Oe Misari , Olff Miranda , Örnkloo Helena , Prakash Krithika , Quaatz Sarah M. , Raghavan Vijaya , Ramakrishnan Muniarajan , Reis Dorota , Şar Vedat , Schnyder Ulrich , Seedat Soraya , Shihab Ibtihal Najm , Vandhana Susilkumar , Wadji Dany Laure , Wamser Rachel , Zabag Reut , Spies Georgina , Pfaltz Monique C.
Published: August 2024

Childhood maltreatment (CM) is thought to be associated with altered responses to social stimuli and interpersonal signals. However, limited evidence exists that CM is linked to larger comfortable interpersonal distance (CID) – the physical distance humans prefer towards others during social interactions. However, no previous study has investigated this association in a comprehensive sample, yielding sufficient statistical power. Moreover, preliminary findings are limited to the European region. Finally, it is unclear how CM affects CID towards different interaction partners, and whether CID is linked to social functioning and attachment. To address these outstanding issues, adults (N = 2986) from diverse cultures and socio-economic strata completed a reaction time task measuring CID towards an approaching stranger and friend. Higher CM was linked to a larger CID towards both friends and strangers. Moreover, insecure attachment and less social support were associated with larger CID. These findings demonstrate for the first time that CM affects CID across countries and cultures, highlighting the robustness of this association.
Noncanonical formation of SNX5 gene-derived circular RNA regulates cancer growth
Authors: Chen Yi-Tung , Tsai Hui-Ju , Kan Chia-Hua , Ma Chung-Pei , Chen Hui-Wen , Chang Ian Yi-Feng , Liu Hsuan , Wu Chih-Ching , Chu Wei-Yun , Wu Ya-Chun , Chang Kai-Ping , Yu Jau-Song , Tan Bertrand Chin-Ming
Published: August 2024

Oral squamous cell carcinoma (OSCC) is a prevalent cancer worldwide, exhibiting unique regional prevalence. Despite advancements in diagnostics and therapy, the 5-year survival rate for patients has seen limited improvement. A deeper understanding of OSCC pathogenesis, especially its molecular underpinnings, is essential for improving detection, prevention, and treatment. In this context, noncoding RNAs, such as circular RNAs (circRNAs), have gained recognition as crucial regulators and potential biomarkers in OSCC progression. Our study highlights the discovery of previously uncharacterized circRNAs, including a SNX5 gene-derived circRNA, circSNX5, through deep sequencing of OSCC patient tissue transcriptomes. We established circSNX5’s tumor-specific expression and its strong correlation with patient survival using structure-specific and quantitative PCR analyses. In vitro and in vivo experiments underscored circSNX5 RNA’s regulatory role in cancer growth and metastasis. Further, our omics profiling and functional assays revealed that ADAM10 is a critical effector in circSNX5-mediated cancer progression, with circSNX5 maintaining ADAM10 expression by sponging miR-323. This novel circRNA-miRNA-mRNA regulatory axis significantly contributes to oral cancer progression and malignancy. Moreover, we discovered that circSNX5 RNA is produced via noncanonical sequential back-splicing of pre-mRNA, a process negatively regulated by the RNA-binding protein STAU1. This finding adds a new dimension to our understanding of exonic circRNA biogenesis in the eukaryotic transcriptome. Collectively, our findings offer a detailed mechanistic dissection and functional interpretation of a novel circRNA, shedding light on the role of the noncoding transcriptome in cancer biology and potentially paving the way for innovative therapeutic strategies.
PINX1 loss confers susceptibility to PARP inhibition in pan-cancer cells
Authors: Huang Mei , Zhu Xiaotong , Wang Chen , He Liying , Li Lei , Wang Haopeng , Fan Gaofeng , Wang Yu
Published: August 2024

PARP1 is crucial in DNA damage repair, chromatin remodeling, and transcriptional regulation. The principle of synthetic lethality has effectively guided the application of PARP inhibitors in treating tumors carrying BRCA1/2 mutations. Meanwhile, PARP inhibitors have exhibited efficacy in BRCA-proficient patients, further highlighting the necessity for a deeper understanding of PARP1 function and its inhibition in cancer therapy. Here, we unveil PIN2/TRF1-interacting telomerase inhibitor 1 (PINX1) as an uncharacterized PARP1-interacting protein that synergizes with PARP inhibitors upon its depletion across various cancer cell lines. Loss of PINX1 compromises DNA damage repair capacity upon etoposide treatment. The vulnerability of PINX1-deficient cells to etoposide and PARP inhibitors could be effectively restored by introducing either a full-length or a mutant form of PINX1 lacking telomerase inhibitory activity. Mechanistically, PINX1 is recruited to DNA lesions through binding to the ZnF3-BRCT domain of PARP1, facilitating the downstream recruitment of the DNA repair factor XRCC1. In the absence of DNA damage, PINX1 constitutively binds to PARP1, promoting PARP1-chromatin association and transcription of specific DNA damage repair proteins, including XRCC1, and transcriptional regulators, including GLIS3. Collectively, our findings identify PINX1 as a multifaceted partner of PARP1, crucial for safeguarding cells against genotoxic stress and emerging as a potential candidate for targeted tumor therapy.
NUP37 promotes the proliferation and invasion of glioma cells through DNMT1-mediated methylation
Authors: Lv Yongqiang , Wang Chaolian , Liu Ruoyu , Wu Shaoxian , Chen Junjun , Zheng Xiao , Jiang Tianwei , Chen Lujun
Published: August 2024

Nuclear regulation has potential in cancer therapy, with the nuclear pore complex (NPC) serving as a critical channel between the nucleus and cytoplasm, playing a role in regulating various biological processes and cancer. DNA methylation, an epigenetic modification mediated by DNA methyltransferases (DNMTs), influences gene expression and cell differentiation, and is crucial for the development and progression of tumor cells. Gliomas are the most common primary brain tumors, with glioblastoma being particularly aggressive, characterized by invasiveness, migration capability, and resistance to conventional treatments, resulting in poor prognosis. Our study revealed that the expression level of NUP37 affects the proliferation and invasion of glioma cells, and that the overexpression of DNMT1 can alleviate the adverse effects caused by NUP37 depletion. These findings suggest that NUP37 promotes the proliferation and invasion of glioma cells through its interaction with DNMT1.
Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network
Authors: Yang Wenyi , Wang Pingping , Xu Shouping , Wang Tao , Luo Meng , Cai Yideng , Xu Chang , Xue Guangfu , Que Jinhao , Ding Qian , Jin Xiyun , Yang Yuexin , Pang Fenglan , Pang Boran , Lin Yi , Nie Huan , Xu Zhaochun , Ji Yong , Jiang Qinghua
Published: August 2024

The inference of cell–cell communication (CCC) is crucial for a better understanding of complex cellular dynamics and regulatory mechanisms in biological systems. However, accurately inferring spatial CCCs at single-cell resolution remains a significant challenge. To address this issue, we present a versatile method, called DeepTalk, to infer spatial CCC at single-cell resolution by integrating single-cell RNA sequencing (scRNA-seq) data and spatial transcriptomics (ST) data. DeepTalk utilizes graph attention network (GAT) to integrate scRNA-seq and ST data, which enables accurate cell-type identification for single-cell ST data and deconvolution for spot-based ST data. Then, DeepTalk can capture the connections among cells at multiple levels using subgraph-based GAT, and further achieve spatially resolved CCC inference at single-cell resolution. DeepTalk achieves excellent performance in discovering meaningful spatial CCCs on multiple cross-platform datasets, which demonstrates its superior ability to dissect cellular behavior within intricate biological processes.
A class I PI3K signalling network regulates primary cilia disassembly in normal physiology and disease
Authors: Conduit Sarah E. , Pearce Wayne , Bhamra Amandeep , Bilanges Benoit , Bozal-Basterra Laura , Foukas Lazaros C. , Cobbaut Mathias , Castillo Sandra D. , Danesh Mohammad Amin , Adil Mahreen , Carracedo Arkaitz , Graupera Mariona , McDonald Neil Q. , Parker Peter J. , Cutillas Pedro R. , Surinova Silvia , Vanhaesebroeck Bart
Published: August 2024

Primary cilia are antenna-like organelles which sense extracellular cues and act as signalling hubs. Cilia dysfunction causes a heterogeneous group of disorders known as ciliopathy syndromes affecting most organs. Cilia disassembly, the process by which cells lose their cilium, is poorly understood but frequently observed in disease and upon cell transformation. Here, we uncover a role for the PI3Kα signalling enzyme in cilia disassembly. Genetic PI3Kα-hyperactivation, as observed in PIK3CA-related overgrowth spectrum (PROS) and cancer, induced a ciliopathy-like phenotype during mouse development. Mechanistically, PI3Kα and PI3Kβ produce the PIP3 lipid at the cilia transition zone upon disassembly stimulation. PI3Kα activation initiates cilia disassembly through a kinase signalling axis via the PDK1/PKCι kinases, the CEP170 centrosomal protein and the KIF2A microtubule-depolymerising kinesin. Our data suggest diseases caused by PI3Kα-activation may be considered ‘Disorders with Ciliary Contributions’, a recently-defined subset of ciliopathies in which some, but not all, of the clinical manifestations result from cilia dysfunction.
Sae2 controls Mre11 endo- and exonuclease activities by different mechanisms
Authors: Tamai Tomoki , Reginato Giordano , Ojiri Ryusei , Morita Issei , Avrutis Alexandra , Cejka Petr , Shinohara Miki , Sugimoto Katsunori
Published: August 2024

DNA double-strand breaks (DSBs) must be repaired to ensure cell survival and genomic integrity. In yeast, the Mre11-Rad50-Xrs2 complex (MRX) collaborates with Sae2 to initiate DSB repair. Sae2 stimulates two MRX nuclease activities, endonuclease and 3’−5’ exonuclease. However, how Sae2 controls the two nuclease activities remains enigmatic. Using a combined genetic and biochemical approach, we identified a separation-of-function rad50 mutation, rad50-C47, that causes a defect in Sae2-dependent MRX 3’−5’ exonuclease activity, but not endonuclease activity. We found that both the endo- and 3’−5’ exonuclease activities are essential to release Spo11 from DNA ends, whereas only the endonuclease activity is required for hairpin removal. We also uncovered that MRX-Sae2 endonuclease introduces a cleavage at defined distances from the Spo11-blocked end with gradually decreasing efficiency. Our findings demonstrate that Sae2 stimulates the MRX endo- and exonuclease activities via Rad50 by different mechanisms, ensuring diverse actions of MRX-Sae2 nuclease at DNA ends.
Control of lysogeny and antiphage defense by a prophage-encoded kinase-phosphatase module
Authors: Guo Yunxue , Tang Kaihao , Sit Brandon , Gu Jiayu , Chen Ran , Shao Xinqi , Lin Shituan , Huang Zixian , Nie Zhaolong , Lin Jianzhong , Liu Xiaoxiao , Wang Weiquan , Gao Xinyu , Liu Tianlang , Liu Fei , Luo Hongbo R. , Waldor Matthew K. , Wang Xiaoxue
Published: August 2024

The filamentous ‘Pf’ bacteriophages of Pseudomonas aeruginosa play roles in biofilm formation and virulence, but mechanisms governing Pf prophage activation in biofilms are unclear. Here, we identify a prophage regulatory module, KKP (kinase-kinase-phosphatase), that controls virion production of co-resident Pf prophages and mediates host defense against diverse lytic phages. KKP consists of Ser/Thr kinases PfkA and PfkB, and phosphatase PfpC. The kinases have multiple host targets, one of which is MvaU, a host nucleoid-binding protein and known prophage-silencing factor. Characterization of KKP deletion and overexpression strains with transcriptional, protein-level and prophage-based approaches indicates that shifts in the balance between kinase and phosphatase activities regulate phage production by controlling MvaU phosphorylation. In addition, KKP acts as a tripartite toxin-antitoxin system that provides defense against some lytic phages. A conserved lytic phage replication protein inhibits the KKP phosphatase PfpC, stimulating toxic kinase activity and blocking lytic phage production. Thus, KKP represents a phosphorylation-based mechanism for prophage regulation and antiphage defense. The conservation of KKP gene clusters in >1000 diverse temperate prophages suggests that integrated control of temperate and lytic phage infection by KKP-like regulatory modules may play a widespread role in shaping host cell physiology.
Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community
Authors: Scarinci Giovanni , Ariens Jan-Luca , Angelidou Georgia , Schmidt Sebastian , Glatter Timo , Paczia Nicole , Sourjik Victor
Published: August 2024

While different stages of mutualism can be observed in natural communities, the dynamics and mechanisms underlying the gradual erosion of independence of the initially autonomous organisms are not yet fully understood. In this study, by conducting the laboratory evolution on an engineered microbial community, we reproduce and molecularly track the stepwise progression towards enhanced partner entanglement. We observe that the evolution of the community both strengthens the existing metabolic interactions and leads to the emergence of de novo interdependence between partners for nitrogen metabolism, which is a common feature of natural symbiotic interactions. Selection for enhanced metabolic entanglement during the community evolution repeatedly occurred indirectly, via pleiotropies and trade-offs within cellular regulatory networks, and with no evidence of group selection. The indirect positive selection of metabolic dependencies between microbial community members, which results from the direct selection of other coupled traits in the same regulatory network, may therefore be a common but underappreciated driving force guiding the evolution of natural mutualistic communities.
METTL3/METTL14 maintain human nucleoli integrity by mediating SUV39H1/H2 degradation
Authors: Shan Yongli , Zhang Yanqi , Wei Yanxing , Zhang Cong , Lin Huaisong , He Jiangping , Wang Junwei , Guo Wenjing , Li Heying , Chen Qianyu , Zhou Tiancheng , Xing Qi , Liu Yancai , Chen Jiekai , Pan Guangjin
Published: August 2024

Nucleoli are fundamentally essential sites for ribosome biogenesis in cells and formed by liquid-liquid phase separation (LLPS) for a multilayer condensate structure. How the nucleoli integrity is maintained remains poorly understood. Here, we reveal that METTL3/METTL14, the typical methyltransferase complex catalyzing N6-methyladnosine (m6A) on mRNAs maintain nucleoli integrity in human embryonic stem cells (hESCs). METTL3/METTL14 deficiency impairs nucleoli and leads to the complete loss of self-renewal in hESCs. We further show that SUV39H1/H2 protein, the methyltransferases catalyzing H3K9me3 were dramatically elevated in METTL3/METTL14 deficient cells, which causes an accumulation and infiltration of H3K9me3 across the whole nucleolus and impairs the LLPS. Mechanistically, METTL3/METTL14 complex serves as an essential adapter for CRL4 E3 ubiquitin ligase targeting SUV39H1/H2 for polyubiquitination and proteasomal degradation and therefore prevents H3K9me3 accumulation in nucleoli. Together, these findings uncover a previously unknown role of METTL3/METTL14 to maintain nucleoli integrity by facilitating SUV39H1/H2 degradation in human cells.
Progress in computational understanding of ferroelectric mechanisms in HfO2
Authors: Zhu Tianyuan , Ma Liyang , Deng Shiqing , Liu Shi
Published: August 2024

Since the first report of ferroelectricity in nanoscale HfO2-based thin films in 2011, this silicon-compatible binary oxide has quickly garnered intense interest in academia and industry, and continues to do so. Despite its deceivingly simple chemical composition, the ferroelectric physics supported by HfO2 is remarkably complex, arguably rivaling that of perovskite ferroelectrics. Computational investigations, especially those utilizing first-principles density functional theory (DFT), have significantly advanced our understanding of the nature of ferroelectricity in these thin films. In this review, we provide an in-depth discussion of the computational efforts to understand ferroelectric hafnia, comparing various metastable polar phases and examining the critical factors necessary for their stabilization. The intricate nature of HfO2 is intimately related to the complex interplay among diverse structural polymorphs, dopants and their charge-compensating oxygen vacancies, and unconventional switching mechanisms of domains and domain walls, which can sometimes yield conflicting theoretical predictions and theoretical-experimental discrepancies. We also discuss opportunities enabled by machine-learning-assisted molecular dynamics and phase-field simulations to go beyond DFT modeling, probing the dynamical properties of ferroelectric HfO2 and tackling pressing issues such as high coercive fields.
Integrating stereotypes and factual evidence in interpersonal communication
Authors: Koch Saskia B. J. , Tyborowska Anna , Niermann Hannah C. M. , Cillessen Antonius H. N. , Roelofs Karin , Bašnáková Jana , Toni Ivan , Stolk Arjen
Published: August 2024

Stereotypes can exert a powerful influence on our interactions with others, potentially leading to prejudice when factual evidence is ignored. Here, we identify neuroanatomical and developmental factors that influence the real-time integration of stereotypes and factual evidence during live social interactions. The study uses precisely quantified communicative exchanges in a longitudinal cohort of seventeen-year-olds followed since infancy, testing their ability to moderate stereotype tendencies toward children as contrary evidence accumulates. Our results indicate that the impact of stereotypes on communicative behavior is linked to individual variations in gray matter density and cortical thickness in the right anterior cingulate gyrus. In contrast, the ability to moderate stereotype tendencies is influenced by developmental exposure to social interactions during the initial years of life, beyond the effects of familial environment and later experiences. These findings pinpoint a key brain structure underlying stereotype tendencies and suggest that early-life social experiences have lasting consequences on how individuals integrate factual evidence in interpersonal communication.
Microbiome of esophageal endoscopic wash samples is associated with resident flora in the esophagus and incidence of cancer
Authors: Shijimaya Takuya , Tahara Tomomitsu , Yamazaki Jumpei , Kobayashi Sanshiro , Matsumoto Yasushi , Nakamura Naohiro , Takahashi Yu , Tomiyama Takashi , Fukui Toshiro , Shibata Tomoyuki , Naganuma Makoto
Published: August 2024

Change in mucosal microbiome is associated with various types of cancer in digestive tract. We hypothesized that microbial communities in the esophageal endoscopic wash fluids reflects resident flora in esophageal mucosa that is associated with esophageal carcinoma (EC) risk and/or directly correlates microbiome derived from EC tumor tissue. Studying microbial communities in esophageal endoscopic wash samples would be therefore useful to predict the incidence or risk of EC. We examined microbial communities of the endoscopic wash samples from 45 primary EC and 20 respective non-EC controls using 16S rRNA V3-V4 amplicon sequencing. The result was also compared with microbial communities in matched endoscopic biopsies from EC and non-cancerous esophageal mucosa. Compared with non-EC controls, 6 discriminative bacterial genera were detected in EC patients. Among them, relative abundance ratio of Prevotella and Shuttlewarthia, as well as decrease of genus Prevotella presented good prognostic performance to discriminate EC from controls (area under curve, 0.86, 0.82, respectively). Multivariate analysis showed occurrence of EC was an independent factor associated with decrease of this bacteria. Abundance of genus Prevotella in the esophageal endoscopic wash samples was significantly correlated with the abundance of this bacteria in the matched endoscopic biopsies from non-cancerous esophageal mucosa but not in the EC tissues. Our findings suggest that microbiome composition in the esophageal endoscopic wash samples reflects resident flora in the esophagus and significantly correlates with the incidence of EC.
NLRP3 inflammasome pathway involved in the pathogenesis of metabolic associated fatty liver disease
Authors: Osman Heba Ahmed , Abuhamdah Sawsan M. A. , Hassan Mohammed H. , Hashim Abdelkader Ahmed , Ahmed Abdelazeem E. , Elsayed Sameh Salaheldin , El-Sawy Samer A. , Gaber Mostafa A. , Abdelhady Marwa
Published: August 2024

The prevalence of Metabolic-associated fatty liver disease (MAFLD) has been steadily increasing worldwide, paralleling the global epidemic of obesity and diabetes. It is estimated that approximately one-quarter of the global population is affected by MAFLD. Despite its high prevalence, MAFLD often goes undiagnosed due to the lack of specific symptoms in its early stages. However, as the disease progresses, it can lead to more severe liver-related complications such as fibrosis, cirrhosis, and hepatocellular carcinoma. Therefore, we aimed to investigate the expression levels of the nucleotide-binding oligomerization domain, leucine-rich repeat (LRR)—containing proteins (NLR) family pyrin domain-containing protein 3 [NLRP3] inflammasome pathway components, NLRP3 and interleukin 1β (IL-1β) genes in patients with MAFLD with various degrees of steatosis and fibrosis. Participants were classified into two equal groups; MAFLD group: consisted of 120 patients with different degrees of hepatic fibrosis and steatosis based on fibro scan results. The non-MAFLD group was comprised of 107 participants. Molecular analysis of pyrin domain-containing protein 3 and IL-1β relative gene expressions was performed in the blood of all participants, using Real-time quantitative polymerase chain reaction (RT-qPCR). Patients with post-MAFLD hepatic fibrosis had significantly higher relative gene expression levels of IL-1β and NLRP3; with IL-1β > 1.1 had AUC of 0.919, sensitivity of 88.33, specificity of 96.26, PPV of 96.4, and NPV of 88 and 92.3 accuracy (p value < 0.001). NLRP3 > 1.33 had a sensitivity of 97.5, specificity of 99.07, PPV of 99.2, NPV of 97.2, and 98.3 accuracy with an AUC of 0.991 (p value < 0.001) as predictors of post-MAFLD hepatic fibrosis.. A significant increase in the mean relative gene expression levels of both IL-1β and NLRP3 found in patients with early fibrosis (F0-F1-2); 31.97 ± 11.8 and 6.76 ± 2.18, respectively; compared with patients with advanced hepatic fibrosis stages (F2-F3); 2.62 ± 3.71 and 4.27 ± 2.99 (p < 0.001 each). The present study provides novel evidence for the possible involvement of IL-1β and NLRP3 inflammasome in metabolic-associated fatty liver disease pathogenesis and could be valid markers for the early detection of post-MAFLD hepatic fibrosis.
Vertical structure of Caribbean deep-reef fishes from the altiphotic to deep-sea boundary
Authors: Jacquemont Juliette , Brandl Simon J. , McFarland Emily P. , Claudet Joachim , Baldwin Carole C. , Barrett Jenna , Tornabene Luke
Published: August 2024

While recent technical breakthroughs have enabled advances in the description of reefs down to 150 m, the structure and depth zonation of deep-reef communities below 150 m remains largely unknown. Here, we present results from over 10 years of deep-reef fish surveys using human-occupied submersibles at four locations across the Caribbean Sea, constituting one of the only continuous reef-fish surveys from 10 to 480 m (1 site) and 40 to 300 m (3 sites). We identify four vertically stratified deep-reef fish communities between 40 and 300 m bordered by an altiphotic (0–10 m) and a deep-sea (300–480 m) community. We found a strong faunal break around 150 m that separates mesophotic and rariphotic zones and secondary breaks at ~ 70 to 90 m and ~ 180 to 200 m subdividing these zones into upper and lower communities. From 300 to 480 m in Roatán, we found a single fish community dominated by deep-sea families, indicating that the lower boundary of the reef-fish realm occurs at 300 m. No differences were found between communities ranging from 20 to 60 m, suggesting that fishes from the lower altiphotic and upper mesophotic form an ecological continuum. While some variability was observed across sites, the overall depth zonation and key species characterizing depth zones were consistent. Most deep-reef species observed were depth specialists restricted to a single depth zone, but many shallow-reef species extended down to mesophotic depths. Depth segregation among species of a genus was found across ten reef-fish genera and likely constitutes one of the mechanisms driving community distinctiveness and thereby fish diversity across depths.
Intraspecific priority effects in response to egg hatching delay in a pond-breeding salamander
Authors: Anderson Thomas L. , Rallo Trevor J.
Published: August 2024

As reproduction phenologies shift with climate change, populations can experience intraspecific priority effects, wherein early hatching cohorts experience an advantage over late-hatching cohorts, resulting in altered demography. Our study objective was to identify how variation in egg hatching phenology alters intraspecific interactions in small-mouthed salamanders, Ambystoma texanum. We addressed two research questions: (Q1) How are demographic responses altered by variation in the temporal duration of hatching between cohorts, and (Q2) How does the seasonality of hatching delays affect demographic responses? We manipulated hatching phenologies of A. texanum eggs and reared larvae in outdoor mesocosms to metamorphosis. For Q1, hatching delay exhibited non-linear relationships with survival and body size, with the greatest asynchrony in cohort additions resulting in the highest mortality and largest body sizes. For Q2, hatching delay effects were stronger (i.e., survival was lower and body sizes larger) when they occurred later in the season, potentially due to temperature differences that larvae experienced. Overall, our results demonstrate that changes in intraspecific interactions due to phenological shifts can be context-dependent, depending on the strength (i.e., temporal duration) and seasonality of such processes. Identifying context-dependencies of phenological shifts will be critical for predicting changes in organismal demographics with climatic shifts.