bluuebunny/crossref_metadata_2025_split huggingface dataset:
NAP1L1 regulates BIRC2 ubiquitination modification via E3 ubiquitin ligase UBR4 and hence determines hepatocellular carcinoma progression
Authors: Zhang Shi-Long , Zhang Shen-Jie , Li Lian , Zhang Ye-Wei , Wang Zhi , Wang Long , Lu Jie-Yu , Chen Teng-Xiang , Zuo Shi 
Published: March 2024

AbstractWe have previously shown that nucleosome assembly protein 1-like 1 (NAP1L1) plays an important role in the abnormal proliferation of hepatocellular carcinoma (HCC) cells. However, the effects of NAP1L1 on the malignant behaviour of HCC cells, including cell migration, invasion and apoptosis, remain unclear. Baculoviral IAP repeat-containing 2 (BIRC2) plays a key role in initiating the abnormal proliferation, apoptotic escape and multidrug resistance of HCC cells; however, the mechanisms through which its stability is regulated in HCC remain elusive. Here, we found that knockdown of NAP1L1 inhibited the proliferation of HCC cells and activated apoptotic pathways but did not remarkably affect the migratory and invasive abilities of HCC cells. In addition, knockdown of NAP1L1 did not alter the expression of BIRC2 at the transcriptional level but substantially reduced its expression at the translational level, suggesting that NAP1L1 is involved in the post-translational modification (such as ubiquitination) of BIRC2. Furthermore, BIRC2 was highly expressed in human HCC tissues and promoted the proliferation and apoptotic escape of HCC cells. Co-immunoprecipitation (Co-IP) assay and mass spectrometry revealed that NAP1L1 and BIRC2 did not bind to each other; however, ubiquitin protein ligase E3 component n-recognin 4 (UBR4) was identified as an intermediate molecule associating NAP1L1 with BIRC2. Knockdown of NAP1L1 promoted the ubiquitin-mediated degradation of BIRC2 through the ubiquitin–protein junction of UBR4, which in turn inhibited the proliferation and apoptotic escape of HCC cells and exerted anti-tumour effects. In conclusion, this study reveals a novel mechanism through which NAP1L1 regulates the ubiquitination of BIRC2 through UBR4, thereby determining the progression of HCC. Based on this mechanism, suppression of NAP1L1 may inhibit tumour progression in patients with HCC with high protein expression of NAP1L1 or BIRC2.
The effects of genetic and modifiable risk factors on brain regions vulnerable to ageing and disease
Authors: Manuello Jordi , Min Joosung , McCarthy Paul , Alfaro-Almagro Fidel , Lee Soojin , Smith Stephen , Elliott Lloyd T. , Winkler Anderson M. , Douaud Gwenaëlle 
Published: March 2024

AbstractWe have previously identified a network of higher-order brain regions particularly vulnerable to the ageing process, schizophrenia and Alzheimer’s disease. However, it remains unknown what the genetic influences on this fragile brain network are, and whether it can be altered by the most common modifiable risk factors for dementia. Here, in ~40,000 UK Biobank participants, we first show significant genome-wide associations between this brain network and seven genetic clusters implicated in cardiovascular deaths, schizophrenia, Alzheimer’s and Parkinson’s disease, and with the two antigens of the XG blood group located in the pseudoautosomal region of the sex chromosomes. We further reveal that the most deleterious modifiable risk factors for this vulnerable brain network are diabetes, nitrogen dioxide – a proxy for traffic-related air pollution – and alcohol intake frequency. The extent of these associations was uncovered by examining these modifiable risk factors in a single model to assess the unique contribution of each on the vulnerable brain network, above and beyond the dominating effects of age and sex. These results provide a comprehensive picture of the role played by genetic and modifiable risk factors on these fragile parts of the brain.
CMOS plus stochastic nanomagnets enabling heterogeneous computers for probabilistic inference and learning
Authors: Singh Nihal Sanjay , Kobayashi Keito , Cao Qixuan , Selcuk Kemal , Hu Tianrui , Niazi Shaila , Aadit Navid Anjum , Kanai Shun , Ohno Hideo , Fukami Shunsuke , Camsari Kerem Y. 
Published: March 2024

AbstractExtending Moore’s law by augmenting complementary-metal-oxide semiconductor (CMOS) transistors with emerging nanotechnologies (X) has become increasingly important. One important class of problems involve sampling-based Monte Carlo algorithms used in probabilistic machine learning, optimization, and quantum simulation. Here, we combine stochastic magnetic tunnel junction (sMTJ)-based probabilistic bits (p-bits) with Field Programmable Gate Arrays (FPGA) to create an energy-efficient CMOS + X (X = sMTJ) prototype. This setup shows how asynchronously driven CMOS circuits controlled by sMTJs can perform probabilistic inference and learning by leveraging the algorithmic update-order-invariance of Gibbs sampling. We show how the stochasticity of sMTJs can augment low-quality random number generators (RNG). Detailed transistor-level comparisons reveal that sMTJ-based p-bits can replace up to 10,000 CMOS transistors while dissipating two orders of magnitude less energy. Integrated versions of our approach can advance probabilistic computing involving deep Boltzmann machines and other energy-based learning algorithms with extremely high throughput and energy efficiency.
iNOS is necessary for GBP-mediated T. gondii clearance in murine macrophages via vacuole nitration and intravacuolar network collapse
Authors: Zhao Xiao-Yu , Lempke Samantha L. , Urbán Arroyo Jan C. , Brown Isabel G. , Yin Bocheng , Magaj Magdalena M. , Holness Nadia K. , Smiley Jamison , Redemann Stefanie , Ewald Sarah E. 
Published: March 2024

AbstractToxoplasma gondii is an obligate intracellular parasite of rodents and humans. Interferon-inducible guanylate binding proteins (GBPs) are mediators of T. gondii clearance, however, this mechanism is incomplete. Here, using automated spatially targeted optical micro proteomics we demonstrate that inducible nitric oxide synthetase (iNOS) is highly enriched at GBP2+ parasitophorous vacuoles (PV) in murine macrophages. iNOS expression in macrophages is necessary to limit T. gondii load in vivo and in vitro. Although iNOS activity is dispensable for GBP2 recruitment and PV membrane ruffling; parasites can replicate, egress and shed GBP2 when iNOS is inhibited. T. gondii clearance by iNOS requires nitric oxide, leading to nitration of the PV and collapse of the intravacuolar network of membranes in a chromosome 3 GBP-dependent manner. We conclude that reactive nitrogen species generated by iNOS cooperate with GBPs to target distinct structures in the PV that are necessary for optimal parasite clearance in macrophages.
Strongly interacting Rydberg atoms in synthetic dimensions with a magnetic flux
Authors: Chen Tao , Huang Chenxi , Velkovsky Ivan , Hazzard Kaden R. A. , Covey Jacob P. , Gadway Bryce 
Published: March 2024

AbstractSynthetic dimensions, wherein dynamics occurs in a set of internal states, have found great success in recent years in exploring topological effects in cold atoms and photonics. However, the phenomena thus far explored have largely been restricted to the non-interacting or weakly interacting regimes. Here, we extend the synthetic dimensions playbook to strongly interacting systems of Rydberg atoms prepared in optical tweezer arrays. We use precise control over driving microwave fields to introduce a tunable U(1) flux in a four-site lattice of coupled Rydberg levels. We find highly coherent dynamics, in good agreement with theory. Single atoms show oscillatory dynamics controllable by the gauge field. Small arrays of interacting atoms exhibit behavior suggestive of the emergence of ergodic and arrested dynamics in the regimes of intermediate and strong interactions, respectively. These demonstrations pave the way for future explorations of strongly interacting dynamics and many-body phases in Rydberg synthetic lattices.
One-photon three-dimensional printed fused silica glass with sub-micron features
Authors: Li Ziyong , Jia Yanwen , Duan Ke , Xiao Ran , Qiao Jingyu , Liang Shuyu , Wang Shixiang , Chen Juzheng , Wu Hao , Lu Yang , Wen Xiewen 
Published: March 2024

AbstractThe applications of silica-based glass have evolved alongside human civilization for thousands of years. High-precision manufacturing of three-dimensional (3D) fused silica glass objects is required in various industries, ranging from everyday life to cutting-edge fields. Advanced 3D printing technologies have emerged as a potent tool for fabricating arbitrary glass objects with ultimate freedom and precision. Stereolithography and femtosecond laser direct writing respectively achieved their resolutions of ~50 μm and ~100 nm. However, fabricating glass structures with centimeter dimensions and sub-micron features remains challenging. Presented here, our study effectively bridges the gap through engineering suitable materials and utilizing one-photon micro-stereolithography (OμSL)-based 3D printing, which flexibly creates transparent and high-performance fused silica glass components with complex, 3D sub-micron architectures. Comprehensive characterizations confirm that the final material is stoichiometrically pure silica with high quality, defect-free morphology, and excellent optical properties. Homogeneous volumetric shrinkage further facilitates the smallest voxel, reducing the size from 2.0 × 2.0 × 1.0 μm3 to 0.8 × 0.8 × 0.5 μm3. This approach can be used to produce fused silica glass components with various 3D geometries featuring sub-micron details and millimetric dimensions. This showcases promising prospects in diverse fields, including micro-optics, microfluidics, mechanical metamaterials, and engineered surfaces.
Intermediate soil acidification induces highest nitrous oxide emissions
Authors: Qiu Yunpeng , Zhang Yi , Zhang Kangcheng , Xu Xinyu , Zhao Yunfeng , Bai Tongshuo , Zhao Yexin , Wang Hao , Sheng Xiongjie , Bloszies Sean , Gillespie Christopher J. , He Tangqing , Wang Yang , Chen Huaihai , Guo Lijin , Song He , Ye Chenglong , Wang Yi , Woodley Alex , Guo Jingheng , Cheng Lei , Bai Yongfei , Zhu Yongguan , Hallin Sara , Firestone Mary K. , Hu Shuijin 
Published: March 2024

AbstractGlobal potent greenhouse gas nitrous oxide (N2O) emissions from soil are accelerating, with increases in the proportion of reactive nitrogen emitted as N2O, i.e., N2O emission factor (EF). Yet, the primary controls and underlying mechanisms of EFs remain unresolved. Based on two independent but complementary global syntheses, and three field studies determining effects of acidity on N2O EFs and soil denitrifying microorganisms, we show that soil pH predominantly controls N2O EFs and emissions by affecting the denitrifier community composition. Analysis of 5438 paired data points of N2O emission fluxes revealed a hump-shaped relationship between soil pH and EFs, with the highest EFs occurring in moderately acidic soils that favored N2O-producing over N2O-consuming microorganisms, and induced high N2O emissions. Our results illustrate that soil pH has a unimodal relationship with soil denitrifiers and EFs, and the net N2O emission depends on both the N2O/(N2O + N2) ratio and overall denitrification rate. These findings can inform strategies to predict and mitigate soil N2O emissions under future nitrogen input scenarios.
Real-time monitoring of replication errors’ fate reveals the origin and dynamics of spontaneous mutations
Authors: Enrico Bena Chiara , Ollion Jean , De Paepe Marianne , Ventroux Magali , Robert Lydia , Elez Marina 
Published: March 2024

AbstractThe efficiency of replication error repair is a critical factor governing the emergence of mutations. However, it has so far been impossible to study this efficiency at the level of individual cells and to investigate if it varies within isogenic cell populations. In addition, why some errors escape repair remains unknown. Here we apply a combination of fluorescent labelling of the Escherichia coli Mismatch Repair (MMR) complex, microfluidics, and time-lapse microscopy, to monitor in real-time the fate of >20000 replication errors. We show that i) many mutations result from errors that are detected by MMR but inefficiently repaired ii) this limited repair efficiency is due to a temporal constraint imposed by the transient nature of the DNA strand discrimination signal, a constraint that is likely conserved across organisms, and iii) repair capacity varies from cell to cell, resulting in a subpopulation of cells with higher mutation rate. Such variations could influence the fitness and adaptability of populations, accelerating for instance the emergence of antibiotic resistance.
Collective incentives reduce over-exploitation of social information in unconstrained human groups
Authors: Deffner Dominik , Mezey David , Kahl Benjamin , Schakowski Alexander , Romanczuk Pawel , Wu Charley M. , Kurvers Ralf H. J. M. 
Published: March 2024

AbstractCollective dynamics emerge from countless individual decisions. Yet, we poorly understand the processes governing dynamically-interacting individuals in human collectives under realistic conditions. We present a naturalistic immersive-reality experiment where groups of participants searched for rewards in different environments, studying how individuals weigh personal and social information and how this shapes individual and collective outcomes. Capturing high-resolution visual-spatial data, behavioral analyses revealed individual-level gains—but group-level losses—of high social information use and spatial proximity in environments with concentrated (vs. distributed) resources. Incentivizing participants at the group (vs. individual) level facilitated adaptation to concentrated environments, buffering apparently excessive scrounging. To infer discrete choices from unconstrained interactions and uncover the underlying decision mechanisms, we developed an unsupervised Social Hidden Markov Decision model. Computational results showed that participants were more sensitive to social information in concentrated environments frequently switching to a social relocation state where they approach successful group members. Group-level incentives reduced participants’ overall responsiveness to social information and promoted higher selectivity over time. Finally, mapping group-level spatio-temporal dynamics through time-lagged regressions revealed a collective exploration-exploitation trade-off across different timescales. Our study unravels the processes linking individual-level strategies to emerging collective dynamics, and provides tools to investigate decision-making in freely-interacting collectives.
In situ detection of spatial distribution information of temperature-pH-strain of sandstone cultural relics
Authors: Xu Changyuan , Li Linyang , Hu Rong , Wu Huihua , Kong Lingnan , Zhong Nianbing , Wan Bo , Wu Lei , Lai Dong , He Yuanyuan , Liu Yang , Peng Xiaoling , Zhao Mingfu , Xie Quanhua 
Published: March 2024

AbstractTo monitor in situ the temperature, pH, and micro-strain change information of sandstone artifacts in the process of oxalic acid corrosion, the temperature, pH, and micro-strain fiber Bragg grating (FBG) sensors are developed. A theoretical model of the sensors is established. The surface morphology, material composition, pore structure, temperature, pH, and micro-strain of sandstone corroded by oxalic acid solutions of different concentrations are investigated. The experimental results show that the higher the concentration of oxalic acid, the stronger the corrosiveness of the sandstone. Ferrous oxalate and calcium oxalate produced by corrosion continuously precipitate from the inside of the rock, and the dual reaction of crystallization and dissolution occurs, reducing the proportion of fine pores in the rock pore suction and gravity. The oxalic acid solution is transported to the middle of the sandstone (3 cm) and undergoes the strongest chemical reaction with ore particles and debris, resulting in the maximum wavelength drift of the temperature, pH, and micro-strain sensors. The results of this study provide important support for analyzing the acid dissolution mechanism of stone cultural relics and the preventive protection of cultural relics.
A genome-wide association study of Chinese and English language phenotypes in Hong Kong Chinese children
Authors: Lin Yu-Ping , Shi Yujia , Zhang Ruoyu , Xue Xiao , Rao Shitao , Yin Liangying , Lui Kelvin Fai Hong , PAN Dora Jue , Maurer Urs , Choy Kwong-Wai , Paracchini Silvia , McBride Catherine , So Hon-Cheong 
Published: March 2024

AbstractDyslexia and developmental language disorders are important learning difficulties. However, their genetic basis remains poorly understood, and most genetic studies were performed on Europeans. There is a lack of genome-wide association studies (GWAS) on literacy phenotypes of Chinese as a native language and English as a second language (ESL) in a Chinese population. In this study, we conducted GWAS on 34 reading/language-related phenotypes in Hong Kong Chinese bilingual children (including both twins and singletons; totalN = 1046). We performed association tests at the single-variant, gene, and pathway levels. In addition, we tested genetic overlap of these phenotypes with other neuropsychiatric disorders, as well as cognitive performance (CP) and educational attainment (EA) using polygenic risk score (PRS) analysis. Totally 5 independent loci (LD-clumped at r2 = 0.01; MAF > 0.05) reached genome-wide significance (p < 5e-08; filtered by imputation quality metric Rsq>0.3 and having at least 2 correlated SNPs (r2 > 0.5) withp < 1e-3). The loci were associated with a range of language/literacy traits such as Chinese vocabulary, character and word reading, and rapid digit naming, as well as English lexical decision. Several SNPs from these loci mapped to genes that were reported to be associated with EA and other neuropsychiatric phenotypes, such asMANEAandPLXNC1. In PRS analysis, EA and CP showed the most consistent and significant polygenic overlap with a variety of language traits, especially English literacy skills. To summarize, this study revealed the genetic basis of Chinese and English abilities in a group of Chinese bilingual children. Further studies are warranted to replicate the findings.
The extrachromosomal circular DNA atlas of aged and young mouse brains
Authors: Hong Xiaoning , Li Jing , Han Peng , Li Shaofu , Yu Jiaying , Zhang Haoran , Li Jiang , Dang Yonghui , Xiang Xi 
Published: March 2024

AbstractExtrachromosomal circular DNA (eccDNA) refers to a distinct class of circular DNA molecules that exist independently from linear chromosomal DNA. Extensive evidence has firmly established the significant involvement of eccDNA in cancer initiation, progression, and evolutionary processes. However, the relationship between eccDNA and brain aging remains elusive. Here, we employed extrachromosomal circular DNA sequencing (Circle-seq) to generate a comprehensive dataset of eccDNA from six brain structures of both young and naturally-aged mice, including the olfactory bulb, medial prefrontal cortex, nucleus accumbens, caudate putamen, hippocampus, and cerebellum. Furthermore, through database annotation, we characterized the properties of mouse brain eccDNA, thereby gaining insights into the potential functions of eccDNA in the mouse brain. In conclusion, our study addresses a previously unexplored area by providing a comprehensive molecular characterization of eccDNA in brain tissues. The data presented in the study can be used as a fundamental resource to associate the molecular phenotypes of eccDNA with brain aging and gain deep insights into the biological role of eccDNA in mammalian brain aging.
Survey data linking coastal visit behaviours to socio-demographic and health profiles
Authors: Hooyberg Alexander , Roose Henk , Lonneville Britt , De Henauw Stefaan , Michels Nathalie , Everaert Gert 
Published: March 2024

AbstractCoastal destinations are highly popular for leisure, yet the effects of spending time at the coast on mental and physical health have remained underexplored. To accelerate the research about the effects of the coast on health, we compiled a dataset from a survey on a sample (N = 1939) of the adult Flemish population about their visits to the Belgian coast. The survey queried the number of days spent at the coast in the previous year or before and the following characteristics of their visits: how often they performed specific activities, which of the 14 municipal seaside resorts they visited, who they were with, what they mentally and physically experienced, and what reasons they had for not visiting the coast more often. The respondents’ geo-demographic (including residential proximity to the coast), socio-economic, and health profile was also collected. We anticipate that investigations on the data will increase our understanding about the social structuring of coastal visits and give context to the effects of the coast on human health.
New role of fat-free mass in cancer risk linked with genetic predisposition
Authors: Harris Benjamin H. L. , Di Giovannantonio Matteo , Zhang Ping , Harris David A. , Lord Simon R. , Allen Naomi E. , Maughan Tim S. , Bryant Richard J. , Harris Adrian L. , Bond Gareth L. , Buffa Francesca M. 
Published: March 2024

AbstractCancer risk is associated with the widely debated measure body mass index (BMI). Fat mass and fat-free mass measurements from bioelectrical impedance may further clarify this association. The UK Biobank is a rare resource in which bioelectrical impedance and BMI data was collected on ~ 500,000 individuals. Using this dataset, a comprehensive analysis using regression, principal component and genome-wide genetic association, provided multiple levels of evidence that increasing whole body fat (WBFM) and fat-free mass (WBFFM) are both associated with increased post-menopausal breast cancer risk, and colorectal cancer risk in men. WBFM was inversely associated with prostate cancer. We also identified rs615029[T] and rs1485995[G] as associated in independent analyses with both PMBC (p = 1.56E–17 and 1.78E–11) and WBFFM (p = 2.88E–08 and 8.24E–12), highlighting splice variants of the intriguing long non-coding RNA CUPID1 (LINC01488) as a potential link between PMBC risk and fat-free mass.
Electrical stimulation of chicken embryo development supports the Inside story scenario of human development and evolution
Authors: Fleury Vincent 
Published: March 2024

AbstractAnimal evolution is driven by random mutations at the genome level. However, it has long been suggested that there exist physical constraints which limit the set of possible outcomes. In craniate evolution, it has been observed that head features, notably in the genus homo, can be ordered in a morphological diagram such that, as the brain expands, the head rocks more forward, face features become less prognathous and the mouth tends to recede. One school of paleontologists suggests that this trend is wired somewhere structurally inside the anatomy, and that random modifications of genes push up or down animal forms along a pre-determined path. No actual experiment has been able to settle the dispute. I present here an experiment of electric stimulation of the head in the chicken embryo which is able to enhance the magnitude of tension forces during development. This experimental intervention causes a correlated brain shrinkage and rotatory movement of the head, congruent with tissue texture, which proves that head dilation and flexure are intimately linked. Numerical modelling explains why the brain curls when it dilates. This gives support to the idea that there exists, in the texture of the vertebrate embryo, a latent dynamic pattern for the observed paleontological trends in craniates towards homo, a concept known as Inside story.