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1.
薛定谔的猫
(2025-04-01 00:19):
#paper doi:https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.124.072226 Natural history and clinical outcomes of patients with DSG2/DSC2 variant-related arrhythmogenic right ventricular cardiomyopathy. Circulation.
DSG2和DSC2通过相互附着构成桥粒的粘附核心,在心脏细胞水平抵抗机械应力方面至关重要。DSG2和DSC2是少见的致心律失常右室心肌病基因,本文收集了271例受试者,其中254例携带DSG2变异。结论:与不进行高强度运动的人相比,进行高强度运动的单变异携带者的发病年龄更小。与单变异携带者相比,多变异携带者更有可能被诊断为ARVC
Circulation,
2025-3-24.
DOI: 10.1161/CIRCULATIONAHA.124.072226
Abstract:
BACKGROUND: Genetic variants in desmosomal cadherins, desmoglein 2 ( DSG2 ) and desmocollin 2 ( DSC2 ), cause a distinct form of arrhythmogenic right ventricular cardiomyopathy (ARVC), which remains poorly …
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BACKGROUND: Genetic variants in desmosomal cadherins, desmoglein 2 ( DSG2 ) and desmocollin 2 ( DSC2 ), cause a distinct form of arrhythmogenic right ventricular cardiomyopathy (ARVC), which remains poorly reported. In this study, we aimed to provide a comprehensive description of the phenotypic expression, natural history, and clinical outcomes of patients with this ARVC subset. METHODS: Genetic and clinical data of DSG2 and DSC2 variant carriers were collected from 5 countries in Europe and Asia. We assessed the phenotypic profile of these patients and their clinical outcomes, focusing on heart failure and ventricular arrhythmia events. RESULTS: Overall, 271 subjects, 254 with DSG2 variants, were included in this study (median age, 38 years [interquartile range, 25–52]; 62.7% male). Of these, 165 were probands, and 200 were diagnosed with definite ARVC. A total of 181 (66.8%) individuals carried missense variants, mainly distributed in the extracellular domains. Notably, we included 78 (28.8%) individuals with multiple variants. Of the 200 cases with diagnosed ARVC, 41 (20.5%) experienced premature cardiac death before the age of 65. Among the 81 individuals for whom both left ventricular ejection fraction and right ventricular fractional area change data were available at presentation, 29 (35.8%) had isolated right ventricular dysfunction, and 16 (19.8%) had biventricular dysfunction. Single-variant carriers who engaged in intense physical exercise were younger at disease onset compared with those who did not ( P =0.001). Compared with single-variant carriers, those with multiple variants were more likely to be diagnosed with ARVC (96.2% versus 64.8%; P <0.001) and exhibited more severe left ventricular dysfunction (44.4% versus 22.1%; P =0.001) and right ventricular dilation (88.9% versus 55.8%, P <0.001). Multiple-variant carriers were significantly younger at ARVC diagnosis compared with single-variant carriers (33 [18–49] years versus 42 [27–54] years; P <0.001]. During follow-up, end-stage heart failure ( P <0.001) and malignant ventricular arrhythmias ( P =0.004) were significantly more frequent in multiple-variant compared with single-variant carriers. Compared with PKP2 patients, DSG2/DSC2 patients exhibited a significantly higher risk of end-stage heart failure ( P <0.001). CONCLUSIONS: ARVC attributable to variants in desmosomal cadherins mostly present with right ventricular or biventricular disease. Multiple variants are common in these patients and are associated with more frequent clinical penetrance, earlier onset of disease, and adverse clinical outcomes.
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2.
林海onrush
(2025-03-31 23:32):
#paper, DOI: 10.1109/GCWkshps45667.2019.9024550, Faking and Discriminating the Navigation Data of a Micro Aerial Vehicle Using Quantum Generative Adversarial Networks, 论文研究了如何利用量子生成对抗网络(QGAN)实施对微型飞行器(MAV)导航数据的伪造与识别。作者提出了一种具体的QGAN设计,探讨了攻击者在完全不掌握目标系统动态信息的前提下,如何通过学习生成虚假的导航数据,以欺骗系统监控和执行隐蔽攻击。同时提出了一个识别真假导航数据的设计方案。具体实现中融合了经典优化算法、量子比特计算和光子量子计算技术,并基于PennyLane量子机器学习平台进行了经典计算机仿真实验。
3.
符毓 Yu
(2025-03-31 23:08):
#paper doi.org/10.1016/j.autcon.2025.105963 Automation in Construction, 2025, Impact of Color and Mixing Proportion of Synthetic Point Clouds on Semantic Segmentation. 合成点云能弥补数据量的不足,本文讨论混合真实数据的比例对模型训练的影响以及点云颜色(真实颜色还是BIM颜色)对模型训练的影响
Automation in Construction,
2025-3.
DOI: 10.1016/j.autcon.2025.105963
Abstract:
No abstract available.
4.
钟鸣
(2025-03-31 22:38):
#paper doi:10.1007/s10071-024-01907-0 Odour generalisation and detection dog training
侦查犬能敏锐辨识特定味道从而在识别爆炸物、病人、药物等领域发挥作用。但受环境等因素影响,目标物质可能会释放出与训犬时不太一样的气味;或者,需要侦查犬捕捉识别出与训练气味相似的气味,因为这或许意味着某种新型但同类别的药物/爆炸物,以上场景统称气味的泛化。目标是训练犬类具有宽严有序的泛化能力,既不错杀也不错放。对单一气味的过度长时间的强化训练会降低犬的概括和泛化能力,作者建议使用目标气味的变化(例如 不同的样品或数量)或将目标气味与各种干扰气味一起或靠近各种干扰气味来克服这个问题。本文还总结了5种推荐的训练方法并作说明:顺序训练、混合训练、交替训练、分类训练、复合训练
Animal Cognition,
2024-11-1.
DOI: 10.1007/s10071-024-01907-0
Abstract:
Abstract Detection dogs are required to search for and alert to specific odours of interest, such as drugs, cadavers, disease markers and explosives. However, the odour released from different samples …
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Abstract Detection dogs are required to search for and alert to specific odours of interest, such as drugs, cadavers, disease markers and explosives. However, the odour released from different samples of the same target substance will vary for a number of reasons, including the production method, evaporation, degradation, or by being mixed with extraneous odours. Generalisation, the tendency to respond in the same manner to stimuli which are different – but similar to – a conditioned stimulus, is therefore a crucial requirement for working detection dogs. Odour is a complex modality which poses unique challenges in terms of reliably predicting generalisation, when compared with auditory or visual stimuli. The primary aim of this review is to explore recent advances in our understanding of generalisation and the factors that influence it, and to consider these in light of detection dog training methods currently used in the field. We identify potential risks associated with certain training practices, and highlight areas where research is lacking and which warrant further investigation.
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5.
庞庞
(2025-03-31 22:14):
#paper https://doi.org/10.1038/s41467-025-57682-0 Major depressive disorder on a neuromorphic continuum 这篇文章很有意思的一点是把抑郁症从连续的角度进行了亚型的划分。因为直接用离散的类别对患者进行划分显然是不合实际的,每个人都有重叠的部分。使用贝叶斯模型对患者的结构数据进行了特征分解,分解到三个因子,每个患者有属于3个因子的概率值;同时获得了三个因子有一个脑图。研究发现这些因子和一些生物过程有关联,并且可以预测治疗的效果。
6.
半面阳光
(2025-03-31 22:08):
#paper https://doi.org/10.1016/j.ajog.2024.08.017. American Journal of Obstetrics & Gynecology. 2024. The use of free DNA for fetal RHD genotyping in the Rh negative pregnant patient—the time has come. 这是2024年发表在AJOG杂志上的评论性文章。文章简要介绍了将检测胎儿RHD基因分型纳入到NIPT检测流程的技术方法,该技术可以检出异常 RHD 假基因和混合 RHD-CE-Ds 基因型,以进一步为临床上使用RhoGAM进行辅助判断。
Abstract:
No abstract available.
7.
哪有情可长
(2025-03-31 19:59):
#paper Resistance to Striga Parasitism through Reduction of Strigolactone Exudation. Cell 12 February 2025, DOI:10.1016/j.cell.2025.01.022. 首先发现高粱在缺磷的环境发现独脚金内酯分泌的多,建立缺磷处理体系后,对缺磷和正常材料进行转录组分析发现ABC转运蛋白家族编码的外排独脚金内酯的基因SbSLT1和SbSLT2高表达。后续利用分子实验鉴定其基因表达模式(qRT-PCR)、原位杂交等实验表明SbSLT1和SbSLT2主要在高粱根系表皮细胞表达,符合其外排SL到土壤中的功能特性。利用酵母、爪蟾卵母细胞以及拟南芥异源表达系统,证实了SbSLT1和SbSLT2均具有显著的SL转运活性。为深入解析SbSLT1和SbSLT2转运SL的分子机制,研究团队利用AlphaFold结合HOLE对SbSLT1和SbSLT2在细胞膜上形成的SL转运通道进行了预测,结合实验结果最终确定了SbSLT1-F693和SbSLT2-F642为关键氨基酸位点,进一步探究发现它们的同源蛋白SbSLT1-LIKE和SbSLT2-LIKE均不具备SL转运活性,强调了SbSLT1和SbSLT2在高粱ABCG家族转运蛋白中的SL转运功能特异性。同源蛋白SbSLT1-LIKE和SbSLT2-LIKE并不存在该保守氨基酸位点,这也解释了二者不具备SL转运活性的现象。通过蛋白序列比对发现,单子叶植物中SbSLT1和SbSLT2的同源蛋白与已知的双子叶SL转运蛋白均具有该保守苯丙氨酸位点,说明在单双子叶植物中可能存在保守的独脚金内酯转运机制。进一步构建高粱SbSLT1和SbSLT2基因编辑敲除株系进行功能验证,发现敲除突变体材料的根系分泌物中独脚金内酯含量较对照株系显著降低,且利用该分泌物处理独脚金种子,萌发率显著下降。田间小区实验发现突变掉SbSLT1和SbSLT2基因的高粱寄生率降低了67-94%以上,同时高粱的产量损失减少了49%-52%。
8.
Vincent
(2025-03-31 16:09):
#paper doi: https://doi.org/10.48550/arXiv.2503.00096 BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology 大语言模型在加速科学发现方面展现出了重要潜力。目前大语言模型智能体在生物信息领域的应用缺乏系统评估,这篇文章整理了近50个真实场景,约300个开放性问题来衡量基于大语言模型的智能体在解决复杂生信问题的能力,作者测试了两个前沿大语言模型(gpt 4o和claude 3.5 sonnet),发现这些模型在回答开放性问题的准确率都较低,回答多选问题的能力也并不比随机选择策略好。这篇文章的贡献在于提供了测试用例与评估框架,为更搭建性能更好的智能体打下了基础
arXiv,
2025-02-28T18:47:57Z.
DOI: 10.48550/arXiv.2503.00096
Abstract:
Large Language Models (LLMs) and LLM-based agents show great promise inaccelerating scientific research. Existing benchmarks for measuring thispotential and guiding future development continue to evolve from pure recalland rote knowledge …
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Large Language Models (LLMs) and LLM-based agents show great promise inaccelerating scientific research. Existing benchmarks for measuring thispotential and guiding future development continue to evolve from pure recalland rote knowledge tasks, towards more practical work such as literature reviewand experimental planning. Bioinformatics is a domain where fully autonomousAI-driven discovery may be near, but no extensive benchmarks for measuringprogress have been introduced to date. We therefore present the BioinformaticsBenchmark (BixBench), a dataset comprising over 50 real-world scenarios ofpractical biological data analysis with nearly 300 associated open-answerquestions designed to measure the ability of LLM-based agents to explorebiological datasets, perform long, multi-step analytical trajectories, andinterpret the nuanced results of those analyses. We evaluate the performance oftwo frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent frameworkwe open source. We find that even the latest frontier models only achieve 17%accuracy in the open-answer regime, and no better than random in amultiple-choice setting. By exposing the current limitations of frontiermodels, we hope BixBench can spur the development of agents capable ofconducting rigorous bioinformatic analysis and accelerate scientific discovery.
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9.
尹志
(2025-03-31 15:06):
#paper:doi:doi.org/10.48550/arXiv.2502.11974, Image Inversion: A Survey from GANs to Diffusion and Beyond(2025).
综述了image inversion常见的算法模型,很新,主要介绍了GAN和diffusion模型,也提了DiT和Rectified Flow框架。image inversion的核心问题涉及latent space, 对其它生成式AI的问题都非常重要。
arXiv,
2025-02-17T16:20:48Z.
DOI: 10.48550/arXiv.2502.11974
Abstract:
Image inversion is a fundamental task in generative models, aiming to mapimages back to their latent representations to enable downstream applicationssuch as editing, restoration, and style transfer. This paper provides …
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Image inversion is a fundamental task in generative models, aiming to mapimages back to their latent representations to enable downstream applicationssuch as editing, restoration, and style transfer. This paper provides acomprehensive review of the latest advancements in image inversion techniques,focusing on two main paradigms: Generative Adversarial Network (GAN) inversionand diffusion model inversion. We categorize these techniques based on theiroptimization methods. For GAN inversion, we systematically classify existingmethods into encoder-based approaches, latent optimization approaches, andhybrid approaches, analyzing their theoretical foundations, technicalinnovations, and practical trade-offs. For diffusion model inversion, weexplore training-free strategies, fine-tuning methods, and the design ofadditional trainable modules, highlighting their unique advantages andlimitations. Additionally, we discuss several popular downstream applicationsand emerging applications beyond image tasks, identifying current challengesand future research directions. By synthesizing the latest developments, thispaper aims to provide researchers and practitioners with a valuable referenceresource, promoting further advancements in the field of image inversion. Wekeep track of the latest works at https://github.com/RyanChenYN/ImageInversion
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10.
白鸟
(2025-03-31 14:35):
#paper:doi:doi.org/10.1038/s41588-024-01883-8, MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution Nat Genet(2024).
通过HLA分子呈递肿瘤新生抗原对于实现肿瘤免疫治疗至关重要。但肿瘤的免疫识别可能会因HLA分子被破坏而受到抑制。HLA被破坏的不同类型(突变、LOH、抑制和可变剪接)在癌症中很常见。
1.检测工具:作者开发了一个工具 MHC Hammer,检测MHC杂合性缺失(LOH) 、等位基因特异性突变及测量HLA表达和抑制。
2.肿瘤HLA变化:肺癌和乳腺癌队列中破坏性的HLA突变很少见,但HLA等位基因的LOH、抑制和肿瘤富集的可变剪接却很普遍。这突出了HLA转录组损坏的程度及其重要性,和HLA抑制和可变剪接在癌症进化中的作用。
3.HLA抑制与甲基化:HLA抑制和替代剪接事件的潜在机制可能是表观遗传。发现甲基化和HLA基因表达之间存在很强的关联。
4.展望:HLA替代剪接和抑制在多大程度上代表一种泛癌症免疫逃避机制需要更多的研究。
Nature Genetics,
2024-10.
DOI: 10.1038/s41588-024-01883-8
Abstract:
AbstractDisruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major histocompatibility complex loss of heterozygosity (LOH), allele-specific mutation …
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AbstractDisruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major histocompatibility complex loss of heterozygosity (LOH), allele-specific mutation and measurement of expression and repression (MHC Hammer). We identified extensive variability in HLA allelic expression and pervasive HLA alternative splicing in normal lung and breast tissue. In lung TRACERx and lung and breast TCGA cohorts, 61% of lung adenocarcinoma (LUAD), 76% of lung squamous cell carcinoma (LUSC) and 35% of estrogen receptor-positive (ER+) cancers harbored class I HLA transcriptional repression, while HLA tumor-enriched alternative splicing occurred in 31%, 11% and 15% of LUAD, LUSC and ER+ cancers. Consistent with the importance of HLA dysfunction in tumor evolution, in LUADs, HLA LOH was associated with metastasis and LUAD primary tumor regions seeding a metastasis had a lower effective neoantigen burden than non-seeding regions. These data highlight the extent and importance of HLA transcriptomic disruption, including repression and alternative splicing in cancer evolution.
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11.
燕赵孤侠
(2025-03-31 11:26):
#paper doi:10.3969/j.issn.1000-0844.2014.03.0599 《川滇地区中小地震震源机制解及构造应力场的研究 》
对于川滇地区底壳环境,他们算出哪些断层现在压力大,再结合以往压力模型,能像天气预报一样实时盯着这些高危地段。能快速判断今年发生的地震是滑着走还是上下跳。就是要要给川滇地壳做了个健康监测系统,做到对防灾减灾心里更有数
12.
李翛然
(2025-03-31 10:04):
#paper doi:doi.org/10.1038/s41467-025-58038-4 Robust enzyme discovery and engineering with deep learning using CataPro.
深度学习赋能酶工程——CataPro模型
1. 研究背景与挑战
酶作为高效生物催化剂在工业中应用广泛,但野生酶性能不足且传统改造方法成本高、效率低。现有深度学习模型在酶动力学参数(如kcat、Km)预测中存在数据偏差和泛化能力不足的问题,阻碍了理性设计进程。
2. 模型创新与优势
研究团队开发的CataPro模型通过整合预训练语言模型(如ProtT5、MolT5)与分子指纹,显著提升了酶动力学参数的预测精度。其核心突破在于采用无偏十折交叉验证数据集(按序列相似性聚类划分),避免模型对训练数据的“记忆性”过拟合,泛化能力优于现有工具。
3. 实际应用验证
在香兰素生物合成案例中,CataPro成功挖掘出活性提升的SsCSO酶,并通过预测指导突变设计获得活性提高3.34倍的突变体。这一成果展示了模型在酶定向进化与工业酶库筛选中的实用性,为生物制造提供高效工具。
4. 局限与未来方向
当前模型对复杂催化机制的表征仍有不足,且kcat预测精度受限于数据覆盖度。未来需融合更多物理化学机制特征,并拓展反应类型数据以增强普适性。
5. 总结评价
CataPro通过深度学习与无偏数据策略的结合,为酶工程提供了高可信度预测工具,推动生物催化从经验驱动向数据驱动转型。其成功案例为绿色化工、合成生物学等领域的高效酶设计开辟了新路径,标志着AI在生物制造中的深度渗透。
Nature Communications,
2025-3-20.
DOI: 10.1038/s41467-025-58038-4
Abstract:
Abstract Accurate prediction of enzyme kinetic parameters is crucial for enzyme exploration and modification. Existing models face the problem of either low accuracy or poor generalization ability due to overfitting. …
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Abstract Accurate prediction of enzyme kinetic parameters is crucial for enzyme exploration and modification. Existing models face the problem of either low accuracy or poor generalization ability due to overfitting. In this work, we first developed unbiased datasets to evaluate the actual performance of these methods and proposed a deep learning model, CataPro, based on pre-trained models and molecular fingerprints to predict turnover number (k c a t ), Michaelis constant (K m ), and catalytic efficiency (k c a t /K m ). Compared with previous baseline models, CataPro demonstrates clearly enhanced accuracy and generalization ability on the unbiased datasets. In a representational enzyme mining project, by combining CataPro with traditional methods, we identified an enzyme (SsCSO) with 19.53 times increased activity compared to the initial enzyme (CSO2) and then successfully engineered it to improve its activity by 3.34 times. This reveals the high potential of CataPro as an effective tool for future enzyme discovery and modification.
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13.
颜林林
(2025-03-26 13:02):
#paper doi:10.1002/mco2.315, MedComm, 2023, Applications of multi-omics analysis in human diseases. 最近我正在做一些多组学数据分析相关的任务,正好翻到这篇综述读了读,用以增强自己对多组学相关技术及分析方法的宏观认识。这篇综述全面介绍了多组学分析在人类疾病研究中的应用,通过整合基因组学、转录组学、蛋白质组学、代谢组学等多种组学数据,既能帮助更深入地理解疾病的发生和发展机制,也能在生物标志物和靶点研究、神经退行性疾病、衰老研究等方面发挥作用。至于分析方法,大致包括两类策略:一是根据相关性或共同映射构建生物网络,揭示分子间相互作用和调控关系;一是使用机器学习或深度学习方法挖掘高维数据,筛选特征或建立预测模式。顺带提一句,这文章已经发表快两年,但在正文Fig 1中的错别字(把MRI错写成MIR)也仍未修正过来。
MedComm,
2023-8.
DOI: 10.1002/mco2.315
Abstract:
AbstractMulti‐omics usually refers to the crossover application of multiple high‐throughput screening technologies represented by genomics, transcriptomics, single‐cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great …
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AbstractMulti‐omics usually refers to the crossover application of multiple high‐throughput screening technologies represented by genomics, transcriptomics, single‐cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi‐omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi‐omics. This review outlines the existing technical categories of multi‐omics, cautions for experimental design, focuses on the integrated analysis methods of multi‐omics, especially the approach of machine learning and deep learning in multi‐omics data integration and the corresponding tools, and the application of multi‐omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open‐source analysis tools and databases, and finally, discusses the challenges and future directions of multi‐omics integration and application in precision medicine. With the development of high‐throughput technologies and data integration algorithms, as important directions of multi‐omics for future disease research, single‐cell multi‐omics and spatial multi‐omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi‐omics medical research.
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14.
DeDe宝
(2025-03-26 11:33):
#paper doi: 10.1101/2024.05.11.593696 bioRxiv, 2025,Prioritizing working memory resources depends on prefrontal cortex工作记忆指的是我们在短时间内存储并处理信息的能力,对记忆的处理包括根据优先级分配工作记忆资源。此前研究指出前额叶皮层与工作记忆存储相关,但是否与记忆处理相关尚不明确。该研究中通过经颅磁刺激(TMS)技术研究了sPCS在工作记忆资源分配中的作用。实验发现,TMS干扰sPCS会破坏工作记忆资源的优先级分配,使得对低优先级项目的记忆表现意外地提高。具体来说,当sPCS的特征选择性活动受到干扰时,原本应该分配更多资源给高优先级项目的机制被破坏,导致资源分配更加均衡,从而提高了低优先级项目的记忆表现。这种现象支持了dlPFC(特别是sPCS)在工作记忆资源分配中的控制功能,而不是单纯的存储功能。
bioRxiv,
2024-10-27.
DOI: 10.1101/2024.05.11.593696
Abstract:
ABSTRACTHow the prefrontal cortex contributes to working memory remains controversial, as theories differ in their emphasis on its role in storing memories versus controlling their content. To adjudicate between these …
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ABSTRACTHow the prefrontal cortex contributes to working memory remains controversial, as theories differ in their emphasis on its role in storing memories versus controlling their content. To adjudicate between these competing ideas, we tested how perturbations to the human (both sexes) lateral prefrontal cortex impact the storage and control aspects of working memory during a task that requires human subjects to allocate resources to memory items based on their behavioral priority. Our computational model made a strong prediction that disruption of this control process would counterintuitively improve memory for low-priority items. Remarkably, transcranial magnetic stimulation of retinotopically-defined superior precentral sulcus, but not intraparietal sulcus, unbalanced the prioritization of resources, improving memory for low-priority items as predicted by the model. Therefore, these results provide direct causal support for models in which the prefrontal cortex controls the allocation of resources that support working memory, rather than simply storing the features of memoranda.SIGNIFICANCE STATEMENTAlthough higher-order cognition depends on working memory, the resources that support our memory are severely limited in capacity. To mitigate this limitation, we allocate memory resources according to the behavioral relevance of items. Nonetheless, the neural basis of these abilities remain unclear. Here, we tested the hypothesis that a region in lateral prefrontal cortex controls prioritization in working memory. Indeed, perturbing this region with transcranial magnetic stimulation disrupted the prioritization of working memory resources. Our results provide causal evidence for the hypothesis that prefrontal cortex primarily controls the allocation of memory resources, rather than storing the contents of working memory.
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15.
徐炳祥
(2025-03-25 21:42):
#paper doi:10.1186/s13059-025-03526-5 Genome Biology, 2025, ASPM mediates nuclear entrapment of FOXM1 via liquid-liquid phase separation to promote progression of hepatocarcinoma。相分离(LLPS)在肿瘤发生发展中的作用是当前相关研究的热门课题。FOXM1是肝癌(HCC)发展的重要标志物,然而其机制尚不明确。本文作者在FOXM1的上下游中筛选了可能与其发生蛋白-蛋白相互作用的基因产物,锁定了基因ASPM,实验和生物信息学均证实ASPM和FOXM1的结合可促使其发生LLPS。细胞和肿瘤移植实验均证实ASPM水平的高低与HCC进展间存在显著的正相关关系。进一步的发现ASPM的存在保护了FOXM1免受降解。最后,作者发现在ASPM的启动子上存在FOXM1的结合位点,二者构成双正反馈表达回路。本文是一项标准的LLPS研究,对学习和掌握LLPS相关实验和分析技术有一定借鉴意义。同时也为肿瘤研究打开了新思路。
16.
刘昊辰
(2025-03-19 16:41):
#paper Implementing the AlphaZero algorithm for Connect Four A deep reinforcement learning approach. 这是一篇关于如何将DeepMind的AlphaZero算法应用于Connect Four(四连棋)游戏的研究论文。论文成功地将AlphaZero算法应用于Connect Four游戏,展示了深度强化学习在复杂棋类游戏中的潜力。下载地址:https://www.researchgate.net/publication/377943555_Implementing_the_AlphaZero_algorithm_for_Connect_Four_A_deep_reinforcement_learning_approach/fulltext/65be3687790074549760c1bc/Implementing-the-AlphaZero-algorithm-for-Connect-Four-A-deep-reinforcement-learning-approach.pdf?_tp=eyJjb250ZXh0Ijp7ImZpcnN0UGFnZSI6InB1YmxpY2F0aW9uIiwicGFnZSI6InB1YmxpY2F0aW9uIn19
Applied and Computational Engineering,
2024-2-4.
DOI: 10.54254/2755-2721/33/20230228
Abstract:
The realm of board games presents a challenging domain for the application of artificial intelligence (AI), given their vast state-action space and inherent complexity. This paper explores the development of …
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The realm of board games presents a challenging domain for the application of artificial intelligence (AI), given their vast state-action space and inherent complexity. This paper explores the development of a proficient AI for Connect Four using DeepMind's AlphaZero algorithm. The algorithm employs a policy-value network for concurrent prediction of action probabilities and state values, and Monte Carlo Tree Search (MCTS) for decision-making, guided by the policy-value network. Through extensive self-play and data augmentation, our AI learns without the need for explicit prior knowledge. Our experiment demonstrated that the AI player showed significant capability in playing Connect Four, exhibiting strategic decision-making that sometimes-surpassed human performance. These results underline the potential of deep reinforcement learning in advancing AI performance in complex board games.
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17.
惊鸿
(2025-03-16 16:46):
#paper Hyperactive histone genes fuel cancer
Pub Date : 2025-03-13
DOI : 10.1038/s41588-025-02145-x
许多癌症类型在整个基因组中表现出非常高水平的转录,这与不良的临床结果相关。为了更好地了解这种现象,Henikoff 等人在靶向可及染色质 (CUTAC) 方法下使用福尔马林固定石蜡包埋 (FFPE) 切割来研究多种癌症样本中 RNA 聚合酶 II (Pol II) 在全基因组范围内的结合。他们在小鼠神经胶质瘤和各种人类肿瘤(乳腺癌、结肠癌、肝脏癌、直肠癌和胃癌)中观察到 Pol II 整体升高。局部 Pol II 增加对应于乳腺癌和结肠癌中的新发 ERBB2 (也称为 HER2) 扩增。有趣的是,在脑膜瘤中发现了 S 期依赖性组蛋白基因的高 Pol II 水平,并与世界卫生组织 (WHO) 等级、快速复发率和全臂染色体丢失相关。脑膜瘤和乳腺癌组蛋白基因 Pol II 的增加表明组蛋白水平可能对 S 期进展至关重要。作者推测,组蛋白基因高转录可能会促进癌细胞的异常增殖,并且过量的 H3 组蛋白可能与着丝粒处的 CENP-A 组蛋白竞争,最终导致癌症中的高非整倍体发生率。
Nature Genetics,
2025-3.
DOI: 10.1038/s41588-025-02145-x
Abstract:
No abstract available.
18.
龙海晨
(2025-03-10 20:43):
#paper Li W, Ma G, Deng Y, Wu Q, Wang Z, Zhou Q. Artesunate exhibits synergistic anti-cancer effects with cisplatin on lung cancer A549 cells by inhibiting MAPK pathway. Gene. 2021 Jan 15;766:145134. doi: 10.1016/j.gene.2020.145134. Epub 2020 Sep 6. PMID: 32898605.这篇文章讲述了青蒿琥酯 (Artesunate,ART)联合顺铂(cisplatin,CIS) 的抗肿瘤作用。青蒿琥酯 (ART) 是一种已在全球范围内广泛用作抗疟疾药物。作者使用肺癌 A549细胞系研究发现,ART 增加剂量或增加时间的方式显着抑制细胞增殖。ART 与顺铂联合使用效果更加明显。与单一处理相比,联合处理显著降低了集落形成率,并增加了 TUNEL 阳性细胞的发生率。机制上,联合处理影响 Bcl-2 、 Bax 、 p-P53 、 Caspase-3/7 、 Caspase-9 、 CyclinB1 、 P34 、 P21 的表达,并协同调节 P38/JNK/ERK1/2 MAPK 通路的活性。
Abstract:
BACKGROUND: Artesunate (ART) has been used extensively as anti-malarial drugs worldwide. Besides, it has also been reported to have anti-cancer activities. This study was aimed to explore the anti-cancer activity …
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BACKGROUND: Artesunate (ART) has been used extensively as anti-malarial drugs worldwide. Besides, it has also been reported to have anti-cancer activities. This study was aimed to explore the anti-cancer activity of ART in combination with cisplatin (CIS) on A549 cells.METHODS: Cells were cultured with different concentrations of ART and/or CIS for 24, 48, or 72 h to test the anti-proliferative effects by CCK-8 assay. Colony formation assay and EdU staining were also performed. TUNEL staining was used to illustrate the morphologic changes. Cell cycle and apoptosis were determined by flow cytometry assay, and Western blot analysis was conducted to detect the expression of apoptosis- and proliferation-related proteins. Caspase activities were determined by colorimetric assay kit. Moreover, the synergistic effect of ART with CIS in A549 cell xenograft model was also determined.RESULTS: ART significantly inhibited cell proliferation in dose- and time-dependent manners. Collectively, the combination treatment remarkably decreased colony formation rates and increased the rates of TUNEL-positive cells compared with mono-treatment. Mechanistically, the combination treatment influenced the expression of Bcl-2, Bax, p-P53, Caspase-3/7, Caspase-9, CyclinB1, P34, P21, and synergistically regulated the activity of P38/JNK/ERK1/2 MAPK pathway. In mice A549 xenograft tumors, the combination strategy significantly increased the anti-cancer efficacy of ART and CIS alone, consistent with the in vitro observations.CONCLUSIONS: ART exhibited significant anti-tumor effect on A549 cells and this efficiency could be enhanced by combination with CIS.
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19.
翁凯
(2025-03-05 21:45):
#paper 【doi】10.1038/s41586-024-07954-4;【发表年份】2024年;【期刊】Nature;【标题】Temporal recording of mammalian development and precancer。该研究旨在突破传统细胞事件追踪技术的局限性,通过开发基于CRISPR的单细胞分子钟平台,实现哺乳动物发育和肿瘤起源的精准时空记录。研究者利用自突变CRISPR条形码技术,在单细胞水平同步捕获基因表达和遗传变异信息,系统解析了小鼠胚胎器官形成过程中细胞增殖、分化和克隆动态,揭示出肠道发育中未被识别的新型祖细胞群体及其功能特征。进一步将此技术应用于人类结直肠癌前病变样本(包含116个息肉的转录组和418个息肉的突变组数据),首次证实约15-30%的腺瘤起源于多个独立正常干细胞,挑战了传统单克隆致癌假说,为癌症早期起源机制研究提供了多维证据支持。
20.
翁凯
(2025-03-02 17:41):
#paper doi:10.1038/s41587-024-02248-6;发表年份:2024;期刊:Nature Biotechnology;标题:High-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits。传统抗原检测技术依赖人类原代T细胞,只能识别少数MHC类型(如人类MHC I类),且无法高效分析低亲和力抗原或跨物种(如小鼠)模型。为了解决这些问题,本研究开发了名为TCR-MAP的新技术,其核心是通过基因工程改造Jurkat细胞(一种实验室常用的T细胞系),使其携带特定T细胞受体(TCR)和一个名为Sortase A的酶;当TCR识别到抗原呈递细胞(如病毒感染的细胞或肿瘤细胞)表面的抗原肽-MHC复合物时,Sortase A会被激活,并在靶细胞表面打上生物素“标记”,随后通过磁珠富集这些标记细胞并测序解析抗原。实验证明,该技术能同时兼容人类和小鼠的MHC I/II类抗原,成功识别了CMV病毒抗原、肿瘤抗原(如CTAG1B)以及自身免疫疾病相关抗原(如心脏中的CKMT2),检测灵敏度达到微摩尔级(可发现极微量的抗原),且无需依赖不稳定的原代T细胞。这一平台为病毒逃逸研究、肿瘤疫苗开发和自身免疫病机制解析提供了高效工具,未来还可扩展至脂类等非蛋白抗原的检测。
Nature Biotechnology,
2024-7-2.
DOI: 10.1038/s41587-024-02248-6
Abstract:
AbstractAntigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs), leaving methods for MHC class II-restricted and mouse TCR reactivities relatively undeveloped. …
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AbstractAntigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs), leaving methods for MHC class II-restricted and mouse TCR reactivities relatively undeveloped. Here we present TCR mapping of antigenic peptides (TCR-MAP), an antigen discovery method that uses a synthetic TCR-stimulated circuit in immortalized T cells to activate sortase-mediated tagging of engineered antigen-presenting cells (APCs) expressing processed peptides on MHCs. Live, tagged APCs can be directly purified for deconvolution by sequencing, enabling TCRs with unknown specificity to be queried against barcoded peptide libraries in a pooled screening context. TCR-MAP accurately captures self-reactivities or viral reactivities with high throughput and sensitivity for both MHC class I-restricted and class II-restricted TCRs. We elucidate problematic cross-reactivities of clinical TCRs targeting the cancer/testis melanoma-associated antigen A3 and discover targets of myocarditis-inciting autoreactive T cells in mice. TCR-MAP has the potential to accelerate T cell antigen discovery efforts in the context of cancer, infectious disease and autoimmunity.
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