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61.
小年 (2025-05-30 17:26):
#paper doi:10.1016/j.stem.2022.12.006 ,Cheng, X., et al. Decoding m6A RNA methylome identifies PRMT6-regulated lipid transport promoting AML stem cell maintenance 研究团队通过MeRIP-seq 测序方法解码了白血病起始细胞(LICs)的RNA m6A修饰组学,确定了3587个高可信度的m6A修饰靶点;与正常造血干祖细胞群体的m6A修饰组进行比较并结合表达水平变化分析,发现在AML发生过程中m6A修饰正调控干细胞自我更新相关基因表达,提示m6A参与白血病起始细胞干性获得。该研究揭示了 PRMT6-MFSD2A 信号轴调控 LSCs 的新机制,为 AML 治疗提供了以 PRMT6 为靶点的潜在策略,IGF2BP2 和 PRMT6 或可作为预后评估生物标志物。
62.
燕赵孤侠 (2025-05-30 14:15):
#paper doi:10.1126/science.adk6635, Returned samples indicate volcanism on the Moon 120 million years ago 之前,我们都觉得月球早就没有活动了,像个死寂的大石头,没想到这篇研究直接打脸 —— 人家 1.2 亿年前还在 “冒火” 搞火山活动呢! 研究团队这次用了超精准的年代测定技术。以前测岩石年龄误差不小,这次靠质谱分析,直接把误差范围缩得超小,还多管齐下交叉验证数据,这波操作简直是科研界严谨的到极致,也给以后研究太空指了条明路。 从这篇论文我特别有感触,科学探索真是永无止境。以前以为铁板钉钉的结论,碰上新技术、新方法,瞬间被颠覆。所以搞研究真不能墨守成规,得大胆创新。而且研究团队这种死磕细节、精益求精的精神,太值得学习了,这才是推动科学进步的关键。
Abstract:
There is extensive geologic evidence of ancient volcanic activity on the Moon, but it is unclear how long that volcanism persisted. Magma fountains produce volcanic glasses, which have previously been … >>>
There is extensive geologic evidence of ancient volcanic activity on the Moon, but it is unclear how long that volcanism persisted. Magma fountains produce volcanic glasses, which have previously been found in samples of the Moon’s surface. We investigated ~3000 glass beads in lunar soil samples collected by the Chang’e-5 mission and identified three as having a volcanic origin on the basis of their textures, chemical compositions, and sulfur isotopes. Uranium-lead dating of the three volcanic glass beads shows that they formed 123 ± 15 million years ago. We measured high abundances of rare earth elements and thorium in these volcanic glass beads, which could indicate that such recent volcanism was related to local enrichment of heat-generating elements in the mantle sources of the magma. <<<
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63.
白鸟 (2025-05-27 15:06):
#paper doi:10.1186/s12859-023-05603-7, A score-based method of immune status evaluation for healthy individuals with complete blood cell counts. 文章介绍了基于16715名健康个体全血细胞计数 (CBC) 的免疫状态评分模型。 主要步骤如下: 1.数据采集:16715 名健康个体的CBC免疫相关的15个免疫指标; 2.数据质控:剔除细菌感染和炎症指标感染的数据; 3.数据归一化:三平台归一化,即log_norm归一化; 4.免疫状态聚类:利用期望最大化(EM-GMM)技术对高斯混合模型优化,聚类,免疫状态分三组,良好/中等/较差; 5.CBC指标与免疫状态的相关性评估:采用 RF、LightGBM 和 XGBoost 算法来评估各CBC指标与免疫状态之间的相关性(权重);权重反映CBC指标与人体免疫状态的相关程度; 6.免疫力评分计算:加权和模型,scores= a1*WBC+a2*NEUT+...+a15*BLR; 7.免疫状态评估:免疫状态曲线(age-score曲线):三阶多项式回归模型; 免疫评分>年龄的拟合值:免疫健康; 免疫评分<年龄的拟合值:免疫状态欠佳或亚健康; 研究意义:健康人的异常免疫状态进行早期预警;
Abstract:
Abstract Background With the COVID-19 outbreak, an increasing number of individuals are concerned about their health, particularly their immune status. However, as of now, there is no available algorithm that … >>>
Abstract Background With the COVID-19 outbreak, an increasing number of individuals are concerned about their health, particularly their immune status. However, as of now, there is no available algorithm that effectively assesses the immune status of normal, healthy individuals. In response to this, a new score-based method is proposed that utilizes complete blood cell counts (CBC) to provide early warning of disease risks, such as COVID-19. Methods First, data on immune-related CBC measurements from 16,715 healthy individuals were collected. Then, a three-platform model was developed to normalize the data, and a Gaussian mixture model was optimized with expectation maximization (EM-GMM) to cluster the immune status of healthy individuals. Based on the results, Random Forest (RF), Light Gradient Boosting Machine (LightGBM) and Extreme Gradient Boosting (XGBoost) were used to determine the correlation of each CBC index with the immune status. Consequently, a weighted sum model was constructed to calculate a continuous immunity score, enabling the evaluation of immune status. Results The results demonstrated a significant negative correlation between the immunity score and the age of healthy individuals, thereby validating the effectiveness of the proposed method. In addition, a nonlinear polynomial regression model was developed to depict this trend. By comparing an individual’s immune status with the reference value corresponding to their age, their immune status can be evaluated. Conclusion In summary, this study has established a novel model for evaluating the immune status of healthy individuals, providing a good approach for early detection of abnormal immune status in healthy individuals. It is helpful in early warning of the risk of infectious diseases and of significant importance. <<<
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64.
徐炳祥 (2025-05-25 14:36):
#paper doi: 10.1186/s13059-025-03617-3 Genome Biology, 2025, Analyzing the relationship of RNA and DNA methylation with gene expression。虽然人们已经对启动子区域的DNA甲基化与基因表达水平之间的负相关关系有了相当程度的了解,但对基因体区域的DNA甲基化和相应的RNA甲基化与基因表达间的关系尚有争议。本文通过牛和羊的三种组织(爪垫、乳腺和脾脏)中DNA 5mC和RNA m6A甲基化测序结果详细对比了启动子和基因体区域DNA和RNA甲基化率与基因表达之间的关系。结果显示了基因体区域DNA和RNA甲基化率与基因表达间的正相关关系,其中RNA甲基化率与基因表达间的此种关系更为强烈。这种关系延续到了哺乳期和非哺乳期母牛乳腺的对比中。本文提供了一个非模式物种DNA和RNA甲基化数据集,对研究甲基化与基因表达间的关系有启发作用。
65.
惊鸿 (2025-05-22 19:55):
#paper DOI: 10.1126/science.adp5540 英文标题: A symbiotic filamentous gut fungus ameliorates MASH via a secondary metabolite–CerS6–ceramide axis 时间: 2025年5月1日 北京大学团队在《Science》发表的这项研究,揭示了肠道共生真菌尖镰孢菌(Fusarium foetens)通过分泌代谢物FF-C1靶向抑制宿主CerS6酶,减少毒性脂质C16:0神经酰胺,从而逆转代谢性脂肪肝炎(MASH)的机制。研究通过无菌小鼠模型验证了因果性,并开发了FOCUS-G技术高效分离厌氧真菌,为肠道真菌功能研究提供了新工具。 亮点:① 突破传统“细菌中心”视角,首次建立“真菌-代谢物-宿主”调控轴;② 代谢产物FF-C1结构明确,具备口服药物开发潜力;③ 技术转化路径清晰,真菌组检测或成代谢病早筛新方向。 不足:FF-C1在人体内的代谢稳定性及长期安全性仍需验证,且研究未涉及其他潜在真菌代谢物的协同作用。 总结:该研究为MASH治疗提供了全新靶点,并推动微生物组研究向真菌领域扩展,未来需深化机制探索并加速临床转化。
Abstract:
The gut microbiota is known to be associated with a variety of human metabolic diseases, including metabolic dysfunction–associated steatohepatitis (MASH). Fungi are increasingly recognized as important members of this community; … >>>
The gut microbiota is known to be associated with a variety of human metabolic diseases, including metabolic dysfunction–associated steatohepatitis (MASH). Fungi are increasingly recognized as important members of this community; however, the role of fungal symbionts in metabolic diseases is unknown. We have systematically isolated and characterized gut fungi, identifying Fusarium foetens as an intestinal symbiotic filamentous fungus in mice. F. foetens reverses MASH progression in mouse models through an intestinal ceramide synthetase 6 (CerS6)–ceramide axis. Moreover, we identified FF-C1, a secondary metabolite from F. foetens , as a CerS6 inhibitor that has an endogenous protective effect on MASH progression. <<<
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66.
龙海晨 (2025-05-22 11:19):
#paper Akar Z. Chemical compositions by using LC-MS/MS and GC-MS and antioxidant activities of methanolic extracts from leaf and flower parts of Scabiosa columbaria subsp. columbaria var. columbaria L. Saudi J Biol Sci. 2021 Nov;28(11):6639-6644. doi: 10.1016/j.sjbs.2021.07.039. Epub 2021 Jul 17. PMID: 34764779; PMCID: PMC8568819. 这是一篇关于植物药物提取的文章。提取蓝盆花属中的有效成分,使用甲醇萃取叶子和花中的有效成分,研究其抗氧化活性。分析了叶片和花朵中的精油成分。叶片中的酚类化合物明显高于花朵。抗氧化活性物质叶片明显高于花朵。
67.
刘昊辰 (2025-05-10 11:40):
#paper doi.org/10.1007/978-3-030-35288-2, The Application of AlphaZero to Wargaming. 这是一篇关于尝试将AlphaZero应用于军事推演游戏 “珊瑚海”,以实现推演自动化的研究论文。军事推演与传统棋盘游戏的差异包括问题表示、游戏不对称、战略深度。通过监督学习引导AlphaZero,结合启发式知识和 MCTS 探索,可有效应对挑战,训练出的模型表现优于训练所用的启发式策略,且计算时间更短。
68.
DeDe宝 (2025-05-09 11:47):
#paper doi.org/10.7554/eLife.100287.4, Elife, Stimulus representation in human frontal cortex supports flexible control in working memory. 工作记忆不仅有存储功能,还有指导决策的功能。然而,这些功能通过哪些脑区实现尚无定论。一方面,一些研究认为视觉相关的工作记忆一般在视觉处理相关脑区进行,但一些研究在前额叶同样检测到特定的工作记忆相关的表征。在这个研究中,研究者提出了一个复杂的工作记忆实验,要求被试在低认知需求的复现任务和高认知需求的分类任务之间快速变化,并用fMRI测量整个大脑的活动模式(重点关注早期视觉皮层、顶内沟以及前额叶皮层)。结果表明,相比于低认知需求的任务,在高认知需求的任务中,只有前额叶皮层表现出更强的刺激表征,且强度与被试的表现相关。这说明了前额叶皮层能够随着任务需求和目标的变化灵活地调整其在工作记忆中的作用。
eLife, 2025-4-24. DOI: 10.7554/eLife.100287.4
Abstract:
When holding visual information temporarily in working memory (WM), the neural representation of the memorandum is distributed across various cortical regions, including visual and frontal cortices. However, the role of … >>>
When holding visual information temporarily in working memory (WM), the neural representation of the memorandum is distributed across various cortical regions, including visual and frontal cortices. However, the role of stimulus representation in visual and frontal cortices during WM has been controversial. Here, we tested the hypothesis that stimulus representation persists in the frontal cortex to facilitate flexible control demands in WM. During functional MRI, participants flexibly switched between simple WM maintenance of visual stimulus or more complex rule-based categorization of maintained stimulus on a trial-by-trial basis. Our results demonstrated enhanced stimulus representation in the frontal cortex that tracked demands for active WM control and enhanced stimulus representation in the visual cortex that tracked demands for precise WM maintenance. This differential frontal stimulus representation traded off with the newly-generated category representation with varying control demands. Simulation using multi-module recurrent neural networks replicated human neural patterns when stimulus information was preserved for network readout. Altogether, these findings help reconcile the long-standing debate in WM research, and provide empirical and computational evidence that flexible stimulus representation in the frontal cortex during WM serves as a potential neural coding scheme to accommodate the ever-changing environment. <<<
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69.
颜林林 (2025-05-03 22:21):
#paper doi:10.1038/s41431-025-01844-7, Eur J Hum Genet, 2025, The value of large-scale programmes in human genomics. 这是一篇会议总结报告,来自UK-FR-D+ GENE(英法德基因组学和伦理网络)。他们在会议上讨论了在英法德等国开展的大规模基因组项目的价值,从社会、经济、临床、科学和人群等角度,分别论述了这些项目的现状、产生的价值、这些价值评估的不足、引起的潜在问题等。例如,癌症筛查确实可能使小部分人受益,但缺乏更大范围的成本效益评估;再如,PRS(多基因风险评分)的解释度有限(20-40%),可能造成高风险结果的人过度诊断,而低风险结果的人因误解而获得虚假保证。这些讨论整体上是全面的、深入的、且是中肯的,相比很多论文仅在讨论部分不痛不痒地叙述下自身课题“社会经济价值”,要有意义得多。他们在说明对这些大型项目价值评估方面的确存在复杂性,不该一刀切地下定论(该做或不该做),也在此基础上提出了一些关于评估标准的建议,即如果要开展此类项目,应该综合考虑哪些方面和问题。无疑,这些建议对于全世界各国都有重要的参考价值;科研投入,尤其是如此大规模的科研投入,努力精打细算确是应该的。
70.
半面阳光 (2025-04-30 22:51):
#paper doi: https://doi.org/10.1016/j.gim.2023.100947. Genetics in Medicine. 2023. The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change. 意义不明变异(Variants of Uncertain Significance,VUS)在基因诊断检测中较为常见,这类变异可能导致临床解读困难,并产生额外的后续成本,包括临床医生额外的时间投入。这篇文章的主要是为了调查多基因panel(Multi-gene Panels,MGPs)和外显子组及基因组测序(Exome and Genome Sequencing,ES/GS)诊断检测报告的VUS结果的发生率,评估不确定结果的影响范围,并探索减少其潜在不良影响的方法。研究收集了2020年至2021年间,北美地区19家临床实验室超过150万份测序检测报告的数据,分析因VUS导致的结果不确定率。结果发现,ES/GS导致的不确定结果(VUS)发生率(22.5%)显著低于MGPs(32.6%;P < .0001)。在MGPs检测中,不确定结果的发生率与检测基因数量呈正相关。与单样本检测相比,家系检测(trios,即父母-子女三人组合)能明显降低不确定结果的发生率(18.9% vs 27.6%;P < .0001),而基因组测序(GS)与外显子组测序(ES)相比在VUS发生率上无显著差异(22.2% vs 22.6%;P = ns)。 在多基因panel(MGPs)的检测中,观察到的VUS高发生率提示需要重新审视现行的变异报告规范。文章提出了一些减少VUS报告率的方法,采用其他方法(如对VUS进行亚分类及提供补充报告信息)或可同时提升两类检测的有效性。文章还根据研究结果的提示,建议将临床资源重点用于对有临床意义的VUS进行进一步跟踪评估。
Abstract: No abstract available.
71.
符毓 (2025-04-30 22:15):
#paper doi: arxiv.org/abs/2504.19193, 2025, Trajectory Planning with Model Predictive Control for Obstacle Avoidance Considering Prediction Uncertainty. 本文介绍了一种用于自主机器人的新型轨迹规划器,在机器人操作系统(ROS2) 和导航框架(Nav2)中融入动态避障功能来增强导航性能。该方法利用模型预测控制 (MPC),重点处理与动态障碍物运动预测相关的不确定性。与主要处理静态障碍物或对动态障碍物当前位置做出反应的现有Nav2轨迹规划器不同,该规划器预测未来障碍物的位置,从而确保机器人避开可能存在障碍物的区间
arXiv, 2025-04-27T11:00:19Z. DOI: 10.48550/arXiv.2504.19193
Abstract:
This paper introduces a novel trajectory planner for autonomous robots,specifically designed to enhance navigation by incorporating dynamic obstacleavoidance within the Robot Operating System 2 (ROS2) and Navigation 2 (Nav2)framework. The … >>>
This paper introduces a novel trajectory planner for autonomous robots,specifically designed to enhance navigation by incorporating dynamic obstacleavoidance within the Robot Operating System 2 (ROS2) and Navigation 2 (Nav2)framework. The proposed method utilizes Model Predictive Control (MPC) with afocus on handling the uncertainties associated with the movement prediction ofdynamic obstacles. Unlike existing Nav2 trajectory planners which primarilydeal with static obstacles or react to the current position of dynamicobstacles, this planner predicts future obstacle positions using a stochasticVector Auto-Regressive Model (VAR). The obstacles' future positions arerepresented by probability distributions, and collision avoidance is achievedthrough constraints based on the Mahalanobis distance, ensuring the robotavoids regions where obstacles are likely to be. This approach considers therobot's kinodynamic constraints, enabling it to track a reference path whileadapting to real-time changes in the environment. The paper details theimplementation, including obstacle prediction, tracking, and the constructionof feasible sets for MPC. Simulation results in a Gazebo environmentdemonstrate the effectiveness of this method in scenarios where robots mustnavigate around each other, showing improved collision avoidance capabilities. <<<
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72.
庞庞 (2025-04-30 21:48):
#paper Connectional axis of individual functional variability: Patterns, structural correlates, and relevance for development and cognition www.pnas.org/doi/10.1073/pnas.2420228122 研究揭示功能连接个体差异的空间分布模式,其结构连接基础,及与儿童青少年发育和高级认知的关系。
Abstract:
The human cerebral cortex exhibits intricate interareal functional synchronization at the macroscale, with substantial individual variability in these functional connections. However, the spatial organization of functional connectivity (FC) variability across … >>>
The human cerebral cortex exhibits intricate interareal functional synchronization at the macroscale, with substantial individual variability in these functional connections. However, the spatial organization of functional connectivity (FC) variability across the human connectome edges and its significance in cognitive development remain unclear. Here, we identified a connectional axis in the edge-level FC variability. The variability declined continuously along this axis from within-network to between-network connections and from the edges linking association networks to those linking the sensorimotor and association networks. This connectional axis of functional variability is associated with spatial pattern of structural connectivity variability. Moreover, the connectional variability axis evolves in youth with an flatter axis slope. We also observed that the slope of the connectional variability axis was positively related to the performance in the higher-order cognition. Together, our results reveal a connectional axis in functional variability that is linked with structural connectome variability, refines during development, and is relevant to cognition. <<<
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73.
哪有情可长 (2025-04-30 21:38):
#paper Reconstructing the Transcriptional Ontogeny of Maize and Sorghum Supports an Inverse Hourglass Model of Inflorescence Development, Current Biology, October 21, 2019. https://doi.org/10.1016/j.cub.2019.08.044.对玉米和高粱的穗构建了不同发育时期的转录组图谱,借助转录本动力学确定了玉米抽穗和高粱穗发育阶段,然后利用随机森林确定了基因表达预测,发现这两个物种在将干细胞命运方面最相似。这个工作对我最近分析多物种的比较转录组很有启发。
74.
白鸟 (2025-04-30 21:37):
#paper doi:10.1016/j.immuni.2023.10.013 Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB−CD8+ memory T cells and accumulation of type 2 memory T cells 文章调研了166名25-85岁人群的200万个PBMC的临床数据和单细胞测序数据;通过分析317个样本55个细胞亚群,寻找健康人群的血液关于年龄相关的变化趋势,发现NKG2C+GZMB−CD8+记忆T细胞亚群随年龄显著减少;随着年龄的增长,2型记忆性CD4+和CD8+T细胞增加,并能产生更多的IL-4。这是一篇从单细胞水平研究免疫年龄,研究人群免疫年龄的共性,寻找免疫在人体衰老过程中的变化。也有不少模型对免疫年龄进行预测,真实性准确性有待商榷。
75.
Vincent (2025-04-30 21:21):
#paper https://doi.org/10.1038/s41467-025-57430-4 DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis, nature communications, 2025. 该研究介绍了由大型语言模型驱动的生物信息学平台 DrBioRight 2.0,旨在以自然语言交互方式支持大规模癌症功能蛋白质组学分析。研究团队整合了来自 TCGA 和 CCLE 的约 9000 个样本,使用近 500 种抗体构建了涵盖主要癌症信号通路的蛋白质组学数据库。DrBioRight 2.0 通过自然语言指令即可实现跨组学数据的查询、分析与可视化,具备自动代码生成、错误校正、插件式可视化等功能,显著提升了非程序员研究者对复杂蛋白质组学数据的可及性与分析效率。该平台现已上线,网址为 https://drbioright.org。
76.
钟鸣 (2025-04-30 20:54):
#paper doi:10.1128/JCM.00329-21 New Pneumococcal Serotype 15D 作者团队通过全基因组测序监测到两株不同的链球菌,他们的荚膜多糖合成基因簇(cps)呈现出独特的结构,其缺失了wcjE基因,并可能因此呈现出不同的荚膜结构。而血清学实验也表明该菌株也确实与其他已知血清型菌株不同。这项研究指引了高通量测序技术在病原微生物分型中的应用方向和价值,同时也提示在研究细菌血清学分型中应关注荚膜多糖合成基因的微进化机制(如基因丢失、移码突变)对血清型转换的影响。
77.
ZĒNG Yíngzhū (Zoo) 曾莹珠 (2025-04-30 16:49):
#paper DOI: 10.1126/sciadv.adn5290 SCIENCE ADVANCES 2024 Generative AI enhances individual creativity but reduces the collective diversity of novel content Reason for recommendation: I don't want to read fear conditioning anymore and don't know what specific topic I want to study in the future. Then I chose the top journal Science and searched CREATIVITY, and found this one that is latest and not very difficult for me to read. Review: 1, Actually GenAI got popular long time ago but it got common this year, I remember after Spring Festival? I should have read this article earlier. 2, Question1: Five GenAI idea condition 的被试平均只使用了2.55次,只有24.5%的人用了5次。他实验设计的时候就是设置了这一组最多能用5次。我想问为啥不定死这个条件呀?就是规定被试必须用5次,然后再写故事。 3, Question2: for exploratory purposes的这种分析,我看它写在正文和放在补充材料。是不是也可以直接留下用于另写一篇新的呀?假如这篇文章没有这部分,会降低它被Science接收的概率吗……
Abstract:
Creativity is core to being human. Generative artificial intelligence (AI)—including powerful large language models (LLMs)—holds promise for humans to be more creative by offering new ideas, or less creative by … >>>
Creativity is core to being human. Generative artificial intelligence (AI)—including powerful large language models (LLMs)—holds promise for humans to be more creative by offering new ideas, or less creative by anchoring on generative AI ideas. We study the causal impact of generative AI ideas on the production of short stories in an online experiment where some writers obtained story ideas from an LLM. We find that access to generative AI ideas causes stories to be evaluated as more creative, better written, and more enjoyable, especially among less creative writers. However, generative AI–enabled stories are more similar to each other than stories by humans alone. These results point to an increase in individual creativity at the risk of losing collective novelty. This dynamic resembles a social dilemma: With generative AI, writers are individually better off, but collectively a narrower scope of novel content is produced. Our results have implications for researchers, policy-makers, and practitioners interested in bolstering creativity. <<<
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78.
尹志 (2025-04-30 15:56):
#paper doi:10.48550/arXiv.2407.20516, Machine Unlearning in Generative AI: A Survey. 很有意思的方向,应该是翻译机器遗忘吧。随着模型越做越大,如何通过对模型的处理达到可控的添加与擦除特定信息,是未来一个重要的主题,不管是从隐私保护还是模型控制的层面上
arXiv, 2024-07-30T03:26:09Z. DOI: 10.48550/arXiv.2407.20516
Abstract:
Generative AI technologies have been deployed in many places, such as(multimodal) large language models and vision generative models. Theirremarkable performance should be attributed to massive training data andemergent reasoning abilities. … >>>
Generative AI technologies have been deployed in many places, such as(multimodal) large language models and vision generative models. Theirremarkable performance should be attributed to massive training data andemergent reasoning abilities. However, the models would memorize and generatesensitive, biased, or dangerous information originated from the training dataespecially those from web crawl. New machine unlearning (MU) techniques arebeing developed to reduce or eliminate undesirable knowledge and its effectsfrom the models, because those that were designed for traditionalclassification tasks could not be applied for Generative AI. We offer acomprehensive survey on many things about MU in Generative AI, such as a newproblem formulation, evaluation methods, and a structured discussion on theadvantages and limitations of different kinds of MU techniques. It alsopresents several critical challenges and promising directions in MU research. Acurated list of readings can be found:https://github.com/franciscoliu/GenAI-MU-Reading. <<<
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79.
李翛然 (2025-04-30 10:14):
#paper Computational design of serine hydrolases doi:doi/10.1126/science.adu2454 baker今年的大文章,这周我精读了一下。 哈哈 接了一个活,和这个非常类似,不过比这个难。 需要化学+酶进化+新的工业级纯化方法。 非常非常好。 baker我觉得自从或诺奖后,全面开挂,一定要证明AI在设计结构生物学上不可撼动的作用,绝不是,生物或者化学专家说的,我也能干~~~哈哈哈 这篇文章写的非常好,逻辑非常舒服
Science, 2025-4-18. DOI: 10.1126/science.adu2454
Abstract:
The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion … >>>
The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies ( k cat / K m ) up to 2.2 × 10 5 M −1 s −1 and crystal structures that closely match the design models (Cα root mean square deviations <1 angstrom). Selection for structural compatibility across the reaction coordinate enabled identification of new catalysts remove with five different folds distinct from those of natural serine hydrolases. Our de novo approach provides insight into the geometric basis of catalysis and a roadmap for designing enzymes that catalyze multistep transformations. <<<
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80.
颜林林 (2025-04-29 10:22):
#paper doi:10.1101/2025.04.27.25326490, medRxiv, 2025, GWAS of macro-scale resting state functional brain networks identify shared biology with brain structure and autism. 这篇文章对来自UK Biobank的54,030名个体的宏观静息态功能脑网络进行全基因组关联研究(GWAS),首先通过rs-fMRI构建功能脑网络,然后用图论方法总结出涵盖全球、半球和区域水平及其不对称性的多种指标,用这些指标结合SNP位点来做关联分析,找到七个显著的遗传位点和十个候选基因。此后,结合使用已发表的单细胞数据,把细胞类型特异表达与基因突变进行关联,并通过孟德尔随机化证明脑结构与神经表型的关系。然而,在针对12种神经疾病的分析中,仅发现孤独症与找到的图论指标存在显著关联。这篇文章综合了常见的各类方法,除了使用的人群规模较大外,并无特别创新之处,但作为方法运用案例进行学习还是不错的。
Abstract:
The topology of the functional brain network has been associated with several neuropsychiatric conditions. However, little is known about its genetic underpinnings, and whether this overlaps with brain structure and … >>>
The topology of the functional brain network has been associated with several neuropsychiatric conditions. However, little is known about its genetic underpinnings, and whether this overlaps with brain structure and neuropsychiatric conditions. Hence, we conducted genome-wide association study across six graph metrics of the macroscale functional networks at global, hemispheric and regional levels and their hemispheric asymmetry in 54,030 individuals. We identified seven experiment-wide significant loci and prioritised ten candidate genes. Both global graph metrics and hemispheric asymmetry are modestly heritable, but phenotypically and genetically form two clusters. Furthermore, cortical macro- and microstructure are causally related to global graph metrics and asymmetry, respectively, suggesting a dual structural constraint on functional network organisation. Finally, amongst twelve common neuropsychiatric conditions, only autism was genetically correlated with graph metrics of the functional network, supporting phenotypic case-control differences in functional connectivity. Overall, our results suggest different genetic axes shaping different aspects of brain functional topology and demonstrate shared biology with brain structure and autism. <<<
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