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201.
muton (2023-12-31 13:31):
#paper Theta mediated dynamics ofhuman hippocampal-neocortical learning systems in memory formation and retrieval https://doi.org/10.1038/s41467-023-44011-6 本研究探讨了人类海马-皮层学习系统在记忆编码和提取过程中的θ节律动力学。研究结果表明,θ节律在记忆形成和检索过程中起着重要的调节作用,并且海马和新皮质之间存在信息传递的动态变化。这些发现对于理解记忆的神经机制和相关疾病具有重要意义。具体而言,文章关心三个研究问题:1)在记忆编码和检索过程中,海马和新皮质之间的信息传递方向是如何的?2)在不同条件下,海马和新皮质之间的信息传递是否存在差异?3)Theta频率范围内的神经振荡是否在海马-新皮质学习系统中发挥重要作用?作者记录了8个颅内病人数据,通过模式分离任务(让被试判断old,lure,new)中的电生理信号来揭示4-5hz的θ节律分别在编码和提取过程的作用,以及这一节律如何贡献于海马和皮层的信息交互。结果发现,4-5hz的θ节律在模式完成和模式分离中表现不同,海马和新皮质无论在模式完成还是模式分离还是编码提取阶段都表现出双向信息交流。但这几种条件下存在一定的偏向性,如模式分离(即能够区分相似的项目)4 - 5hz介导了新皮层→海马方向偏差,而如果4-5hz可以在编码阶段介导海马→新皮层方向偏差,那么被试在提取阶段可以更好的识别学过的项目。总体来说海马和新皮层的交互在记忆编码提取以及模式分离和模式整合等不同阶段和条件下展现出了非常动态性的过程,4-5hz的θ震荡在其中起到一定的作用。
IF:14.700Q1 Nature communications, 2023-Dec-21. DOI: 10.1038/s41467-023-44011-6 PMID: 38129375
Abstract:
Episodic memory arises as a function of dynamic interactions between the hippocampus and the neocortex, yet the mechanisms have remained elusive. Here, using human intracranial recordings during a mnemonic discrimination … >>>
Episodic memory arises as a function of dynamic interactions between the hippocampus and the neocortex, yet the mechanisms have remained elusive. Here, using human intracranial recordings during a mnemonic discrimination task, we report that 4-5 Hz (theta) power is differentially recruited during discrimination vs. overgeneralization, and its phase supports hippocampal-neocortical when memories are being formed and correctly retrieved. Interactions were largely bidirectional, with small but significant net directional biases; a hippocampus-to-neocortex bias during acquisition of new information that was subsequently correctly discriminated, and a neocortex-to-hippocampus bias during accurate discrimination of new stimuli from similar previously learned stimuli. The 4-5 Hz rhythm may facilitate the initial stages of information acquisition by neocortex during learning and the recall of stored information from cortex during retrieval. Future work should further probe these dynamics across different types of tasks and stimuli and computational models may need to be expanded accordingly to accommodate these findings. <<<
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202.
庞庞 (2023-12-30 20:07):
#paper Brain aging in major depressive disorder: results from the ENIGMA major depressive disorder working group doi: 10.1038/s41380-020-0754-0 研究者使用大样本数据集(ENIGMA)探究了抑郁症患者脑龄相对正常人的差异。具体而言,他们使用正常人的脑结构信息,构建了预测脑龄的模型,并将抑郁症患者作为测试集对他们的脑龄进行了预测。研究发现,抑郁症患者的脑龄相比正常人更高,并且和临床症状无关。
IF:9.600Q1 Molecular psychiatry, 2021-09. DOI: 10.1038/s41380-020-0754-0 PMID: 32424236
Laura K M Han, Richard Dinga, Tim Hahn, Christopher R K Ching, Lisa T Eyler, Lyubomir Aftanas, Moji Aghajani, André Aleman, Bernhard T Baune, Klaus Berger, Ivan Brak, Geraldo Busatto Filho, Angela Carballedo, Colm G Connolly, Baptiste Couvy-Duchesne, Kathryn R Cullen, Udo Dannlowski, Christopher G Davey, Danai Dima, Fabio L S Duran, Verena Enneking, Elena Filimonova, Stefan Frenzel, Thomas Frodl, Cynthia H Y Fu, Beata R Godlewska, Ian H Gotlib, Hans J Grabe, Nynke A Groenewold, Dominik Grotegerd, Oliver Gruber, Geoffrey B Hall, Ben J Harrison, Sean N Hatton, Marco Hermesdorf, Ian B Hickie, Tiffany C Ho, Norbert Hosten, Andreas Jansen, Claas Kähler, Tilo Kircher, Bonnie Klimes-Dougan, Bernd Krämer, Axel Krug, Jim Lagopoulos, Ramona Leenings, Frank P MacMaster, Glenda MacQueen, Andrew McIntosh, Quinn McLellan, Katie L McMahon, Sarah E Medland, Bryon A Mueller, Benson Mwangi, Evgeny Osipov, Maria J Portella, Elena Pozzi, Liesbeth Reneman, Jonathan Repple, Pedro G P Rosa, Matthew D Sacchet, Philipp G Sämann, Knut Schnell, Anouk Schrantee, Egle Simulionyte, Jair C Soares, Jens Sommer, Dan J Stein, Olaf Steinsträter, Lachlan T Strike, Sophia I Thomopoulos, Marie-José van Tol, Ilya M Veer, Robert R J M Vermeiren, Henrik Walter, Nic J A van der Wee, Steven J A van der Werff, Heather Whalley, Nils R Winter, Katharina Wittfeld, Margaret J Wright, Mon-Ju Wu, Henry Völzke, Tony T Yang, Vasileios Zannias, Greig I de Zubicaray, Giovana B Zunta-Soares, Christoph Abé, Martin Alda, Ole A Andreassen, Erlend Bøen, Caterina M Bonnin, Erick J Canales-Rodriguez, Dara Cannon, Xavier Caseras, Tiffany M Chaim-Avancini, Torbjørn Elvsåshagen, Pauline Favre, Sonya F Foley, Janice M Fullerton, Jose M Goikolea, Bartholomeus C M Haarman, Tomas Hajek, Chantal Henry, Josselin Houenou, Fleur M Howells, Martin Ingvar, Rayus Kuplicki, Beny Lafer, Mikael Landén, Rodrigo Machado-Vieira, Ulrik F Malt, Colm McDonald, Philip B Mitchell, Leila Nabulsi, Maria Concepcion Garcia Otaduy, Bronwyn J Overs, Mircea Polosan, Edith Pomarol-Clotet, Joaquim Radua, Maria M Rive, Gloria Roberts, Henricus G Ruhe, Raymond Salvador, Salvador Sarró, Theodore D Satterthwaite, Jonathan Savitz, Aart H Schene, Peter R Schofield, Mauricio H Serpa, Kang Sim, Marcio Gerhardt Soeiro-de-Souza, Ashley N Sutherland, Henk S Temmingh, Garrett M Timmons, Anne Uhlmann, Eduard Vieta, Daniel H Wolf, Marcus V Zanetti, Neda Jahanshad, Paul M Thompson, Dick J Veltman, Brenda W J H Penninx, Andre F Marquand, James H Cole, Lianne Schmaal <<<
Abstract:
Major depressive disorder (MDD) is associated with an increased risk of brain atrophy, aging-related diseases, and mortality. We examined potential advanced brain aging in adult MDD patients, and whether this … >>>
Major depressive disorder (MDD) is associated with an increased risk of brain atrophy, aging-related diseases, and mortality. We examined potential advanced brain aging in adult MDD patients, and whether this process is associated with clinical characteristics in a large multicenter international dataset. We performed a mega-analysis by pooling brain measures derived from T1-weighted MRI scans from 19 samples worldwide. Healthy brain aging was estimated by predicting chronological age (18-75 years) from 7 subcortical volumes, 34 cortical thickness and 34 surface area, lateral ventricles and total intracranial volume measures separately in 952 male and 1236 female controls from the ENIGMA MDD working group. The learned model coefficients were applied to 927 male controls and 986 depressed males, and 1199 female controls and 1689 depressed females to obtain independent unbiased brain-based age predictions. The difference between predicted "brain age" and chronological age was calculated to indicate brain-predicted age difference (brain-PAD). On average, MDD patients showed a higher brain-PAD of +1.08 (SE 0.22) years (Cohen's d = 0.14, 95% CI: 0.08-0.20) compared with controls. However, this difference did not seem to be driven by specific clinical characteristics (recurrent status, remission status, antidepressant medication use, age of onset, or symptom severity). This highly powered collaborative effort showed subtle patterns of age-related structural brain abnormalities in MDD. Substantial within-group variance and overlap between groups were observed. Longitudinal studies of MDD and somatic health outcomes are needed to further assess the clinical value of these brain-PAD estimates. <<<
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203.
哪有情可长 (2023-12-30 19:00):
#paper Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks, Nature Communications, 18 November 2023, https://doi.org/10.1038/s41467-023-43077-6 。利用转录组和全基因组关联分析鉴定控制水稻穗型结构的基因。研究人员利用275份水稻1-2mm幼穗转录组数据,鉴定出表达水平与性状相关的基因,后续又对鉴定到的显著的基因和受小效应位点影响,对等位基因差异选择影响基因的表达和穗部性状,后续利用顺式表达成分和和反式表达成分来构建了水稻穗发育的基因表达调控网络。
IF:14.700Q1 Nature communications, 2023-Nov-18. DOI: 10.1038/s41467-023-43077-6 PMID: 37980346
Abstract:
Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm … >>>
Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits. <<<
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204.
李翛然 (2023-12-30 10:31):
#paper doi:10.4161/bioe.28791 Bioengineered collagens: Emerging directions for biomedical materials 1. 胶原蛋白作为生物医学材料的历史和应用。 2. 动物胶原蛋白的局限性及疾病传播风险。 3. 重组胶原蛋白技术的发展,特别是在大肠杆菌中表达的细菌胶原蛋白的特性和潜在应用。 4. 生物工程方法改善胶原蛋白稳定性和功能的可能性。 5. 不同系统(如酵母、昆虫细胞、植物、微生物)用于胶原蛋白的生产。 6. 细菌胶原蛋白的特性、稳定性、非免疫原性和生产方法。 7. 结合生物工程技术,设计出具有特定功能的胶原蛋白结构。
IF:4.200Q2 Bioengineered, 2014 Jul-Aug. DOI: 10.4161/bioe.28791 PMID: 24717980
Abstract:
Mammalian collagen has been widely used as a biomedical material. Nevertheless, there are still concerns about the variability between preparations, particularly with the possibility that the products may transmit animal-based … >>>
Mammalian collagen has been widely used as a biomedical material. Nevertheless, there are still concerns about the variability between preparations, particularly with the possibility that the products may transmit animal-based diseases. Many groups have examined the possible application of bioengineered mammalian collagens. However, translating laboratory studies into large-scale manufacturing has often proved difficult, although certain yeast and plant systems seem effective. Production of full-length mammalian collagens, with the required secondary modification to give proline hydroxylation, has proved difficult in E. coli. However, recently, a new group of collagens, which have the characteristic triple helical structure of collagen, has been identified in bacteria. These proteins are stable without the need for hydroxyproline and are able to be produced and purified from E. coli in high yield. Initial studies indicate that they would be suitable for biomedical applications. <<<
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205.
徐炳祥 (2023-12-30 09:37):
#paper doi: 10.1186/s13073-020-00810-w Genome Medicine, 2023, DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies。成人中DNA甲基化图谱与肥胖间存在关联这一事实已为人们所知,然而此关联性是否在少儿期存在,二者间是否存在因果关系尚不明确。本文作为一项Meta分析,检查了来自全球23项研究的超过1万名儿童青少年参与者,分析了其血液DNA甲基化图谱和体重指数(BMI)的关系。通过横断面研究识别了在儿童青少年时期与BMI有显著关联的DNA甲基化位点,通过纵向研究探讨了其因果性。结果发现,仅少量血液DNA甲基化位点与BMI显著关联,且有证据显示其可能为高BMI的结果。本研究是一项典型的分子流行病学研究,其结构和方法有很多可取之处。
Abstract:
AbstractBackgroundDNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely … >>>
AbstractBackgroundDNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unknown. More insight into this relationship at younger ages may have implications for future prevention of obesity and its related traits.MethodsWe examined whether DNA methylation in cord blood and whole blood in childhood and adolescence was associated with BMI in the age range from 2 to 18 years using both cross-sectional and longitudinal models. We performed meta-analyses of epigenome-wide association studies including up to 4133 children from 23 studies. We examined the overlap of findings reported in previous studies in children and adults with those in our analyses and calculated enrichment.ResultsDNA methylation at three CpGs (cg05937453, cg25212453, and cg10040131), each in a different age range, was associated with BMI at Bonferroni significance,P < 1.06 × 10−7, with a 0.96 standard deviation score (SDS) (standard error (SE) 0.17), 0.32 SDS (SE 0.06), and 0.32 BMI SDS (SE 0.06) higher BMI per 10% increase in methylation, respectively. DNA methylation at nine additional CpGs in the cross-sectional childhood model was associated with BMI at false discovery rate significance. The strength of the associations of DNA methylation at the 187 CpGs previously identified to be associated with adult BMI, increased with advancing age across childhood and adolescence in our analyses. In addition, correlation coefficients between effect estimates for those CpGs in adults and in children and adolescents also increased. Among the top findings for each age range, we observed increasing enrichment for the CpGs that were previously identified in adults (birthPenrichment = 1; childhoodPenrichment = 2.00 × 10−4; adolescencePenrichment = 2.10 × 10−7).ConclusionsThere were only minimal associations of DNA methylation with childhood and adolescent BMI. With the advancing age of the participants across childhood and adolescence, we observed increasing overlap with altered DNA methylation loci reported in association with adult BMI. These findings may be compatible with the hypothesis that DNA methylation differences are mostly a consequence rather than a cause of obesity. <<<
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206.
惊鸿 (2023-12-30 08:42):
#paper The quantum house of cards 10.1073/pnas.2313269120 Pub Date  : 2023-12-26 量子计算机已被提议解决许多重要问题,例如发现新药、肥料生产的新催化剂、破解加密协议、优化金融投资组合或实施新的人工智能应用。然而,迄今为止,诸如 3 乘以 5 之类的简单任务超出了现有的量子硬件的能力。本文探讨了量子计算机兑现其承诺需要解决的困难。我讨论了构建量子计算机的整个技术堆栈,从顶层(实际算法和相关应用程序)到最底层(量子硬件、其控制电子设备、低温等),而不是忘记了量子纠错的关键中间层。
Abstract:
Quantum computers have been proposed to solve a number of important problems such as discovering new drugs, new catalysts for fertilizer production, breaking encryption protocols, optimizing financial portfolios, or implementing … >>>
Quantum computers have been proposed to solve a number of important problems such as discovering new drugs, new catalysts for fertilizer production, breaking encryption protocols, optimizing financial portfolios, or implementing new artificial intelligence applications. Yet, to date, a simple task such as multiplying 3 by 5 is beyond existing quantum hardware. This article examines the difficulties that would need to be solved for quantum computers to live up to their promises. I discuss the whole stack of technologies that has been envisioned to build a quantum computer from the top layers (the actual algorithms and associated applications) down to the very bottom ones (the quantum hardware, its control electronics, cryogeny, etc.) while not forgetting the crucial intermediate layer of quantum error correction. <<<
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207.
林海onrush (2023-12-30 00:06):
#paper,Using sequences of life-events to predict human lives. Nat Comput Sci (2023). Lives,https://doi.org/10.1038/s43588-023-00573-5,大语言模型可以精准算命了吗?是的!发表于Nature Computational Science的论文提出预测人生走向的模型,用与语言结构相似的方式来表示人类生活,将一系列人类行为事件构建为生命序列。该论文提出了一个名为life2vec的深度学习模型,用于预测人类生活轨迹的各种结果,比如早逝风险和个性特质。该模型基于Transformer架构,可以学习表示人生事件序列的稠密向量表示。研究使用了丹麦全国范围内约600万居民近10年的详细劳动力和医疗数据,构建了生活事件序列。L2V模型的Accuracy达到了78.8%(0.788 [0.782, 0.794])。 该模型包含三个组件:嵌入层、编码器和特定任务的解码器。模型首先通过masked language modeling任务和sequence ordering预测任务进行预训练,学习事件表示和序列结构。之后进行微调,通过早逝预测和个性特质预测等下游任务学习整个生活轨迹的向量表示。结果显示,该模型能够准确预测各种不同领域的结果,在早逝预测任务上明显优于当前最先进的方法。 研究同时分析了模型学习的事件表示空间和个体表示空间,发现它们具有明显的结构,能够体现事件之间的语义关联。该研究也证明了Transformer模型和大规模数据集可用于预测和理解个体生活轨迹,为社会科学和医疗健康领域的新研究打开了新的可能性。需要注意的是,该模型目前只用于研究目的,实际应用中有许多伦理考量需要谨慎对待。那么问题来了,还有什么是大模型所不能的呢。
Abstract:
Here we represent human lives in a way that shares structural similarity to language, and we exploit this similarity to adapt natural language processing techniques to examine the evolution and … >>>
Here we represent human lives in a way that shares structural similarity to language, and we exploit this similarity to adapt natural language processing techniques to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on a comprehensive registry dataset, which is available for Denmark across several years, and that includes information about life-events related to health, education, occupation, income, address and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space, showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to discover potential mechanisms that impact life outcomes as well as the associated possibilities for personalized interventions. <<<
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208.
🐼太真实 (2023-12-28 20:39):
#paper https://doi.org/10.48550/arXiv.2312.03701 , Self-conditioned Image Generation via Generating Representations 这篇文章介绍了一种名为“表示条件图像生成”(RCG)的新型图像生成框架。RCG 不依赖于人类标注,而是基于自监督的表示分布来生成图像。使用预训练的编码器将图像分布映射到表示分布,然后通过表示扩散模型(RDM)从中采样,最后通过像素生成器根据采样的表示生成图像。RCG 在 ImageNet 256×256 数据集上实现了显著的性能提升,其 FID 和 IS 分别达到了 3.31 和 253.4。这个方法不仅显著提升了类无条件图像生成的水平,而且与当前领先的类条件图像生成方法相比也具有竞争力,弥补了这两种任务之间长期存在的性能差距。
Abstract:
This paper presents $\textbf{R}$epresentation-$\textbf{C}$onditioned image$\textbf{G}$eneration (RCG), a simple yet effective image generation frameworkwhich sets a new benchmark in class-unconditional image generation. RCG doesnot condition on any human annotations. Instead, it … >>>
This paper presents $\textbf{R}$epresentation-$\textbf{C}$onditioned image$\textbf{G}$eneration (RCG), a simple yet effective image generation frameworkwhich sets a new benchmark in class-unconditional image generation. RCG doesnot condition on any human annotations. Instead, it conditions on aself-supervised representation distribution which is mapped from the imagedistribution using a pre-trained encoder. During generation, RCG samples fromsuch representation distribution using a representation diffusion model (RDM),and employs a pixel generator to craft image pixels conditioned on the sampledrepresentation. Such a design provides substantial guidance during thegenerative process, resulting in high-quality image generation. Tested onImageNet 256$\times$256, RCG achieves a Frechet Inception Distance (FID) of3.31 and an Inception Score (IS) of 253.4. These results not only significantlyimprove the state-of-the-art of class-unconditional image generation but alsorival the current leading methods in class-conditional image generation,bridging the long-standing performance gap between these two tasks. Code isavailable at https://github.com/LTH14/rcg. <<<
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209.
钟鸣 (2023-12-28 19:27):
#paper doi:10.1002/cyto.a.23690 , Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry 本文是一篇综述,描述了从组织制备单细胞悬液的一般性经验和原则。制备单细胞悬液的本质是消化和降解掉细胞间的连接物,即胶原蛋白、蛋白聚糖和糖蛋白,同时也要注意试剂不能破坏细胞膜的完整性,以保护细胞表面分子的完整性,避免造成表位丢失。 分散酶、胶原酶、透明质酸酶用作将组织解离成小细胞团块,其中分散酶可能会破坏细胞表位。细胞-细胞间存在3种链接:1)闭塞连接、2)通信连接和3)锚定连接,使用胰蛋白酶或木瓜蛋白酶破坏他们。胰蛋白酶会对细胞膜蛋白有非常严重的影响,且会导致游离DNA诱导的细胞聚集,因此要避免使用。一种替代方案是木瓜蛋白酶,但其同样会导致游离 DNA 诱导的细胞聚集。还需要引入DNA酶来降解游离的DNA,通常使用DNase-I而非DNase-II,因为前者不启动细胞凋亡途径。钙离子在这一步是必要的,因其能充当DNA酶的激活剂。 关于酶的使用,确定酶解中所用酶的最佳强度和浓度是经验性的,对于正确分离细胞和成功消化组织至关重要。根据酶的不同,酶解也可以在 4°C或冰上进行,这些较低的温度可能会减慢酶的反应速率并延长潜伏期,但有助于最大限度地减少细胞死亡。 酶解结束后推荐使用流式计数,添加核染色剂可以区分完整细胞和细胞碎片,添加活性染料可以定量死细胞的百分比。如果下游是流式分析且需要保存一段时间,最好使用多聚甲醛固定,特别是对于脆弱/异质群体(例如肺单细胞)。 文章最后还提供了其他有益建议。
Abstract:
Preparing a single cell suspension is a critical step in any solid tissue flow cytometry experiment. Tissue dissection, enzymatic digestion, and mechanical dissociation are three significant steps leading to the … >>>
Preparing a single cell suspension is a critical step in any solid tissue flow cytometry experiment. Tissue dissection, enzymatic digestion, and mechanical dissociation are three significant steps leading to the degradation of the extracellular matrix and the isolation of single cells, allowing the generation of high-quality flow cytometry data. Cells and the extracellular matrix contain various proteins and other structures which must be considered when designing a tissue digestion protocol to preserve the viability of cells and the presence of relevant antigens while digesting matrix components and cleaving cell-cell junctions. Evaluation of the single cell suspension is essential before proceeding with the labeling of the cells as high viability and absence of cell debris and aggregates are critical for flow cytometry. The information presented should be used as a general guide of steps to consider when preparing a single cell suspension from solid tissues for flow cytometry experiments. © 2018 International Society for Advancement of Cytometry. <<<
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210.
Jarvi Coa (2023-12-28 11:25):
#paper doi:10.1021/jacs.2c04325,JACS,2022,DNA Strand-Displacement Temporal Logic Circuits 这篇文章通过时间记忆的策略,结合DNA电路链置换反应,实现逻辑与门,用n个输入可以得到附带时序信息的n!个组合,对比传统电路只能得到n个输出结果的电路,很大程度提高了可拓展性,并在研究过程中发现改进门中杂交链的错配可用于降低电路设计的复杂性,缩短特定的立足点可用于提高电路行为的鲁棒性。为以后在更复杂的DNA计算提供了可能,该作者也正在研发此此类电路与神经网路和机器学习结合的新方法。
Abstract:
Molecular circuits capable of processing temporal information are essential for complex decision making in response to both the presence and history of a molecular environment. A particular type of temporal … >>>
Molecular circuits capable of processing temporal information are essential for complex decision making in response to both the presence and history of a molecular environment. A particular type of temporal information that has been recognized to be important is the relative timing of signals. Here we demonstrate the strategy of temporal memory combined with logic computation in DNA strand-displacement circuits capable of making decisions based on specific combinations of inputs as well as their relative timing. The circuit encodes the timing information on inputs in a set of memory strands, which allows for the construction of logic gates that act on current and historical signals. We show that mismatches can be employed to reduce the complexity of circuit design and that shortening specific toeholds can be useful for improving the robustness of circuit behavior. We also show that a detailed model can provide critical insights for guiding certain aspects of experimental investigations that an abstract model cannot. We envision that the design principles explored in this study can be generalized to more complex temporal logic circuits and incorporated into other types of circuit architectures, including DNA-based neural networks, enabling the implementation of timing-dependent learning rules and opening up new opportunities for embedding intelligent behaviors into artificial molecular machines. <<<
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211.
前进 (2023-12-27 15:11):
#paper arXiv:2312.11514v1 ,2023, LLM in a flash: Efficient Large Language Model Inference with Limited Memory 大型语言模型(LLMs)在现代自然语言处理中具有重要作用,但其高昂的计算和内存需求对于内存有限的设备构成了挑战。为了高效运行超过可用DRAM容量的LLMs,该论文采用了存储模型参数在闪存上,并按需将其调入DRAM的方法。研究方法包括构建与闪存行为协调的推理模型,并在两个关键领域进行优化:减少闪存传输的数据量和以更大、更连续的块来读取数据。在这个框架下,引入了两种主要技术:“windowing”策略通过重复使用先前激活的神经元减少数据传输,“row-column bunding”则充分利用了闪存的顺序数据访问特性,增加了从闪存中读取的数据块的大小。这些方法使得可以在有限DRAM上运行比原先两倍大的模型,相较于朴素的加载方法,在CPU和GPU上推断速度分别提高了4-5倍和20-25倍。
Abstract:
Large language models (LLMs) are central to modern natural languageprocessing, delivering exceptional performance in various tasks. However, theirintensive computational and memory requirements present challenges, especiallyfor devices with limited DRAM capacity. … >>>
Large language models (LLMs) are central to modern natural languageprocessing, delivering exceptional performance in various tasks. However, theirintensive computational and memory requirements present challenges, especiallyfor devices with limited DRAM capacity. This paper tackles the challenge ofefficiently running LLMs that exceed the available DRAM capacity by storing themodel parameters on flash memory but bringing them on demand to DRAM. Ourmethod involves constructing an inference cost model that harmonizes with theflash memory behavior, guiding us to optimize in two critical areas: reducingthe volume of data transferred from flash and reading data in larger, morecontiguous chunks. Within this flash memory-informed framework, we introducetwo principal techniques. First, "windowing'" strategically reduces datatransfer by reusing previously activated neurons, and second, "row-columnbundling", tailored to the sequential data access strengths of flash memory,increases the size of data chunks read from flash memory. These methodscollectively enable running models up to twice the size of the available DRAM,with a 4-5x and 20-25x increase in inference speed compared to naive loadingapproaches in CPU and GPU, respectively. Our integration of sparsity awareness,context-adaptive loading, and a hardware-oriented design paves the way foreffective inference of LLMs on devices with limited memory. <<<
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212.
颜林林 (2023-12-27 12:42):
#paper doi:10.1101/2023.10.04.560604. bioRxiv, 2023, Federated Learning for multi-omics: a performance evaluation in Parkinson's disease. 这篇文章基于两个帕金森病研究的数据集(PPMI和PDBP),这两个数据集都入组了数百例患者和对照健康人,分别都进行了WGS和RNA-seq,获得了多组学检测的分析特征结果。通过将PPMI拆分为K折,留出一折后所剩余K-1折用于模型训练,再将模型放到PPMI预先留出的一折数据和PBMP上进行测试和性能评估。建模分别使用了集中化的机器学习方法,以及将数据拆分到多个节点(site)以采取联邦学习法,并使用了不同的联邦学习策略。结果显示,虽然样本在不同site的分散程度、联邦学习的策略等都会对最终性能有所影响,但联邦学习的最优结果,能与集中化训练的性能相当。此外,本文对联邦学习的训练时间进行评估,比集中化的方法至少高出一个数量级。虽然如此,由于联邦学习可以避免大规模数据在不同sites之间分享和传输,对于整合更广泛的数据,提升模型性能,还是有优势的。提供了对联邦学习在多组学和特别是在帕金森病预测中的应用的深入分析,展示了其作为一种协作工具在处理大规模异构数据时的潜力和挑战。
Abstract:
While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML … >>>
While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated Learning (FL) represents an opportunity to enable collaborative curation of such datasets among participating institutions. We compare the simulated performance of several models trained using FL against classically trained ML models on the task of multi-omics Parkinson's Disease prediction. We find that FL model performance tracks centrally trained ML models, where the most performant FL model achieves an AUC-PR of 0.876 ± 0.009, 0.014 ± 0.003 less than its centrally trained variation. We also determine that the dispersion of samples within a federation plays a meaningful role in model performance. Our study implements several open source FL frameworks and aims to highlight some of the challenges and opportunities when applying these collaborative methods in multi-omics studies. <<<
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213.
DeDe宝 (2023-12-13 23:02):
#paper,https://doi.org/10.7554/eLife.55389,A Bayesian and efficient observer model explains concurrent attractive and repulsive history biases in visual perception,人类的视觉感知受到历史经验的影响,同时产生排斥性偏差和吸引性偏差,且二者具有不同的时间尺度:吸引性偏差的衰减速度快,只由上一个试次刺激影响产生,排斥性偏差衰减速度慢,可以持续受到过去数分钟的刺激的影响,暗示吸引性和排斥性偏差的机制是分离的。但是,目前仍不清楚吸引性的偏差和排斥性的偏差在知觉决策过程中是否相互作用以及如何相互作用。这篇研究结合了快速编码框架和贝叶斯解码模型,同时捕获了吸引性偏差和排斥性偏差的关键特征。
IF:6.400Q1 eLife, 2020-06-01. DOI: 10.7554/eLife.55389 PMID: 32479264
Abstract:
Human perceptual decisions can be repelled away from (repulsive adaptation) or attracted towards recent visual experience (attractive serial dependence). It is currently unclear whether and how these repulsive and attractive … >>>
Human perceptual decisions can be repelled away from (repulsive adaptation) or attracted towards recent visual experience (attractive serial dependence). It is currently unclear whether and how these repulsive and attractive biases interact during visual processing and what computational principles underlie these history dependencies. Here we disentangle repulsive and attractive biases by exploring their respective timescales. We find that perceptual decisions are concurrently attracted towards the short-term perceptual history and repelled from stimuli experienced up to minutes into the past. The temporal pattern of short-term attraction and long-term repulsion cannot be captured by an ideal Bayesian observer model alone. Instead, it is well captured by an ideal observer model with efficient encoding and Bayesian decoding of visual information in a slowly changing environment. Concurrent attractive and repulsive history biases in perceptual decisions may thus be the consequence of the need for visual processing to simultaneously satisfy constraints of efficiency and stability. <<<
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214.
林海onrush (2023-12-01 00:00):
#paper, https://doi.org/10.1038/s41562-019-0804-2,Quantum reinforcement learning during human decision-making,这篇nature子刊很有意思,探讨了量子强化学习(QRL)在人类决策中的应用。QRL在人类决策中的新颖应用:该研究是首次将QRL应用于人类决策的实证研究。QRL在计算机模拟中表现出色,但此研究首次在人类决策环境中对其进行了特殊测试。研究利用了参与者在执行爱荷华赌博任务时的行为数据和功能性磁共振成像(fMRI)数据,将2个QRL模型与12个已建立的CRL模型进行了对比。研究者开发了两种新的QRL模型:量子叠加状态学习(QSL)和量子叠加状态加持续性(QSPP)。这些模型的表现在某些方面优于最好的CRL模型。这一发现在包括健康个体和吸烟者在内的不同受试者群体中得到了确认,表明这些模型的稳健性和普遍适用性。量子类过程的神经表征:该研究的一个重要创新是确定了表示量子类过程的神经基质。例如,QSPP模型显示了在大脑中如何表征量子距离和转换幅度——QRL的关键概念。这一发现弥合了认知量子模型和神经科学之间的差距,为决策中的量子类过程提供了神经生物学基础。对于决策中的不确定性理解,论文还探讨了决策中不确定性的角色。通过将QSPP模型与CRL模型(VPPDecayTIC)进行比较,突出了大脑如何不同地处理由不稳定的外部环境影响的内部状态不确定性。这一研究方面强调了QRL模型在提供对决策认知过程更细微洞察方面的潜力。​​
IF:21.400Q1 Nature human behaviour, 2020-03. DOI: 10.1038/s41562-019-0804-2 PMID: 31959921
Abstract:
Classical reinforcement learning (CRL) has been widely applied in neuroscience and psychology; however, quantum reinforcement learning (QRL), which shows superior performance in computer simulations, has never been empirically tested on … >>>
Classical reinforcement learning (CRL) has been widely applied in neuroscience and psychology; however, quantum reinforcement learning (QRL), which shows superior performance in computer simulations, has never been empirically tested on human decision-making. Moreover, all current successful quantum models for human cognition lack connections to neuroscience. Here we studied whether QRL can properly explain value-based decision-making. We compared 2 QRL and 12 CRL models by using behavioural and functional magnetic resonance imaging data from healthy and cigarette-smoking subjects performing the Iowa Gambling Task. In all groups, the QRL models performed well when compared with the best CRL models and further revealed the representation of quantum-like internal-state-related variables in the medial frontal gyrus in both healthy subjects and smokers, suggesting that value-based decision-making can be illustrated by QRL at both the behavioural and neural levels. <<<
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215.
小W (2023-11-30 23:40):
#paper doi:doi.org/10.1038/s41551-023-01114-1 Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand 本文介绍了利用CRISPR相关蛋白(Cas)-Cas12a 检测活细胞表面受体分子力事件的方法,其技术路径:激活剂是固定在表面(如玻璃载玻片)上的ssDNA,激活剂通过与互补链杂交而被隐藏,互补链又与配体肽结合;当细胞被植入该表面时,表面受体和配体结合,并施加力,超过双链的机械耐受性的力会导致其断裂,暴露激活剂;激活Cas12a会高效地催化切割荧光性ssDNA报告基因。在作为测试的血小板力检测中,其具有以下优势1.活细胞2.只需要~5 μl或更少的血液来进行每次测量,降低了高通量筛选的难度3.检测结果与出血风险更高的相关4.更短的时间(30min),更易识别的信号,可能更低的成本。对 CRISPR 检测不太了解,欢迎斧正。
Abstract:
Molecular forces generated by cell receptors are infrequent and transient, and hence difficult to detect. Here we report an assay that leverages the CRISPR-associated protein 12a (Cas12a) to amplify the … >>>
Molecular forces generated by cell receptors are infrequent and transient, and hence difficult to detect. Here we report an assay that leverages the CRISPR-associated protein 12a (Cas12a) to amplify the detection of cellular traction forces generated by as few as 50 adherent cells. The assay involves the immobilization of a DNA duplex modified with a ligand specific for a cell receptor. Traction forces of tens of piconewtons trigger the dehybridization of the duplex, exposing a cryptic Cas12-activating strand that sets off the indiscriminate Cas12-mediated cleavage of a fluorogenic reporter strand. We used the assay to perform hundreds of force measurements using human platelets from a single blood draw to extract individualized dose-response curves and half-maximal inhibitory concentrations for a panel of antiplatelet drugs. For seven patients who had undergone cardiopulmonary bypass, platelet dysfunction strongly correlated with the need for platelet transfusion to limit bleeding. The Cas12a-mediated detection of cellular traction forces may be used to assess cell state, and to screen for genes, cell-adhesion ligands, drugs or metabolites that modulate cell mechanics. <<<
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216.
钟鸣 (2023-11-30 23:39):
#paper doi: 10.1002/ctm2.1354 IMPACT: A web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers 这是一篇临床转化医学的数据库的文章,作者来自燃石、中国国家肿瘤中心等单位。数据库纳入了23000+样品、覆盖37种肿瘤,数据来源包括公共数据库、文献来源的数据集以及作者自己收集的一系列数据。数据库的主旨是挖掘和分析影响肿瘤预后的生物标志物。数据库功能还是比较多的,与既有的数据库相比更加灵活和细化,操作比较简便和直观,界面简洁一目了然,使用者可快速执行感兴趣的操作,提高分析效率。
217.
Ricardo (2023-11-30 23:19):
#paper 10.1109/TMI.2022.3174827 PTNet3D: A 3D High-Resolution Longitudinal Infant Brain MRI Synthesizer Based on Transformers 最近看了一些基于GAN的医学图像生成的文章(当然现在的热点都转向diffusion model了),感觉都很没有创意,有点无聊,并且都存在一些共性问题。第一,纵向婴幼儿图像生成算法仅仅是通过在每个年龄段训练模型来构建,完全可以把年龄作为条件直接生成;第二,为了缓解数据维度高且数据量小的问题,大多数这类生成算法都基于slice或者patch的生成方式,不可避免的会导致生成图像的不连续性,而且基本上所有文章都没解决这个问题。在我的新工作(不是单纯的图像生成任务)里,这些问题都得到了重视并予以解决,估计年后会release预印本出来,敬请期待。
Abstract:
An increased interest in longitudinal neurodevelopment during the first few years after birth has emerged in recent years. Noninvasive magnetic resonance imaging (MRI) can provide crucial information about the development … >>>
An increased interest in longitudinal neurodevelopment during the first few years after birth has emerged in recent years. Noninvasive magnetic resonance imaging (MRI) can provide crucial information about the development of brain structures in the early months of life. Despite the success of MRI collections and analysis for adults, it remains a challenge for researchers to collect high-quality multimodal MRIs from developing infant brains because of their irregular sleep pattern, limited attention, inability to follow instructions to stay still during scanning. In addition, there are limited analytic approaches available. These challenges often lead to a significant reduction of usable MRI scans and pose a problem for modeling neurodevelopmental trajectories. Researchers have explored solving this problem by synthesizing realistic MRIs to replace corrupted ones. Among synthesis methods, the convolutional neural network-based (CNN-based) generative adversarial networks (GANs) have demonstrated promising performance. In this study, we introduced a novel 3D MRI synthesis framework- pyramid transformer network (PTNet3D)- which relies on attention mechanisms through transformer and performer layers. We conducted extensive experiments on high-resolution Developing Human Connectome Project (dHCP) and longitudinal Baby Connectome Project (BCP) datasets. Compared with CNN-based GANs, PTNet3D consistently shows superior synthesis accuracy and superior generalization on two independent, large-scale infant brain MRI datasets. Notably, we demonstrate that PTNet3D synthesized more realistic scans than CNN-based models when the input is from multi-age subjects. Potential applications of PTNet3D include synthesizing corrupted or missing images. By replacing corrupted scans with synthesized ones, we observed significant improvement in infant whole brain segmentation. <<<
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218.
符毓 Yu (2023-11-30 23:11):
#paper doi.org/10.48550/arXiv.2311.05332, 2023, On the Road with GPT-4V(ision): Early Explorations of Visual-Language Model on Autonomous Driving. 文远知行的团队近期的论文,把GPT应用在自动驾驶领域。测试结果显示GPT在图像识别,点云识别,天气识别,V2X图像,模拟图像识别,多角度图片识别都有较高准确率;在交通灯识别,左右空间区分上容易出错
Abstract:
The pursuit of autonomous driving technology hinges on the sophisticatedintegration of perception, decision-making, and control systems. Traditionalapproaches, both data-driven and rule-based, have been hindered by theirinability to grasp the nuance … >>>
The pursuit of autonomous driving technology hinges on the sophisticatedintegration of perception, decision-making, and control systems. Traditionalapproaches, both data-driven and rule-based, have been hindered by theirinability to grasp the nuance of complex driving environments and theintentions of other road users. This has been a significant bottleneck,particularly in the development of common sense reasoning and nuanced sceneunderstanding necessary for safe and reliable autonomous driving. The advent ofVisual Language Models (VLM) represents a novel frontier in realizing fullyautonomous vehicle driving. This report provides an exhaustive evaluation ofthe latest state-of-the-art VLM, GPT-4V(ision), and its application inautonomous driving scenarios. We explore the model's abilities to understandand reason about driving scenes, make decisions, and ultimately act in thecapacity of a driver. Our comprehensive tests span from basic scene recognitionto complex causal reasoning and real-time decision-making under varyingconditions. Our findings reveal that GPT-4V demonstrates superior performancein scene understanding and causal reasoning compared to existing autonomoussystems. It showcases the potential to handle out-of-distribution scenarios,recognize intentions, and make informed decisions in real driving contexts.However, challenges remain, particularly in direction discernment, trafficlight recognition, vision grounding, and spatial reasoning tasks. Theselimitations underscore the need for further research and development. Projectis now available on GitHub for interested parties to access and utilize:\url{https://github.com/PJLab-ADG/GPT4V-AD-Exploration} <<<
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219.
muton (2023-11-30 23:05):
#paper: Schonhaut, D. R., Aghajan, Z. M., Kahana, M. J., & Fried, I. (2023). A neural code for time and space in the human brain. Cell Reports, 42(11). https://doi.org/10.1016/j.celrep.2023.113238 时间和空间对人类的记忆来说是非常重要的两个维度,不仅可以帮助构建我们的经验,也可以帮助我们预测未来。以往有部分研究发现了时间和空间的神经关联,比如时间细胞和位置细胞的发现等。但是这两个维度是如何在个体记忆中被整合的仍未可知。作者基于这一问题记录了在定时性空间导航虚拟游戏中10个病人的单细胞放电情况,任务分为延迟等待阶段,寻金时间(编码阶段),下一个延迟等待阶段和挖金阶段(提取阶段)。结果发现,内侧颞叶和前额叶皮层神经元在无任务延迟期间编码时间信息,在空间探索过程中,时间和位置是独立表征的,时间细胞会在相似的事件下重新编码(remap)但是位置细胞仍会以稳定的模式放电,群体神经活动代表序列中多个事件的时间信息。本文的亮点在于首次在人类中同时研究了时间和空间信息在记忆形成中的放电特征。
IF:7.500Q1 Cell reports, 2023-11-28. DOI: 10.1016/j.celrep.2023.113238 PMID: 37906595
Abstract:
Time and space are primary dimensions of human experience. Separate lines of investigation have identified neural correlates of time and space, yet little is known about how these representations converge … >>>
Time and space are primary dimensions of human experience. Separate lines of investigation have identified neural correlates of time and space, yet little is known about how these representations converge during self-guided experience. Here, 10 subjects with intracranially implanted microelectrodes play a timed, virtual navigation game featuring object search and retrieval tasks separated by fixed delays. Time cells and place cells activate in parallel during timed navigation intervals, whereas a separate time cell sequence spans inter-task delays. The prevalence, firing rates, and behavioral coding strengths of time cells and place cells are indistinguishable-yet time cells selectively remap between search and retrieval tasks, while place cell responses remain stable. Thus, the brain can represent time and space as overlapping but dissociable dimensions. Time cells and place cells may constitute a biological basis for the cognitive map of spatiotemporal context onto which memories are written. <<<
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220.
白鸟 (2023-11-30 22:58):
#paper https://doi.org/10.1111/imm.13441 Velikkakam, T, Gollob, KJ, and Dutra, WO. Double-negative T cells: setting the stage for disease control or progression. Immunology. (2022) 165:371–85. 这篇文献是关于双阴性T细胞DNT的综述文章。DNT是一群独特的T细胞,缺乏CD4和CD8辅助受体,但表达αβ TCR或γδ TCR,在人外周血中占比较低。DNT细胞能有效产生细胞因子,是免疫反应的关键协调者。1.DNT从哪里来?DNT 的确切来源仍有很多盲点,有研究表明DNT细胞可以源自胸腺和外周环境。外周血中DNT细胞可以通过可能逃避胸腺中的负选择以及随后在外周中的激活和扩增。另外,体外也可诱导产生DNT细胞。2.DNT亚群:存在高度异质性,未有正式定义,来源不同研究课题,如初始nDNT和激活态aDNT。3.DNT与疾病:它是多种人类疾病的发病机制的主角,特别是自身免疫疾病、炎症性疾病和移植。其调节功能损害了必要的炎症效应机制,或者介导细胞死亡和组织破坏。多数文献DNT研究源自小鼠模型,许多是转基因的。人类DNT会有所区别,还是需要系统的梳理DNT细胞的功能和在疾病中的作用。
IF:4.900Q2 Immunology, 2022-04. DOI: 10.1111/imm.13441 PMID: 34939192
Abstract:
Double-negative (DN) T cells are present at relatively low frequencies in human peripheral blood, and are characterized as expressing the alpha-beta or gamma-delta T-cell receptor (TCR), but not the CD4 … >>>
Double-negative (DN) T cells are present at relatively low frequencies in human peripheral blood, and are characterized as expressing the alpha-beta or gamma-delta T-cell receptor (TCR), but not the CD4 nor the CD8 co-receptors. Despite their low frequencies, these cells are potent producers of cytokines and, thus, are key orchestrators of immune responses. DN T cells were initially associated with induction of peripheral immunological tolerance and immunomodulatory activities related to disease prevention. However, other studies demonstrated that these cells can also display effector functions associated with pathology development. This apparent contradiction highlighted the heterogeneity of the DN T-cell population. Here, we review phenotypic and functional characteristics of DN T cells, emphasizing their role in human diseases. The need for developing biomarkers to facilitate the translation of studies from animal models to humans will also be discussed. Finally, we will examine DN T cells as promising therapeutic targets to prevent or inhibit human disease development. <<<
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