当前共找到 1294 篇文献分享,本页显示第 1201 - 1220 篇。
1201.
Ricardo
(2022-04-30 20:52):
#paper https://doi.org/10.1016/j.media.2021.102292 Deformable MR-CT image registration using an unsupervised, dual-channel network for neurosurgical guidance. MIA(2022) 微创颅内神经外科手术的精度可能会受到变形的脑组织结构的影响,例如,在神经内窥镜路径中,由于脑脊液的流出导致脑组织变形达10毫米。这篇文章提出了一种基于深度学习的无监督配准方法,用于术前MR和术中CT之间的配准。MR和CT之间的配准属于跨模态配准问题,由于难以衡量不同模态图像之间的相似性, 跨模态配准问题一直以来都比较难做。这篇文章的主要思路就是利用cyclegan将不同模态的图像转换成同模态图像,从而进行模态内的配准。另一方面,与其使用determistic cyclegan, 作者使用了probabilitic cyclegan,这样就可以输出模型对于预测的形变场的不准确度的估计,这种不准确度的估计可以进一步拿来作为形变场的约束。
IF:10.700Q1
Medical image analysis,
2022-01.
DOI: 10.1016/j.media.2021.102292
PMID: 34784539
PMCID:PMC10229200
Abstract:
PURPOSE: The accuracy of minimally invasive, intracranial neurosurgery can be challenged by deformation of brain tissue - e.g., up to 10 mm due to egress of cerebrospinal fluid during neuroendoscopic …
>>>
PURPOSE: The accuracy of minimally invasive, intracranial neurosurgery can be challenged by deformation of brain tissue - e.g., up to 10 mm due to egress of cerebrospinal fluid during neuroendoscopic approach. We report an unsupervised, deep learning-based registration framework to resolve such deformations between preoperative MR and intraoperative CT with fast runtime for neurosurgical guidance.METHOD: The framework incorporates subnetworks for MR and CT image synthesis with a dual-channel registration subnetwork (with synthesis uncertainty providing spatially varying weights on the dual-channel loss) to estimate a diffeomorphic deformation field from both the MR and CT channels. An end-to-end training is proposed that jointly optimizes both the synthesis and registration subnetworks. The proposed framework was investigated using three datasets: (1) paired MR/CT with simulated deformations; (2) paired MR/CT with real deformations; and (3) a neurosurgery dataset with real deformation. Two state-of-the-art methods (Symmetric Normalization and VoxelMorph) were implemented as a basis of comparison, and variations in the proposed dual-channel network were investigated, including single-channel registration, fusion without uncertainty weighting, and conventional sequential training of the synthesis and registration subnetworks.RESULTS: The proposed method achieved: (1) Dice coefficient = 0.82±0.07 and TRE = 1.2 ± 0.6 mm on paired MR/CT with simulated deformations; (2) Dice coefficient = 0.83 ± 0.07 and TRE = 1.4 ± 0.7 mm on paired MR/CT with real deformations; and (3) Dice = 0.79 ± 0.13 and TRE = 1.6 ± 1.0 mm on the neurosurgery dataset with real deformations. The dual-channel registration with uncertainty weighting demonstrated superior performance (e.g., TRE = 1.2 ± 0.6 mm) compared to single-channel registration (TRE = 1.6 ± 1.0 mm, p < 0.05 for CT channel and TRE = 1.3 ± 0.7 mm for MR channel) and dual-channel registration without uncertainty weighting (TRE = 1.4 ± 0.8 mm, p < 0.05). End-to-end training of the synthesis and registration subnetworks also improved performance compared to the conventional sequential training strategy (TRE = 1.3 ± 0.6 mm). Registration runtime with the proposed network was ∼3 s.CONCLUSION: The deformable registration framework based on dual-channel MR/CT registration with spatially varying weights and end-to-end training achieved geometric accuracy and runtime that was superior to state-of-the-art baseline methods and various ablations of the proposed network. The accuracy and runtime of the method may be compatible with the requirements of high-precision neurosurgery.
<<<
翻译
1202.
Ricardo
(2022-04-30 20:39):
#paper https://doi.org/10.48550/arXiv.1806.09055 DARTS: differentiable architecture search ICLR(2019) Neural Architectural Search (NAS) 这个问题是出了名的消耗算力,动不动就需要消耗上千个gpu hour,基本也只能在顶级的研究机构做这类研究。这篇文章没有使用类似于进化算法或者强化学习这样的方法在离散和不可微的空间中搜索网络架构, 而是通过对神经网络的架构表征进行松弛,将NAS问题转化为一个可微分的形式,从而能够使用梯度下降法在连续空间中搜索神经网络架构。作者将这个问题建模成一个bilevel的优化问题,然后提出了一个类似于EM算法的优化方法,通过交替优化模型架构参数\alpha和模型权重w来找到较优的模型架构\alpha 。由于优化过程中涉及二阶导的计算,作者进一步对二阶导的计算做了松弛,将其转化为形式为一阶导的估计,从而进一步降低了方法的复杂度。结果也都很漂亮,相比于之前那些动辄需要上千个gpu day的计算量,darts方法只需要几个gpu day的计算,而且也能达到差不多的效果。
arXiv,
2019.
DOI: 10.48550/arXiv.1806.09055
Abstract:
This paper addresses the scalability challenge of architecture search by formulating the task in a differentiable manner. Unlike conventional approaches of applying evolution or reinforcement learning over a discrete and …
>>>
This paper addresses the scalability challenge of architecture search by formulating the task in a differentiable manner. Unlike conventional approaches of applying evolution or reinforcement learning over a discrete and non-differentiable search space, our method is based on the continuous relaxation of the architecture representation, allowing efficient search of the architecture using gradient descent. Extensive experiments on CIFAR-10, ImageNet, Penn Treebank and WikiText-2 show that our algorithm excels in discovering high-performance convolutional architectures for image classification and recurrent architectures for language modeling, while being orders of magnitude faster than state-of-the-art non-differentiable techniques. Our implementation has been made publicly available to facilitate further research on efficient architecture search algorithms.
<<<
翻译
1203.
张贝
(2022-04-30 20:39):
#paper DOI: 10.1038/s41580-021-00407-0 Nat Rev Mol Cell Biol.,2021,A guide to machine learning for biologists. 近几十年来,随着生物数据集规模与复杂性的大幅增长,机器学习越来越多的用于为潜在生物过程构建信息与预测模型。然而具体的机器学习方法多种多样,令人眼花缭乱。对于不同类型的生物数据,该如何选择特定的机器学习技术?本文是一篇2021年发表在Nature Reviews Molecular Cell Biology 上的综述文章,向读者简要介绍了一些关键的机器学习技术:既包括分类、回归、聚类模型等传统机器学习方法,也包括最近开发和广泛使用的涉及深度神经网络的技术。本文描述了不同的技术如何适用于特定类型的生物学数据,并指出着手进行涉及机器学习的实验时需要考虑的要点。最后,本文还讨论了一些机器学习研究的新方向。
Abstract:
The expanding scale and inherent complexity of biological data have encouraged a growing use of machine learning in biology to build informative and predictive models of the underlying biological processes. …
>>>
The expanding scale and inherent complexity of biological data have encouraged a growing use of machine learning in biology to build informative and predictive models of the underlying biological processes. All machine learning techniques fit models to data; however, the specific methods are quite varied and can at first glance seem bewildering. In this Review, we aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to specific types of biological data, and also discuss some best practices and points to consider when one is embarking on experiments involving machine learning. Some emerging directions in machine learning methodology are also discussed.
<<<
翻译
1204.
颜林林
(2022-04-30 18:41):
#paper doi:10.1016/j.ccell.2022.04.002 Cancer Cell, 2022, The translational challenges of precision oncology. 这是一篇新近发表在Cancer Cell上的关于精准肿瘤学(precision oncology)的综述。所谓精准肿瘤学,是指基于肿瘤分子特征进行肿瘤诊治决策。这篇综述回顾了与肿瘤分子特征相关的研究历史和当前研究进展,从肿瘤发生、肿瘤预防、早期检测、新辅助治疗、微小病变残留监测、药物耐受、肿瘤演化过程、肿瘤转移等诊治不同阶段环节,讨论了相应重要分子特征的发现及应用。本文对于目前在肿瘤基因检测行业中涉及到的各类应用,包括涉及的临床队列研究和相关资源,都有提及,整体上内容全面、逻辑脉络清晰。比较适合初学者,快速了解这个方向的产业应用和临床应用,并强烈建议可追溯其参考文献,对各个具体应用场景,进行深入探索和学习。
Abstract:
The translational challenges in the field of precision oncology are in part related to the biological complexity and diversity of this disease. Technological advances in genomics have facilitated large sequencing …
>>>
The translational challenges in the field of precision oncology are in part related to the biological complexity and diversity of this disease. Technological advances in genomics have facilitated large sequencing efforts and discoveries that have further supported this notion. In this review, we reflect on the impact of these discoveries on our understanding of several concepts: cancer initiation, cancer prevention, early detection, adjuvant therapy and minimal residual disease monitoring, cancer drug resistance, and cancer evolution in metastasis. We discuss key areas of focus for improving cancer outcomes, from biological insights to clinical application, and suggest where the development of these technologies will lead us. Finally, we discuss practical challenges to the wider adoption of molecular profiling in the clinic and the need for robust translational infrastructure.
<<<
翻译
1205.
June
(2022-04-30 14:29):
#paper https://doi.org/10.1038/s41392-022-00936-w该研究通过将 RT 与核酸酶野生型 Cas9 (WT-PE) 融合来进行大规模基因组操作,设计了一种新的先导编辑系统。与传统的先导编辑器(PE2)不同,这种新系统同时在目标位点引入了一个 DSB 和一个 3' 延伸的瓣,然后通过内源机制将它们整合到基因组中。当它与配对的 pegRNA 结合时,WT-PE 实现了高效的大规模基因组编辑,包括大片段缺失和染色体易位。因此, WT-PE 系统可能有助于建模或治疗与大片段畸变相关的疾病。
IF:40.800Q1
Signal transduction and targeted therapy,
2022-04-20.
DOI: 10.1038/s41392-022-00936-w
PMID: 35440051
PMCID:PMC9018734
Abstract:
Large scale genomic aberrations including duplication, deletion, translocation, and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer. …
>>>
Large scale genomic aberrations including duplication, deletion, translocation, and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer. The current prime editor, PE2, consisting of Cas9-nickase and reverse transcriptase enables efficient editing of genomic deletion and insertion, however, at small scale. Here, we designed a novel prime editor by fusing reverse transcriptase (RT) to nuclease wild-type Cas9 (WT-PE) to edit large genomic fragment. WT-PE system simultaneously introduced a double strand break (DSB) and a single 3' extended flap in the target site. Coupled with paired prime editing guide RNAs (pegRNAs) that have complementary sequences in their 3' terminus while target different genomic regions, WT-PE produced bi-directional prime editing, which enabled efficient and versatile large-scale genome editing, including large fragment deletion up to 16.8 megabase (Mb) pairs and chromosomal translocation. Therefore, our WT-PE system has great potential to model or treat diseases related to large-fragment aberrations.
<<<
翻译
1206.
大象城南
(2022-04-30 14:19):
#paper https://doi.org/10.1002/hbm.25739 推测为血管源性的脑白质高信号(WMH)常在健康老年人群的MRI上有发现。WMH还与衰老和认知能力下降有关。本文使用包含认知健康老年人MRI数据的纵向数据集(基线N=231人,年龄范围在64~87岁之间),比较并验证了FreeSurfer (T1w)、UBO Detector (T1W + FLAIR)和FSL-BIANCA(T1w+FLAIR)三种脑白质高信号提取的算法的有效性。作为参考,我们在T1w、3D (3D) FLAIR和二维(2D) FLAIR图像中手动分割WMH,并用于评估不同自动化算法的分割精度。此外,我们评估了算法提供的WMH体积与Fazekas评分和年龄的关系。FreeSurfer低估了WMH的体积,其骰子相似系数最差(DSC = 0.434),但其WMH的体积与Fazekas得分有很强的相关性(rs = 0.73)。BIANCA在3D FLAIR图像中实现了最高DSC(0.602)。然而,在2D FLAIR图像中(rs = 0.41),与Fazekas得分的关系仅为中等,在探索人体内轨迹时检测到许多异常值WMH体积(2D FLAIR: ~30%)。UBO Detector在DSC中与BIANCA在两种模式下的表现相似,在2D FLAIR(0.531)中达到了最佳DSC,无需定制训练数据集。此外,它与Fazekas评分有很高的相关性(2D FLAIR: rs = 0.80)。总之,我们的结果强调了仔细考虑选择的WMH分割算法和mr模态的重要性。
Abstract:
White matter hyperintensities (WMH) of presumed vascular origin are frequently found in MRIs of healthy older adults. WMH are also associated with aging and cognitive decline. Here, we compared and …
>>>
White matter hyperintensities (WMH) of presumed vascular origin are frequently found in MRIs of healthy older adults. WMH are also associated with aging and cognitive decline. Here, we compared and validated three algorithms for WMH extraction: FreeSurfer (T1w), UBO Detector (T1w + FLAIR), and FSL's Brain Intensity AbNormality Classification Algorithm (BIANCA; T1w + FLAIR) using a longitudinal dataset comprising MRI data of cognitively healthy older adults (baseline N = 231, age range 64-87 years). As reference we manually segmented WMH in T1w, three-dimensional (3D) FLAIR, and two-dimensional (2D) FLAIR images which were used to assess the segmentation accuracy of the different automated algorithms. Further, we assessed the relationships of WMH volumes provided by the algorithms with Fazekas scores and age. FreeSurfer underestimated the WMH volumes and scored worst in Dice Similarity Coefficient (DSC = 0.434) but its WMH volumes strongly correlated with the Fazekas scores (r = 0.73). BIANCA accomplished the highest DSC (0.602) in 3D FLAIR images. However, the relations with the Fazekas scores were only moderate, especially in the 2D FLAIR images (r = 0.41), and many outlier WMH volumes were detected when exploring within-person trajectories (2D FLAIR: ~30%). UBO Detector performed similarly to BIANCA in DSC with both modalities and reached the best DSC in 2D FLAIR (0.531) without requiring a tailored training dataset. In addition, it achieved very high associations with the Fazekas scores (2D FLAIR: r = 0.80). In summary, our results emphasize the importance of carefully contemplating the choice of the WMH segmentation algorithm and MR-modality.
<<<
翻译
1207.
吴增丁
(2022-04-29 16:29):
#paper https://doi.org/10.1038/s43018-022-00356-3
Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology (2022)
最近为了能从bulkRNAseq数据中分析出肿瘤一致性,所以在找一款比较好用的cellar deconvolution的软件。这方面引用量最好的是CIBERSORT及CIBERSORTx,但是这两款软件存在显示的缺点是只能online分析,不能本地化部署。看到前几天(2022年4月25日)刚在Nature Cancer上发表的BayesPrism,它可以本地化部署且提供的源码,赶紧读一读且拿来了试用。
该软件采用了贝叶斯统计模型,利用已经对cell type/ cell states注释过的single cell data作为 Reference,实现了从bulk RNAseq中推断出不同肿瘤细胞的组成及比例,而且还估计除了不同cell type的gene expression。而且从文章自己展示的性能看,已经超过了CIBERSORT/CIBERSORTx/Bisque/MUSiC 了,并且在肿瘤细胞10%以上的样本中,得到的表达谱和真实表达谱相关性大于0.9。
Abstract:
Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction …
>>>
Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction inferred using statistical marginalization (BayesPrism), a Bayesian method to predict cellular composition and gene expression in individual cell types from bulk RNA-seq, using patient-derived, scRNA-seq as prior information. We conduct integrative analyses in primary glioblastoma, head and neck squamous cell carcinoma and skin cutaneous melanoma to correlate cell type composition with clinical outcomes across tumor types, and explore spatial heterogeneity in malignant and nonmalignant cell states. We refine current cancer subtypes using gene expression annotation after exclusion of confounding nonmalignant cells. Finally, we identify genes whose expression in malignant cells correlates with macrophage infiltration, T cells, fibroblasts and endothelial cells across multiple tumor types. Our work introduces a new lens to accurately infer cellular composition and expression in large cohorts of bulk RNA-seq data.
<<<
翻译
1208.
尹志
(2022-04-28 22:10):
#paper https://doi.org/10.48550/arXiv.1503.03585 Deep Unsupervised Learning using Nonequilibrium Thermodynamics ICML (2015). 这是一篇还没完全看懂的论文,但是非常有意思。说起这篇文章的扩散模型大家一不定熟悉,但是提到最近大火的openai的工作dall-e 2,大家可能会更熟悉一点。对,Dall-E 2最早的启发就是这篇文章。本文受非平衡热力学的启发,设计了一个称之为扩散模型(diffusion model)的生成模型。我们知道,在机器学习中,对一堆数据的分布进行估计是一个极具挑战的事情。特别是要兼顾模型的灵活性(flexible)和过程的可解性(tractable)。如果把建模隐变量z到观测量x的映射作为任务,那么扩散模型的想法是,
假设整个映射是一个马尔科夫链(MC),然后数据的初始状态是由一步步不断添加高斯噪声,最终获得某种最终形态,那么反过来,可以将去噪的过程看做是生成的过程。我们针对这个MC过程进行训练,那么逆过程则可以作为生成模型生成符合分布的数据。是的,很像VAE。考虑到这类生成模型通过不断的改进,已经达到Dall-E 2的效果,值得我们深入理解背后的机制,以及是否可以在数据合成上产生更好的效果。
arXiv,
2015.
DOI: 10.48550/arXiv.1503.03585
Abstract:
A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. …
>>>
A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. Here, we develop an approach that simultaneously achieves both flexibility and tractability. The essential idea, inspired by non-equilibrium statistical physics, is to systematically and slowly destroy structure in a data distribution through an iterative forward diffusion process. We then learn a reverse diffusion process that restores structure in data, yielding a highly flexible and tractable generative model of the data. This approach allows us to rapidly learn, sample from, and evaluate probabilities in deep generative models with thousands of layers or time steps, as well as to compute conditional and posterior probabilities under the learned model. We additionally release an open source reference implementation of the algorithm.
<<<
翻译
1209.
李翛然
(2022-04-28 21:30):
#paper Wohlert and Edholm (2006) J. Chem. Phys. 125: 204703
Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion 本论文提出了不同脂分子的面积,相转变温度,等各种参数的得出方法,并列举出了模拟当中的一些参数选择背后的原因。最近正在深耕细挖分子动力学,因为接下来要和量子计算进行合作了,需要充分理解目前的原理及参数选择,以便找到一个最适合用量子计算的场景。
Abstract:
It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of …
>>>
It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of the chains and lateral diffusion of lipids. It is shown that the reorientational correlation functions exhibits an algebraic decay (rather than exponential) for several orders of magnitude in time. The calculated nuclear magnetic resonance relaxation rates agree with experiments for carbons at the C7 position while there are some differences for C3. Lateral diffusion can be divided into two stages. In a first stage occurring at short times, t<5 ns, the center of mass of the lipid moves due to conformational changes of the chains while the headgroup position remains relatively fixed. In this stage, the center of mass can move up to approximately 0.8 nm. The fitted short-time diffusion coefficient is D(1)=13 x 10(-7) cm(2) s(-1) On a longer time scale, the diffusion coefficient becomes D(2)=0.79 x 10(-7) cm(2) s(-1).
<<<
翻译
1210.
小W
(2022-04-28 10:15):
#paper doi.org/10.1038/s43018-022-00352-7 Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity Nat Cancer (2022). 一篇介绍新生抗原疫苗(ADP 依赖性葡糖激酶突变的 9 聚体 (ADPGK))和免疫检查点抑制剂联合治疗的文章。作者通过对 MC38 模型进行新抗原疫苗接种、抗 PD-L1 治疗和联合治疗期间 DLN 和肿瘤组织中的 T 细胞进行了单细胞 RNA 测序 (scRNA-seq)。通过聚类表征,对簇间 TCR 的相似性 、克隆共享迁移分数、T 细胞进化轨迹、迁移抑制等分析跟踪 TME 的时空状态转换,1.验证了联合治疗通过对 TME 诱导 防止 Teff 细胞向终末耗竭 T 细胞的转变,以及 来自 DLN 的新浸润新抗原特异 T 细胞迁移对促进持久的免疫反应至关重要2.另一种 MC38 表位特异的 T 细胞百分比在联合治疗后也显着增加,Teff 细胞可能在原始肿瘤抗原初始引发后经历表位扩散。3.使用 IFN-γ 途径中的三个基因:Ifngr1、Zfp36l2 和 Gimap4 和两个趋化因子相关基因(Ccl5 和CXCR3) 刻画 MC38 癌症模型 ADPGK 新抗原特异性 T 细胞 (CAST) 评分,ICB 治疗增加了四分之三患者的 CAST 评分, ICB 在扩大 TME 中抗原特异性 T 细胞中的作用。作者分析使用了 10d 和 20d 的时间点的测序数据,从本文来看其分析和模型还是受到 小鼠模型 、疫苗特异性 、 临床数据 、时间梯度 的局限性。
免疫检查点阻断剂的同时递送可调节 T 细胞动力学,以增强新抗原疫苗产生的抗肿瘤免疫力
Abstract:
Neoantigen vaccines aiming to induce tumor-specific T cell responses have achieved promising antitumor effects in early clinical trials. However, the underlying mechanism regarding response or resistance to this treatment is …
>>>
Neoantigen vaccines aiming to induce tumor-specific T cell responses have achieved promising antitumor effects in early clinical trials. However, the underlying mechanism regarding response or resistance to this treatment is unclear. Here we observe that neoantigen vaccine-generated T cells can synergize with the immune checkpoint blockade for effective tumor control. Specifically, we performed single-cell sequencing on over 100,000 T cells and uncovered that combined therapy induces an antigen-specific CD8 T cell population with active chemokine signaling (Cxcr3/Ccl5), lower co-inhibitory receptor expression (Lag3/Havcr2) and higher cytotoxicity (Fasl/Gzma). Furthermore, generation of neoantigen-specific T cells in the draining lymph node is required for combination treatment. Signature genes of this unique population are associated with T cell clonal frequency and better survival in humans. Our study profiles the dynamics of tumor-infiltrating T cells during neoantigen vaccine and immune checkpoint blockade treatments and high-dimensionally identifies neoantigen-reactive T cell signatures for future development of therapeutic strategies.
<<<
翻译
旨在诱导肿瘤特异性T细胞反应的新抗原疫苗在早期临床试验中取得了有希望的抗肿瘤效果。然而,关于对这种治疗的反应或耐药的潜在机制尚不清楚。在这里,我们观察到新抗原疫苗产生的T细胞可以与免疫检查点阻断协同作用,从而有效控制肿瘤。具体来说,我们对超过 100,000 个 T 细胞进行了单细胞测序,发现联合疗法诱导抗原特异性 CD8 T 细胞群,具有活性趋化因子信号传导 (Cxcr3/Ccl5)、较低的共抑制受体表达 (Lag3/Havcr2) 和更高的细胞毒性 (Fasl/Gzma)。此外,联合治疗需要在引流淋巴结中产生新抗原特异性 T 细胞。这个独特群体的特征基因与T细胞克隆频率和人类更好的存活率有关。我们的研究描绘了新抗原疫苗和免疫检查点阻断治疗过程中肿瘤浸润 T 细胞的动力学,并高维识别新抗原反应性 T 细胞特征,用于未来治疗策略的开发。
1211.
洪媛媛
(2022-04-26 18:22):
#paper Cell-free DNA methylation markers for differential diagnosis of hepatocellular
carcinoma. 2022 20:8. https://doi.org/10.1186/s12916-021-02201-3.这篇文献技术路线是DNA提取,重硫酸盐转化,单链建库,探针捕获,二代测序,数据建模(SVM和多项式逻辑回归),独立验证集测试肝癌、肝硬化、健康人互相的区分效果。分类效果是The screening model can effectively discriminate HCC patients from non-HCC controls,including liver cirrhotic patients,asymptomatic HBsAg+ and healthy individuals,achieving an AUC of 0.957 (95%CI 0.939–0.975),wherea AFP only achieved an AUC of 0.803(95%CI 0.758–0.847).
IF:7.000Q1
BMC medicine,
2022-01-14.
DOI: 10.1186/s12916-021-02201-3
PMID: 35027051
PMCID:PMC8759185
Abstract:
BACKGROUND: Aberrant DNA methylation may offer opportunities in revolutionizing cancer screening and diagnosis. We sought to identify a non-invasive DNA methylation-based screening approach using cell-free DNA (cfDNA) for early detection …
>>>
BACKGROUND: Aberrant DNA methylation may offer opportunities in revolutionizing cancer screening and diagnosis. We sought to identify a non-invasive DNA methylation-based screening approach using cell-free DNA (cfDNA) for early detection of hepatocellular carcinoma (HCC).METHODS: Differentially, DNA methylation blocks were determined by comparing methylation profiles of biopsy-proven HCC, liver cirrhosis, and normal tissue samples with high throughput DNA bisulfite sequencing. A multi-layer HCC screening model was subsequently constructed based on tissue-derived differentially methylated blocks (DMBs). This model was tested in a cohort consisting of 120 HCC, 92 liver cirrhotic, and 290 healthy plasma samples including 65 hepatitis B surface antigen-seropositive (HBsAg+) samples, independently validated in a cohort consisting of 67 HCC, 111 liver cirrhotic, and 242 healthy plasma samples including 56 HBsAg+ samples.RESULTS: Based on methylation profiling of tissue samples, 2321 DMBs were identified, which were subsequently used to construct a cfDNA-based HCC screening model, achieved a sensitivity of 86% and specificity of 98% in the training cohort and a sensitivity of 84% and specificity of 96% in the independent validation cohort. This model obtained a sensitivity of 76% in 37 early-stage HCC (Barcelona clinical liver cancer [BCLC] stage 0-A) patients. The screening model can effectively discriminate HCC patients from non-HCC controls, including liver cirrhotic patients, asymptomatic HBsAg+ and healthy individuals, achieving an AUC of 0.957(95% CI 0.939-0.975), whereas serum α-fetoprotein (AFP) only achieved an AUC of 0.803 (95% CI 0.758-0.847). Besides detecting patients with early-stage HCC from non-HCC controls, this model showed high capacity for distinguishing early-stage HCC from a high risk population (AUC=0.934; 95% CI 0.905-0.963), also significantly outperforming AFP. Furthermore, our model also showed superior performance in distinguishing HCC with normal AFP (< 20ng ml-1) from high risk population (AUC=0.93; 95% CI 0.892-0.969).CONCLUSIONS: We have developed a sensitive blood-based non-invasive HCC screening model which can effectively distinguish early-stage HCC patients from high risk population and demonstrated its performance through an independent validation cohort.TRIAL REGISTRATION: The study was approved by the ethic committee of The Second Xiangya Hospital of Central South University (KYLL2018072) and Chongqing University Cancer Hospital (2019167). The study is registered at ClinicalTrials.gov(# NCT04383353 ).
<<<
翻译
1212.
张浩彬
(2022-04-23 15:36):
#paper Salinas, D., Flunkert, V., Gasthaus, J., & Januschowski, T. (2020). DeepAR: Probabilistic forecasting with autoregressive recurrent networks. International Journal of Forecasting, 36(3), 1181–1191. https://doi.org/10.1016/j.ijforecast.2019.07.001
2020的DeepAR算法,个人觉得还是蛮有启发性的。相比于大部分在时序问题这种的点预测,DeepAR用概率模型的思路,在每个时间点去预测期概率分布;这其实也可能更符合显示,毕竟本身时序过程就是有非常强的随机属性,概率分布本身也更贴近本质。文章本身对鲁棒性讨论不多,但DeepAR的鲁棒性应该比较好。另外就是DeepAR自身强调的是,他可以很方便地对多个相关的序列(数千上万)个进行建模并提取其中的关系,这一点确实也是比较强的。所以作者也特别提到,仅需要少量的特征工程及超参数调整,即能获得比传统模型更好的效果。(论文中的模型对比,我个人觉得确实也相对规范)。
论文本身写得很精炼,但是因为是Amazon的论文,所以亲生儿子是用Mxnet上搭建的,用起来确实有点不太方便。Pytprch和TF倒是有实现,但是实现细节也有些魔改的地方。方便性来看,确实比不过Prophet,哈哈
Abstract:
Probabilistic forecasting, i.e., estimating a time series’ future probability distribution given its past, is a key enabler for optimizing business processes. In retail businesses, for example, probabilistic demand forecasts are …
>>>
Probabilistic forecasting, i.e., estimating a time series’ future probability distribution given its past, is a key enabler for optimizing business processes. In retail businesses, for example, probabilistic demand forecasts are crucial for having the right inventory available at the right time and in the right place. This paper proposes DeepAR, a methodology for producing accurate probabilistic forecasts, based on training an autoregressive recurrent neural network model on a large number of related time series. We demonstrate how the application of deep learning techniques to forecasting can overcome many of the challenges that are faced by widely-used classical approaches to the problem. By means of extensive empirical evaluations on several real-world forecasting datasets, we show that our methodology produces more accurate forecasts than other state-of-the-art methods, while requiring minimal manual work.
<<<
翻译
1213.
张德祥
(2022-04-19 21:45):
#paper http://dx.doi.org/10.31234/osf.io/tdw82 逆向海马体高级认知: 作者分析了生物高级slam功能是生物高级认知的基础,论文第三部分调查梳理了大量生物认知文献,论文第二部分提到了作者之前实现的类生物的slam框架,更多介绍可以参考https://mp.weixin.qq.com/s/R7doxKN6ylz7QXAIMiWQlQ
PsyArXiv,
2022.
DOI: 10.31234/osf.io/tdw82
Abstract:
Simultaneous localization and mapping (SLAM) represents a fundamental problem for autonomous embodied systems, for which the hippocampal/entorhinal system (H/E-S) has been optimized over the course of evolution. We have developed …
>>>
Simultaneous localization and mapping (SLAM) represents a fundamental problem for autonomous embodied systems, for which the hippocampal/entorhinal system (H/E-S) has been optimized over the course of evolution. We have developed a biologically-inspired SLAM architecture based on latent variable generative modeling within the Free Energy Principle and Active Inference (FEP-AI) framework, which affords flexible navigation and planning in mobile robots. We have primarily focused on attempting to reverse engineer H/E-S ‘design’ properties, but here we consider ways in which SLAM principles from robotics may help us better understand nervous systems and emergent minds. After reviewing LatentSLAM and notable features of this control architecture, we consider how the H/E-S may realize these functional properties not only for physical navigation, but also with respect to high-level cognition understood as generalized simultaneous localization and mapping (G-SLAM). We focus on loop-closure, graph-relaxation, and node duplication as particularly impactful architectural features, suggesting these computational phenomena may contribute to understanding cognitive insight (as proto-causal-inference), accommodation (as integration into existing schemas), and assimilation (as category formation). All these operations can similarly be describable in terms of structure/category learning on multiple levels of abstraction. However, here we adopt an ecological rationality perspective, framing H/E-S functions as orchestrating SLAM processes within both concrete and abstract hypothesis spaces. In this navigation/search process, adaptive cognitive equilibration between assimilation and accommodation involves balancing tradeoffs between exploration and exploitation; this dynamic equilibrium may be near optimally realized in FEP-AI, wherein control systems governed by expected free energy objective functions naturally balance model simplicity and accuracy. With respect to structure learning, such a balance would involve constructing models and categories that are neither too inclusive nor exclusive. We propose these (generalized) SLAM phenomena may represent some of the most impactful sources of variation in cognition both within and between individuals, suggesting that modulators of H/E-S functioning may potentially illuminate their adaptive significances as fundamental cybernetic control parameters. Finally, we discuss how understanding H/E-S contributions to G-SLAM may provide a unifying framework for high-level cognition and its potential realization in artificial intelligences.
<<<
翻译
1214.
张浩彬
(2022-04-19 21:09):
#paper 10.7287/peerj.preprints.3190v1 Taylor, S. J., & Letham, B. (2017, August 25). Forecasting at Scale. PeerJ Prepr 17年Facebook开源的Prophet。原理不复杂,时序分成3个部分,趋势项,周期项,节假日项。之前用在我司的一个预测模型里面,但是最近算是正儿八经的把论文给读了。Prophet被诟病最多应该还是没啥理论,尤其是趋势项的部分分解过于粗暴了,把时序上的所有点,分解的所有项都看作是t的函数,确实带有一股工业界浓浓的ML气息。虽然粗暴,但不得不说使用体验却是很好。prophet特别适用于商业时间序列的预测,并且这个包中集成了很多方便使用的工具,例如可以方便地定义节假日,方便地定于周期,中间时间序列有缺失值也不仅要,集成了异常检测识别,模型评估方法,时间序列分解图,所以说,即使不是很了解理论的人,也能够很容易使用这个包,简单而言,对数据分析师,非常友好。
PeerJ Preprints,
2017.
DOI: 10.7287/peerj.preprints.3190
Abstract:
Forecasting is a common data science task that helps organizations with capacity planning, goal setting, and anomaly detection. Despite its importance, there are serious challenges associated with producing reliable and …
>>>
Forecasting is a common data science task that helps organizations with capacity planning, goal setting, and anomaly detection. Despite its importance, there are serious challenges associated with producing reliable and high quality forecasts — especially when there are a variety of time series and analysts with expertise in time series modeling are relatively rare. To address these challenges, we describe a practical approach to forecasting “at scale” that combines configurable models with analyst-in-the-loop performance analysis. We propose a modular regression model with interpretable parameters that can be intuitively adjusted by analysts with domain knowledge about the time series. We describe performance analyses to compare and evaluate forecasting procedures, and automatically flag forecasts for manual review and adjustment. Tools that help analysts to use their expertise most effectively enable reliable, practical forecasting of business time series.
<<<
翻译
1215.
龙海晨
(2022-04-10 12:28):
#paper Heat Shock Protein Beta 1 is a Prognostic
Biomarker and Correlated with Immune Infiltrates
in Hepatocellular Carcinoma PMID: 34531676
PMCID: PMC8439715
DOI: 10.2147/IJGM.S330608
推荐理由,最近在尝试自己做生信分析,这是我尝试复现文中生信分析方法的文章,文章使用生信分析和自己做免疫组化验证相结合的方法进行实验。
文章研究目的:研究旨在阐明HSPB1在肝癌中的表达及其潜在的治疗和预后价值。方法:从癌症基因组图谱和基因表达综合数据库中收集了肝癌和正常肝组织中HSPB1表达水平的数据。用免疫组织化学(IHC)对其进行了验证。ROC和Kaplan-Meier 生存曲线研究分析HSPB1在肝癌预后中的作用。生信分析部分包含:RNA-Sequencing Data and Bioinformatics(使用TCGA数据库数据GEO分析,免疫组化实验验证)ROC和Kaplan-Meier 生存曲线分析HSPB1在肝癌患者中的预后。单变量和多变量回归分析,分析HSPB1表达与肝癌生存率之间的相关性。用(STRING) 构建HSPB1的蛋白质相互作用(PPI)网络。HSPB1和HSPB1基因信号通路预测使用Gene Ontology (GO)和Kyoto Encyclopedia of Genes and Genomes (KEGG).用Tumor Immune Estimation Resource (TIMER) 和single sample Gene Set Enrichment Analysis (ssGSEA)分析HSPB1与肿瘤之间的关系。免疫细胞,包括B细胞、中性粒细胞、巨噬细胞、CD4+T细胞和CD8+T细胞。文章结论:HSPB1表达和免疫细胞浸润和肝癌患者预后之间存在显著相关性。HSPB1的表达可能对肝癌患者有明显的预后价值,而且可能是肝癌免疫治疗的潜在靶点。
IF:2.100Q2
International journal of general medicine,
2021.
DOI: 10.2147/IJGM.S330608
PMID: 34531676
PMCID:PMC8439715
Abstract:
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most serious malignancies. The main features of HCC are vascular invasion and drug resistance. Ferroptosis is a novel cell program that is …
>>>
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most serious malignancies. The main features of HCC are vascular invasion and drug resistance. Ferroptosis is a novel cell program that is involved in several diseases, such as cancer. Heat shock protein beta 1 (HSPB1) is a major component of heat shock proteins. A recent study showed that HSPB1 could be a new therapeutic target for colorectal cancer with 5-fluorouracil-acquired resistance. However, the functional role of HSPB1 in HCC remains unclear.AIM: The aim of this study is to clarify HSPB1 expression in HCC and its potential therapeutic and prognostic value.METHODS: We collected data on HSPB1 expression levels in HCC and normal liver tissues from The Cancer Genome Atlas and Gene Expression Omnibus databases. We then validated it using immunohistochemistry (IHC). Receiver operating characteristic and Kaplan-Meier survival curves were used to investigate the role of HSPB1 in the prognosis analysis of HCC. Further, we used the online Search Tool for the Retrieval of Interacting Genes/Proteins website, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes to conduct enrichment analysis and identify the predictive signaling pathways. Meanwhile, we used the TIMER and GSVA package of R (v3.6.3) to analyze the association between HSPB1 and immunocyte infiltration.RESULTS: Compared to normal tissues, there was differential expression of HSPB1 in pan-cancers. HSPB1 expression was higher in HCC tissues than in normal tissues (p<0.05). There was an evident significant difference between HSPB1 mRNA levels and histologic grade, vascular invasion, and alpha-fetoprotein level (all p values<0.05). Univariate analysis indicated that HCC patients with high HSPB1 levels had shorter overall survival rates than those with low HSPB1 levels (p<0.05). MAPK14, HSPA8, MAPKAPK3, MAPKAPK5, and MAPKAPK2 are essential proteins that interact with HSPB1. There was a significant correlation between HSPB1 expression levels and immune cell infiltration, including CD4+ T cells (r=0.203, p<0.05).CONCLUSION: High HSPB1 expression is closely associated with a worse prognosis in HCC patients, and HSPB1 may be a target of immunotherapy in HCC.
<<<
翻译
1216.
魏魏魏
(2022-04-05 00:36):
#paper doi:10.1007/s10826-015-0349-6 Journal of Child and Family Studies, (2016), Emotion Regulation in Relation to Emerging Adults’ Mental Health and Delinquency: A Multi-informant Approach. 父母的教养方式是其教养态度和价值观的反映,并体现在其具体的教养行为中,最终影响子女各方面的发展。此前研究证实,权威型教养方式有更多优点能促进子女积极发展,而威权型教养方式和溺爱型教养方式则会带来更多消极结果。当前研究探讨了父母教养方式与子女情绪调控技能和心理健康及越轨行为的关系,以及情绪调控的中介作用。不过,当前研究的被试不同于此前研究中的儿童或青少年被试,该研究以刚刚成年的子女为研究对象。该研究采用的是问卷法。结果发现,被试报告的情绪调控能力部分中介了权威型教养方式与心理健康的关系,而权威型教养方式通过情绪调控间接与子女的越轨行为发生关系。威权型和溺爱型两种消极的教养方式没有与情绪调控能力发生关系。这一结果提示家庭教育工作者,父母权威型教养方式是有利于子女情绪调控能力发展和心理健康的,不过,未来研究需要建立在干预研究或者追踪研究的基础上才更好。
Abstract:
Relative to the merits of authoritative parenting, potential adverse outcomes are well documented for authoritarian and permissive parenting. However, conclusions are typically drawn from single informants. The ability of youths’ …
>>>
Relative to the merits of authoritative parenting, potential adverse outcomes are well documented for authoritarian and permissive parenting. However, conclusions are typically drawn from single informants. The ability of youths’ emotion regulation skills to mediate outcomes in emerging adults has also not been fully explored. This study investigated whether emotion regulation mediated parenting style history and potential outcomes of mental health and delinquency. Parenting style history and emerging adults’ emotion regulation ability were reported by 110 youth and their caregivers; youth reported on mental health functioning and delinquency. Emerging adults’ emotion regulation ability partially mediated the association between authoritative parenting history and mental health functioning and authoritative parenting history was indirectly related to delinquency through emotion regulation; however, based on all reporters, emotion regulation ability was not associated with authoritarian or permissive parenting style history. Results support that the merits of authoritative parenting may lie in fostering better emotion regulation skills.
<<<
翻译
1217.
魏魏魏
(2022-04-04 23:41):
#paper doi:10.1007/s10802-021-00833-w Research on Child and Adolescent Psychopathology, (2021), Adolescent Emotionality and Emotion Regulation in the Context of Parent Emotion Socialization Among Adolescents with Neurodevelopmental Disorders: A Call to Action with Pilot Data. 父母的情绪社会化影响儿童和青少年的神经发展障碍,该领域的研究目前并不多,该研究也只是一个预备性研究,而且被试量也并不多,只有18个有神经发育障碍的青少年和他们的抚养者。研究中的青少年被试有注意力缺陷多动障碍(ADHD)以及系列共生障碍,比如焦虑、抑郁以及自闭症谱系障碍。当前研究采用了冲突讨论任务、观察法和问卷法。最后发现,父母支持性的情绪社会化行为与观察得到的子女适应性的情绪调控策略显著相关,与观察得到的负性情绪以及青少年报告的负性情绪的减少正相关,而父母非支持性情绪社会化行为与观察到的消极情绪相关。因此,当前研究发现支持了适应性父母情绪社会化抚养行为有助于减少有神经发育障碍子女的消极情绪体验,或者使之能更好地进行情绪调控。当前研究对探讨父母教养行为与子女神经发育障碍的关系提供了一个启发,希望后续能够看到更多此类研究。
IF:2.900Q2
Research on child and adolescent psychopathology,
2022-01.
DOI: 10.1007/s10802-021-00833-w
PMID: 34195911
Abstract:
To date, only three studies have examined the role of emotion socialization in the emotional functioning of youth with neurodevelopmental disorders. As such, this review article with pilot data sought …
>>>
To date, only three studies have examined the role of emotion socialization in the emotional functioning of youth with neurodevelopmental disorders. As such, this review article with pilot data sought to provide a call to action and first step in addressing this limited research body. Pilot data was collected with 18 adolescents (Mage = 13.5, SD = 1.6; 70% male) with a neurodevelopmental disorder and their primary caregiver. All adolescents were diagnosed with attention-deficit/hyperactivity disorder and displayed a range of comorbid disorders: autism spectrum disorder (27.8%), anxiety (66.7%), depression (44.4%), and disruptive behavior disorders (50%). Adolescents and caregivers completed a conflict discussion task while physiological, observational, and self-report measures of emotion socialization and emotional functioning were measured. Observed supportive parent emotion socialization behaviors were significantly associated with more observed adaptive emotion regulation strategies, and decreased observed and adolescent-reported negative affect, whereas non-supportive emotion socialization behaviors were associated with more observed negative affect and less observed adaptive emotion regulation strategies. Our pilot findings support growing research suggesting that adaptive parent emotion socialization practices can help foster less negative emotionality and better emotion regulation in youth with neurodevelopment disorders. We make a call to action for more emotion socialization research focused on youth with neurodevelopmental disorders, and propose four important directions for future research: 1) Research examining emotion socialization behaviors during daily life, 2) Understanding the nuanced role of emotion socialization practices, 3) Considering diversity in emotion socialization practices with clinical populations, and 4) Longitudinal and intervention research studies.
<<<
翻译
1218.
吴增丁
(2022-04-02 17:54):
#paper Lang, F., Schrörs, B., Löwer, M. et al. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat Rev Drug Discov 21, 261–282 (2022). https://doi.org/10.1038/s41573-021-00387-y
这篇最近发表在Nat Rev Drug Discov的综述文章用较长的篇幅介绍了新抗原neoantigen疫苗在肿瘤临床个性化治疗的应用。核心内容包括三个方面:1.新抗原能够产生免疫治疗效果前提与机理,即新抗原的呈递和被免疫细胞的识别;2.提出了一种新的新抗原的分类;3.鉴定新抗原的方法。
篇幅有限,此处1/3两点不做更多详述。重点介绍下第2点--新抗原的分类。传统上一般根据产生新抗原的somatic 突变类型进行分类的,比如SNV/INDEL/FUSION/splice variants等。但是作者根据临床表现来将新抗原分为Guarding neoantigen、Restrained neoantigen、Ignored neoantigen。
其中Guarding Neo是能够自然天然的帮助身体产生对肿瘤细胞的免疫反应,再不需要而外干预的情况抑制了肿瘤细胞的生长。这主要两种情况,一是肿瘤细胞正好有很强的免疫原性,激活了native T,并进一步激活了整个免疫反应;二是由于cross- reactive 效果,即机体可能再产生肿瘤细胞前因为病原感染产生了对某种多肽的免疫,并有了记忆T细胞,正好新生肿瘤中的新抗原含有这个多肽;其二Restrained neoantigen,这个是为什么PD-L1抑制剂能起作用的原因;其三Ignored neoantigen ,这是最有潜力用于免疫治疗的新抗原。
Abstract:
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are …
>>>
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are not expressed in healthy tissues, they are attractive targets for therapeutic cancer vaccines. Because the vast majority of cancer mutations are unique to the individual patient, harnessing the full potential of this rich source of targets requires individualized treatment approaches. Many computational algorithms and machine-learning tools have been developed to identify mutations in sequence data, to prioritize those that are more likely to be recognized by T cells and to design tailored vaccines for every patient. In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing between guarding, restrained and ignored neoantigens, based on how they confer proficient antitumour immunity in a given clinical context. Such context-based differentiation will contribute to a framework that connects neoantigen biology to the clinical setting and medical peculiarities of cancer, and will enable future neoantigen-based therapies to provide greater clinical benefit.
<<<
翻译
1219.
白义民
(2022-04-02 13:40):
#paper 《密契经验的比较研究》,对神秘主义感兴趣的同学可能比较关心,密契经验是从哲学跃迁到宗教的必经步骤,有助于你切身感受到另外维度空间的存在,或曰彼岸或曰净土或曰天堂地狱;如果缺乏宗教经验,哲学理性的归宿基本上都是悖论死胡同,走向不可知论;密契的非理性突破是走出死胡同,打开新世界天地的钥匙。本文是神学博士的比较宗教学研究作品,很合学术章法。对相关主题想深度研究的同学,可读书《宗教经验种种》
2012.
Abstract:
在本文当中,我们首先定义密契经验的内涵、特质以及说明为何选择此四人的主要原因。其次,则分别阐析王重阳等四人之生平大要、开悟的详细经过及开悟的内涵与特质。最后,则进一步分析及比较此四人之密契经验的异同以及我们可以从此探讨当中归纳出的重要结论。藉由如是的探讨,除了可以具体了解中印宗教、哲学的内涵、特质以及其形成与发展的一种重要途径外,也可使我们对于哲学、宗教学及心理学等学科中的重要问题,带来关键的启发。最后,密契经验做为一种了悟真理及彻底解决生命问题的可能方式,对其探讨,亦能给人类的生命,带来重要的启示及指引。
>>>
在本文当中,我们首先定义密契经验的内涵、特质以及说明为何选择此四人的主要原因。其次,则分别阐析王重阳等四人之生平大要、开悟的详细经过及开悟的内涵与特质。最后,则进一步分析及比较此四人之密契经验的异同以及我们可以从此探讨当中归纳出的重要结论。藉由如是的探讨,除了可以具体了解中印宗教、哲学的内涵、特质以及其形成与发展的一种重要途径外,也可使我们对于哲学、宗教学及心理学等学科中的重要问题,带来关键的启发。最后,密契经验做为一种了悟真理及彻底解决生命问题的可能方式,对其探讨,亦能给人类的生命,带来重要的启示及指引。
<<<
翻译
1220.
吴增丁
(2022-04-02 11:39):
#paper Sahin, U., Oehm, P., Derhovanessian, E. et al. An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma. Nature 585, 107–112 (2020). doi:org/10.1038/s41586-020-2537-9
这篇2020年发表在Nautre文章介绍了BioNtech关于FixVac BNT111的I期临床结果,它是2016年pre-clinical 研究( doi.org/10.1038/nature18300)的clinical 研究的延续。该文章首先介绍了临床研究设计:
1.药物核心还是用临川前验证有效的RNA-LPX载体递送四个TAA (NY-ESO-1/Tyrosinase/MAGE-A3/TPTE); 2.通过总共纳入了89例黑色素瘤患者,做了 a.剂量爬坡 、b.剂量范围(7.2-400ug totalRNA)、c. 单用及联合PD-1 抑制剂分别进行cohort验证药效和安全性分析。
最终结果显示单独或与PD1抑制剂联用,都可以介导晚期无法手术的患者产生客观缓解(OR)。通过进一步研究分析产生客观缓解的患者体内伴随着很强的CD4+和CD8+ T 细胞,这个水平几乎和T-cell治疗的水平相当,并且有持久效果。综合显示,TAA BNT111对治疗黑色素瘤取得较好效果。
Abstract:
Treating patients who have cancer with vaccines that stimulate a targeted immune response is conceptually appealing, but cancer vaccine trials have not been successful in late-stage patients with treatment-refractory tumours. …
>>>
Treating patients who have cancer with vaccines that stimulate a targeted immune response is conceptually appealing, but cancer vaccine trials have not been successful in late-stage patients with treatment-refractory tumours. We are testing melanoma FixVac (BNT111)-an intravenously administered liposomal RNA (RNA-LPX) vaccine, which targets four non-mutated, tumour-associated antigens that are prevalent in melanoma-in an ongoing, first-in-human, dose-escalation phase I trial in patients with advanced melanoma (Lipo-MERIT trial, ClinicalTrials.gov identifier NCT02410733). We report here data from an exploratory interim analysis that show that melanoma FixVac, alone or in combination with blockade of the checkpoint inhibitor PD1, mediates durable objective responses in checkpoint-inhibitor (CPI)-experienced patients with unresectable melanoma. Clinical responses are accompanied by the induction of strong CD4 and CD8 T cell immunity against the vaccine antigens. The antigen-specific cytotoxic T-cell responses in some responders reach magnitudes typically reported for adoptive T-cell therapy, and are durable. Our findings indicate that RNA-LPX vaccination is a potent immunotherapy in patients with CPI-experienced melanoma, and suggest the general utility of non-mutant shared tumour antigens as targets for cancer vaccination.
<<<
翻译