来自用户 孤舟蓑笠翁 的文献。
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41.
孤舟蓑笠翁 (2022-06-30 22:15):
#paper 10.1038/s41588-018-0129-5。Nature Genetics。2018。Genetic identification of brain cell types underlying schizophrenia。貌似是第一批利用单细胞转录组来定位遗传学研究积累的候选致病基因富集在哪些细胞类型。这有利于进行更细致的机制研究。
IF:31.700Q1 Nature genetics, 2018-06. DOI: 10.1038/s41588-018-0129-5 PMID: 29785013 PMCID:PMC6477180
精神分裂症脑细胞类型的基因鉴定
Abstract:
With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying … >>>
With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells. These enrichments were due to sets of genes that were specifically expressed in each of these cell types. We also found that many of the diverse gene sets previously associated with schizophrenia (genes involved in synaptic function, those encoding mRNAs that interact with FMRP, antipsychotic targets, etc.) generally implicated the same brain cell types. Our results suggest a parsimonious explanation: the common-variant genetic results for schizophrenia point at a limited set of neurons, and the gene sets point to the same cells. The genetic risk associated with MSNs did not overlap with that of glutamatergic pyramidal cells and interneurons, suggesting that different cell types have biologically distinct roles in schizophrenia. <<<
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除了少数例外,关于精神分裂症遗传基础的知识的显着进展并没有集中在可以自信地用于精确实验建模的发现上。通过应用来自单细胞RNA测序的大脑细胞分类学知识,我们评估了与精神分裂症有关的基因组位点是否映射到特定的脑细胞类型。我们发现,常见变异的基因组结果一致地映射到锥体细胞、中棘神经元(MSN)和某些中间神经元,但对胚胎细胞、祖细胞或神经胶质细胞的一致性要低得多。这些富集是由于在这些细胞类型中的每一种中特异性表达的基因集造成的。我们还发现,许多以前与精神分裂症相关的不同基因集(参与突触功能的基因,编码与FMRP相互作用的mRNA,抗精神病靶点等)通常与相同的脑细胞类型有关。我们的研究结果提出了一个简洁的解释:精神分裂症的常见变异遗传结果指向有限的神经元集,而基因集指向相同的细胞。与MSNs相关的遗传风险与谷氨酸能锥体细胞和中间神经元的遗传风险没有重叠,这表明不同的细胞类型在精神分裂症中具有生物学上不同的作用。
42.
孤舟蓑笠翁 (2022-05-23 19:00):
#paper 10.1080/01621459.2020.1721245。Journal of the American Statistical Association。2020。The Book of Why: The New Science of Cause and Effect。 这是对Judea Pearl的《the book of why》的书评。从这个书评来看,Judea Pearl的《the book of why》有较大的局限。比如,Judea Pearl在《the book of why》只处理了因果分析,而忽略了因果结构的确定。但有时往往连因果结构也是不清楚或者不确定的。基于我的阅读理解,这个书评还指出,Judea Pearl认为随机实验不重要,只要看起来没有受到干扰就可以了。但书评作者认为,随机实验的作用在于能让研究者对实验设计和过程做检查。另外,实验允许我们不知道因果结构。然后,书评作者认为Judea Pearl的因果分析模型的表达能力不够强;还说Judea Pearl虽然回顾了因果研究的历史,但他的回顾是不完整的,忽略了其它因果研究方向;说Judea Pearl认为不接受他的理论的研究者是“文化抵触”,但其实是因为他的理论用处不大;说Judea Pearl的理论和之前Robin的因果理论关系密切,仅仅是多了一些独立性假设,但Robin没提这些假设不是因为他提不出来,而是因为认为太牵强,而且也无法得到实验验证。看了这个书评后我估计不会优先看The Book of Why了。
43.
孤舟蓑笠翁 (2022-04-30 23:23):
#paper DOI: 10.1126/science.1192788 science, 2011, How to Grow a Mind: Statistics, Structure, and Abstraction. 这是一篇综述,提出了在我看来比较可信的关于人脑如何学习的解释。人脑学习的一个特点是只需少量样本量(或者说数据很稀疏)就能学得很好,尤其是对因果关联的学习。作者认为学习效率高是因为用了抽象知识指导学习,并认为贝叶斯定理能很好地解释是如何用抽象知识指导学习的。而且贝叶斯方法可以有效利用多种形式的抽象知识,从而避免了传统方法需要穷举各种可能(一个个很长的数值向量)的需要。至于是如何从数据学到抽象知识的,比如是如何知道哪种形式是正确的,作者提到了各种形式(树、空间、环、次序……)都可以用graph表示,然后可以用分层贝叶斯模型来生成所需的graph,并且非参形式的分层贝叶斯模型自动蕴含了奥卡姆剃刀,只在数据需要时引入更多变量。不过,有些重要问题仍然没有被分层贝叶斯模型解决,比如学习到底是如何开始的?总得有什么作为基础吧?作者指出,有些贝叶斯建模者认为哪怕是最抽象的概念(比如因果关系的概念)原则上也是可以被学习的。作者还有一些讨论,比如什么Turing complete compositional representations,还有人脑具体如何实现贝叶斯算法,但目前不是我的兴趣(或者其实更是今晚我没有时间重新仔细看了……虽然2011年这篇文献出来的时候我就读过)。有兴趣的朋友可以直接找文献看。
Abstract:
In coming to understand the world-in learning concepts, acquiring language, and grasping causal relations-our minds make inferences that appear to go far beyond the data available. How do we do … >>>
In coming to understand the world-in learning concepts, acquiring language, and grasping causal relations-our minds make inferences that appear to go far beyond the data available. How do we do it? This review describes recent approaches to reverse-engineering human learning and cognitive development and, in parallel, engineering more humanlike machine learning systems. Computational models that perform probabilistic inference over hierarchies of flexibly structured representations can address some of the deepest questions about the nature and origins of human thought: How does abstract knowledge guide learning and reasoning from sparse data? What forms does our knowledge take, across different domains and tasks? And how is that abstract knowledge itself acquired? <<<
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