当前共找到 1194 篇文献分享,本页显示第 1001 - 1020 篇。
1001.
洪媛媛 (2022-06-30 22:36):
#paper doi:10.1126/science.aav1898 Science 362, 420 (2018). The chromatin accessibility landscape of primary human cancers。推荐理由:这篇文章对TCGA数据库的23种癌症的410份肿瘤组织的ATAC-seq数据进行了分析,得到562,709个染色质开发区域。其中远端调控区域具有癌种特异性,将癌种间差异最大的250,000个区域通过tSNE分成18个cluster,发现这18个cluster based clustering schemes和mRNA based clustering schemes相关性很好,和癌种也有强相关性。
Abstract:
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend … >>>
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy. <<<
翻译
1002.
旺旺小小酥 (2022-06-30 22:25):
#paper 早进城的回报:农村移民的城市经历和就业表现[J].经济研究,2021,56(12):168-186.这篇文章是我随机找的一篇,更多的是满足好奇心。论文用两阶段最小二乘法,以进城年龄为主要依据,通过对中国流动人口数据(数据来源于:2017年国家卫计委流动人口动态监测数据,感兴趣的各位可以把数据集下载下来试试看)识别进行分析,结果表明农村移民要“趁早”,早期的农村移民表现出的城市学习效应,这里的学习效应并不是在学校接受教育所致,而是真正在城市中稳定就业带来的,城市越大效果越明显。作者随后分析这种学习效应的内在机制,利用流动人口监测数据,区分移民进城和从事当前工作的先后顺序,表明非认知能力的提高确实是进城生活后获得的,同样,不同的工作也会带来不同的学习效应,如现代服务业优于第二产业等等,但文中并未进一步区分。至于论文中部分系数的拟定,尚待考究和确认,部分结果也因篇幅原因没有做进一步的解释说明~ 最后,文章指出,如何建设对青年人和低收入人群体更包容的城市,是除政府提供的公共服务之外更重要的问题。
经济研究, 2021.
Abstract:
移民通过尽早进城,在青少年时期获得城市生活经历,可以提升其非认知能力,增加进入现代服务业就业的概率,改善其劳动力市场收入。基于流动人口监测数据的实证研究表明,农村移民首次进城年龄越小,其小时工资越高。以农村移民进城当年户籍地春季旱涝等级作为首次进城年龄的工具变量,两阶段最小二乘法估计表明,户籍地当年春季降水量越多,农民越早进城,其日后的劳动力市场表现越好。机制分析表明,农村移民早进城能提高其非认知能力,提升其进入收入较高的现代服务业的概率。本文的政策含义是,破除体制障碍让更多农村人口尽早进城,以改善其日后的就业和收入。 >>>
移民通过尽早进城,在青少年时期获得城市生活经历,可以提升其非认知能力,增加进入现代服务业就业的概率,改善其劳动力市场收入。基于流动人口监测数据的实证研究表明,农村移民首次进城年龄越小,其小时工资越高。以农村移民进城当年户籍地春季旱涝等级作为首次进城年龄的工具变量,两阶段最小二乘法估计表明,户籍地当年春季降水量越多,农民越早进城,其日后的劳动力市场表现越好。机制分析表明,农村移民早进城能提高其非认知能力,提升其进入收入较高的现代服务业的概率。本文的政策含义是,破除体制障碍让更多农村人口尽早进城,以改善其日后的就业和收入。 <<<
翻译
1003.
翁凯 (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. <<<
翻译
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。
1004.
魏魏魏 (2022-06-30 21:45):
#paper doi:10.1111/cdep.12275 Child Development Perspectives, (2018), Fathers Are Parents, Too! Widening the Lens on Parenting for Children’s Development. 此前谈到亲子关系一般讨论和研究的都是母子关系,最近这些年人们开始关注父亲的作用,然而,父亲为什么会在亲子关系中起作用呢?最近的研究发现,父亲对子女成长的影响既有直接的影响也有间接的影响。儿童发展处于一个非常丰富的生态系统里,这个系统有助于全面解释儿童的发展,其中,亲子关系,尤其是父子关系是一个非常重要的影响因素。父子关系反映了当下的家庭生活,对父子关系进行界定和评估是研究中非常重要的事情,然而,此前的研究中父亲一直都是缺失的,这篇文章首先讨论了父亲缺失的原因。然而,父亲是家庭系统中不可缺少的一部分,家庭是一个生态系统,父子关系是其中的一个子系统。相关模型告诉我们父子关系具有多样性,而且父子关系是如何变化的。最新的模型是基于动态系统的,这更有助于理解父亲在子女发展中的影响,人们很容易发现父亲在以直接和间接地方式影响子女成长。比如以教育水平和收入水平为指标的父亲的社会阶层在直接影响子女成长。父亲也会通过母亲这个中介间接影响子女成长。最后文章探讨了父子关系的评估方法,比如问卷法、视频记录法、质性研究法和神经科学方法等,多个研究方法的使用有助于更好地父亲与母亲在子女成长中所起作用的不同,也有助于确定研究结果的效度。
Abstract:
Why do fathers matter? Recent conceptual and theoretical advances regarding father–child relationships have demonstrated that fathers affect children's outcomes both directly and indirectly. To attain a complete developmental account of … >>>
Why do fathers matter? Recent conceptual and theoretical advances regarding father–child relationships have demonstrated that fathers affect children's outcomes both directly and indirectly. To attain a complete developmental account of the ecologically rich contexts of child development, in this article, we recommend best practices regarding the conceptualization and assessment of father–child relationships that reflect contemporary family life. We also discuss conceptual and measurement issues pertaining to father–child relationships in different family configurations, including those with resident and nonresident fathers. We conclude with recommendations that can help developmental researchers advance our understanding of fathering, parenting, and children's development. <<<
翻译
1005.
前进 (2022-06-30 17:14):
#paper doi:10.1109/CVPR42600.2020.00470 CVPR 2020 Fast Symmetric Diffeomorphic Image Registration with Convolutional Neural Networks 这篇图像配准论文的思路新颖,不同于以往浮动图像朝着固定图像配准的思路,本文将浮动图像和固定图像同时朝着中间图像进行配准。在图像配准过程中,需要保证变形场的微分同胚性,即需要保留图像的拓扑结构,保证变形场是可逆的(不发生折叠)。以往的基于学习的方法通常通过给变形场施加一个全局的正则化来实现这一要求。但是这种做法引入了超参数,要么容易导致变形场过度平坦使得配准精度下降,要么变形场变形过大无法保证变形场不发生折叠。受到传统的对称图像归一化方法的启发,本文提出了一种新的、有效的无监督对称图像配准方法,该方法使微分纯映射空间内图像之间的相似性最大化,并同时估计正变换和逆变换,使得输入的图像从两个方向朝中间对齐,能够同时保证配准精度和变形场的微分同胚性。
Abstract:
Diffeomorphic deformable image registration is crucial in many medical image studies, as it offers unique, special features including topology preservation and invertibility of the transformation. Recent deep learning-based deformable image … >>>
Diffeomorphic deformable image registration is crucial in many medical image studies, as it offers unique, special features including topology preservation and invertibility of the transformation. Recent deep learning-based deformable image registration methods achieve fast image registration by leveraging a convolutional neural network (CNN) to learn the spatial transformation from the synthetic ground truth or the similarity metric. However, these approaches often ignore the topology preservation of the transformation and the smoothness of the transformation which is enforced by a global smoothing energy function alone. Moreover, deep learning-based approaches often estimate the displacement field directly, which cannot guarantee the existence of the inverse transformation. In this paper, we present a novel, efficient unsupervised symmetric image registration method which maximizes the similarity between images within the space of diffeomorphic maps and estimates both forward and inverse transformations simultaneously. We evaluate our method on 3D image registration with a large scale brain image dataset. Our method achieves state-of-the-art registration accuracy and running time while maintaining desirable diffeomorphic properties. <<<
翻译
1006.
王昊 (2022-06-30 17:08):
#paper doi:https://doi.org/10.48550/arXiv.2201.12086 BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation. arXiv:2201.12086 [cs]. BLIP 是一个统一的视觉语言预训练(vision-language pre-training, VLP)框架,从有噪声的图像文本对中学习。 BLIP 通过自展标注(bootstrapping the captions),可以有效地利用带有噪声的 web 数据,其中标注器(captioner)生成标注,过滤器(filter)去除有噪声的标注。本模型属于开源的视觉语言模型中性能较好的(2022年6月),可以直接docker部署,应用于多个视觉语言下游任务。我们尝试了以后可以一定程度上实现zero-shot的功能。在VQA 2.0数据集上性能较好。思考下一步将其作为预训练模型,微调后应用于落地的其它下游任务。
Abstract:
Vision-Language Pre-training (VLP) has advanced the performance for many vision-language tasks. However, most existing pre-trained models only excel in either understanding-based tasks or generation-based tasks. Furthermore, performance improvement has been … >>>
Vision-Language Pre-training (VLP) has advanced the performance for many vision-language tasks. However, most existing pre-trained models only excel in either understanding-based tasks or generation-based tasks. Furthermore, performance improvement has been largely achieved by scaling up the dataset with noisy image-text pairs collected from the web, which is a suboptimal source of supervision. In this paper, we propose BLIP, a new VLP framework which transfers flexibly to both vision-language understanding and generation tasks. BLIP effectively utilizes the noisy web data by bootstrapping the captions, where a captioner generates synthetic captions and a filter removes the noisy ones. We achieve state-of-the-art results on a wide range of vision-language tasks, such as image-text retrieval (+2.7% in average recall@1), image captioning (+2.8% in CIDEr), and VQA (+1.6% in VQA score). BLIP also demonstrates strong generalization ability when directly transferred to video-language tasks in a zero-shot manner. Code, models, and datasets are released at this https URL. <<<
翻译
1007.
魏魏魏 (2022-06-30 16:52):
#paper doi:10.1111/jftr.12227 Journal of Family Theory & Review, (2018), Father Love and Mother Love: Contributions of Parental Acceptance to Children’s Psychological Adjustment. 在家庭教育中,父亲的作用不容忽视,在子女心理发展中和母亲一样各自起着独特作用,只是,这种独特性和相对重要性仍然没有定论。此前研究更多从实证研究的角度探讨父亲教养方式在子女心理问题或健康中的作用,该研究则从元分析的视角比较了子女感知到的父亲和母亲的接纳对子女成长的影响。该研究基于127份研究进行,这些研究都采用子女报告的方式获取数据,自变量均是父亲和母亲对子女的接纳,结果变量是子女发展指标。首先,不论父母性别如何,子女都能够从感知到的父母的接纳中受益并积极发展,父母的接纳都能够显著预测子女的适应状况。但是,在具体指标方面可以发现父母影响的差异,父亲接纳通常与子女的问题行为和精神病理学等指标密切相关,而母亲的接纳则往往有助于子女在社会情绪方面的积极发展。当然,父母接纳也会共同影响子女适应,即通过交互影响的方式以及与其他因素交互影响的方式影响子女。父母的接纳与子女发展的关系会因子女的性别不同而有所不同,当然,这一关系也会因文化不同而有差异。这一结果对推进积极父子关系的建立和科学家庭教育是有利的,父亲不应该在家庭教育中缺失。
Abstract:
Research on child development increasingly includes data on both parents and from different cultures. However, the relative importance of fathers versus mothers for child adjustment is still under debate. The … >>>
Research on child development increasingly includes data on both parents and from different cultures. However, the relative importance of fathers versus mothers for child adjustment is still under debate. The present review compares the contributions of perceived paternal and maternal acceptance to various child adjustment indicators among samples of families around the world. We reviewed 127 published studies that included child-reported paternal and maternal acceptance and developmental outcomes. Regardless of the sex of parent, children benefited from perceived parental acceptance. Fathers and mothers were often found to both predict adjustment significantly to varying degrees. Paternal acceptance tended to be related to children's problem behavior and psychopathology, whereas maternal acceptance was more likely to contribute to socioemotional development. Paternal and maternal acceptance also often jointly contributed to child adjustment through their interaction with each other and with other predictors. Moreover, the link between parental acceptance and adjustment was often moderated by child gender and cultural context. <<<
翻译
1008.
吴增丁 (2022-06-30 16:51):
#paper . doi:10.1038/s41392-021-00572-w 分享一篇发表在2021年nature子刊Signal Transduction and Targeted Therapy的有关肿瘤靶向治疗小分子药物研发的综述:Small molecules in targeted cancer therapy: advances, challenges, and future perspectives. Signal Transduction and Targeted Therapy。 这篇文章汇总了自2001年第一个靶向治疗药物伊马替尼(格列卫--我不是药神)上市以来二十年间89种抗肿瘤小分子药,其对应的靶点涵盖了酪受体氨酸激酶抑制剂(ALK/c-MET/EGFR/FLT3/VEGFR/FGFR/PDGFR/NTRK)、非受体酪氨酸激酶抑制剂(BCR-ABL/BTK/JAK)、丝氨酸/苏氨酸激酶抑制剂(BRAF/MEK/ERK/CDK/PI3K/AKT/mTOR)、酪氨酸激酶样激酶抑制剂(BRAF/MEK/ERK/CDK/PI3K/AKT/mTOR)、 表观遗传抑制剂(EZH/HDAC/IDH1,2)、BCL-2 抑制剂、PROTEASOME 抑制剂、以及合成致死(PARP)。这些靶点中酪氨酸激酶获批的药物最多。本文章并没有太多新颖之处,主要是以量取胜,几乎每一种药物都有相关内容的阐述,所以工作量还是蛮大的。这篇文章适合当做字典对靶向药的查询使用。
Abstract:
Due to the advantages in efficacy and safety compared with traditional chemotherapy drugs, targeted therapeutic drugs have become mainstream cancer treatments. Since the first tyrosine kinase inhibitor imatinib was approved … >>>
Due to the advantages in efficacy and safety compared with traditional chemotherapy drugs, targeted therapeutic drugs have become mainstream cancer treatments. Since the first tyrosine kinase inhibitor imatinib was approved to enter the market by the US Food and Drug Administration (FDA) in 2001, an increasing number of small-molecule targeted drugs have been developed for the treatment of malignancies. By December 2020, 89 small-molecule targeted antitumor drugs have been approved by the US FDA and the National Medical Products Administration (NMPA) of China. Despite great progress, small-molecule targeted anti-cancer drugs still face many challenges, such as a low response rate and drug resistance. To better promote the development of targeted anti-cancer drugs, we conducted a comprehensive review of small-molecule targeted anti-cancer drugs according to the target classification. We present all the approved drugs as well as important drug candidates in clinical trials for each target, discuss the current challenges, and provide insights and perspectives for the research and development of anti-cancer drugs. <<<
翻译
1009.
张德祥 (2022-06-30 16:36):
#paper https://doi.org/10.3390/e24060819 Competency in Navigating Arbitrary Spaces as an Invariant for Analyzing Cognition in Diverse Embodiments 我们在3d空间的导航能力熟视无睹,其实不然,很多女士对方位非常困惑;另外从认知角度看,各种认知能力及不同的知识的掌握都类似于在特定的数学空间的导航能力。这篇论文分析了生物空间的不同导航情况,比如dna的展开,身体发育的展开;这些空间的适用性行为在大脑之前就存在,而且很稳定,很智能;作者从自由能的主动推理推导出一个动作空间的抽象,更多可参考:https://mp.weixin.qq.com/s/e6xmn7Xo-mp9UuuxKWVJ6g
Abstract:
One of the most salient features of life is its capacity to handle novelty and namely to thrive and adapt to new circumstances and changes in both the environment and … >>>
One of the most salient features of life is its capacity to handle novelty and namely to thrive and adapt to new circumstances and changes in both the environment and internal components. An understanding of this capacity is central to several fields: the evolution of form and function, the design of effective strategies for biomedicine, and the creation of novel life forms via chimeric and bioengineering technologies. Here, we review instructive examples of living organisms solving diverse problems and propose competent navigation in arbitrary spaces as an invariant for thinking about the scaling of cognition during evolution. We argue that our innate capacity to recognize agency and intelligence in unfamiliar guises lags far behind our ability to detect it in familiar behavioral contexts. The multi-scale competency of life is essential to adaptive function, potentiating evolution and providing strategies for top-down control (not micromanagement) to address complex disease and injury. We propose an observer-focused viewpoint that is agnostic about scale and implementation, illustrating how evolution pivoted similar strategies to explore and exploit metabolic, transcriptional, morphological, and finally 3D motion spaces. By generalizing the concept of behavior, we gain novel perspectives on evolution, strategies for system-level biomedical interventions, and the construction of bioengineered intelligences. This framework is a first step toward relating to intelligence in highly unfamiliar embodiments, which will be essential for progress in artificial intelligence and regenerative medicine and for thriving in a world increasingly populated by synthetic, bio-robotic, and hybrid beings. <<<
翻译
1010.
张德祥 (2022-06-30 16:23):
#paper https://doi.org/10.3389/fncom.2020.00041 An Active Inference Approach to Modeling Structure Learning: Concept Learning as an Example Case 概念学习是AI的难点,如果学习新概念,去掉冗余概念或冗余认识,提高认知的泛化,及使用无监督学习,这几个难点合在一起更难,这篇论文对概念学习进行了尝试和验证,给出了良好结果的实验,值得参考:https://mp.weixin.qq.com/s/lSkIsuTiDESVBxZcm9PY-w
Abstract:
Within computational neuroscience, the algorithmic and neural basis of structure learning remains poorly understood. Concept learning is one primary example, which requires both a type of internal model expansion process … >>>
Within computational neuroscience, the algorithmic and neural basis of structure learning remains poorly understood. Concept learning is one primary example, which requires both a type of internal model expansion process (adding novel hidden states that explain new observations), and a model reduction process (merging different states into one underlying cause and thus reducing model complexity via meta-learning). Although various algorithmic models of concept learning have been proposed within machine learning and cognitive science, many are limited to various degrees by an inability to generalize, the need for very large amounts of training data, and/or insufficiently established biological plausibility. Using concept learning as an example case, we introduce a novel approach for modeling structure learning-and specifically state-space expansion and reduction-within the active inference framework and its accompanying neural process theory. Our aim is to demonstrate its potential to facilitate a novel line of active inference research in this area. The approach we lay out is based on the idea that a generative model can be equipped with extra (hidden state or cause) "slots" that can be engaged when an agent learns about novel concepts. This can be combined with a Bayesian model reduction process, in which any concept learning-associated with these slots-can be reset in favor of a simpler model with higher model evidence. We use simulations to illustrate this model's ability to add new concepts to its state space (with relatively few observations) and increase the granularity of the concepts it currently possesses. We also simulate the predicted neural basis of these processes. We further show that it can accomplish a simple form of "one-shot" generalization to new stimuli. Although deliberately simple, these simulation results highlight ways in which active inference could offer useful resources in developing neurocomputational models of structure learning. They provide a template for how future active inference research could apply this approach to real-world structure learning problems and assess the added utility it may offer. <<<
翻译
1011.
张德祥 (2022-06-30 16:22):
#paper https://doi.org/10.1016/j.neunet.2021.09.011 World model learning and inference 最近lecun 提出了他的AGI世界模型架构,lecun名气从深度学习的奠基而来,生物认知方面还是有所欠缺,这篇论文的第二部分的概述层次深入,逐步递进,讲解了从感知的不同时间维度,从感知到动作到推理的层次递进。很有深度,看参考:https://mp.weixin.qq.com/s/MwBCBIvRG5HdcDwJL0rK5w
Abstract:
Understanding information processing in the brain-and creating general-purpose artificial intelligence-are long-standing aspirations of scientists and engineers worldwide. The distinctive features of human intelligence are high-level cognition and control in various … >>>
Understanding information processing in the brain-and creating general-purpose artificial intelligence-are long-standing aspirations of scientists and engineers worldwide. The distinctive features of human intelligence are high-level cognition and control in various interactions with the world including the self, which are not defined in advance and are vary over time. The challenge of building human-like intelligent machines, as well as progress in brain science and behavioural analyses, robotics, and their associated theoretical formalisations, speaks to the importance of the world-model learning and inference. In this article, after briefly surveying the history and challenges of internal model learning and probabilistic learning, we introduce the free energy principle, which provides a useful framework within which to consider neuronal computation and probabilistic world models. Next, we showcase examples of human behaviour and cognition explained under that principle. We then describe symbol emergence in the context of probabilistic modelling, as a topic at the frontiers of cognitive robotics. Lastly, we review recent progress in creating human-like intelligence by using novel probabilistic programming languages. The striking consensus that emerges from these studies is that probabilistic descriptions of learning and inference are powerful and effective ways to create human-like artificial intelligent machines and to understand intelligence in the context of how humans interact with their world. <<<
翻译
1012.
prayer (2022-06-30 11:49):
#paper doi:10.1016/j.cell.2022.04.003; Cell, 2022, Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays:华大基因5月Cell发文,使用Stereo-seq技术(大视野,单细胞分辨率,灵敏度高)绘制了不同胚胎时期小鼠器官发生的时空转录组图谱。技术方法不是看的很懂,有待进一步学习。 附原始数据链接:CNP0001543(https://db.cngb.org/search/project/CNP0001543)
IF:45.500Q1 Cell, 2022-05-12. DOI: 10.1016/j.cell.2022.04.003 PMID: 35512705
Abstract:
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies … >>>
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development. <<<
翻译
1013.
masion (2022-06-30 04:24):
#paper doi:10.1111/1365-2745.12025. Identification of 100 fundamental ecological questions. Journal of Ecology. 2013.01作者William J. Sutherland领衔一众科学家对基础生态学研究关键性科学问题的评选活动。他们希望以此为契机,梳理生态学研究的现状并对未来的优先性研究进行展望。评选首先由388位参与人提交了754个问题。然后通过反复的讨论、词语重组织、投票等进一步筛选,最终挑选出100个基础的生态学问题。在Journal of Ecology这篇文章中,这100个问题被划分为与7个主题相关的大类。7个主题分别是:生态与演化(ecology and evolution)、种群(populations)、疾病与微生物(disease and micro-organisms)、群落与多样性(communities and diversity)、生态系统及其功能(ecosystems and functioning)、人类影响与全球变化(human impacts and global change)和方法(methods)。时至今日,其中的一些问题有了显著的进展,比如生态系统恢复力的度量。而更多的问题,仍然有待探索。重新思考这些问题,或许可以对生态学未来的发展,有一定的助益。
Abstract:
Fundamental ecological research is both intrinsically interesting and provides the basic knowledge required to answer applied questions of importance to the management of the natural world. The 100th anniversary of … >>>
Fundamental ecological research is both intrinsically interesting and provides the basic knowledge required to answer applied questions of importance to the management of the natural world. The 100th anniversary of the British Ecological Society in 2013 is an opportune moment to reflect on the current status of ecology as a science and look forward to high-light priorities for future work. To do this, we identified 100 important questions of fundamental importance in pure ecology. We elicited questions from ecologists working across a wide range of systems and disciplines. The 754 questions submitted (listed in the online appendix) from 388 participants were narrowed down to the final 100 through a process of discussion, rewording and repeated rounds of voting. This was done during a two-day workshop and thereafter. The questions reflect many of the important current conceptual and technical pre-occupations of ecology. For example, many questions concerned the dynamics of environmental change and complex ecosystem interactions, as well as the interaction between ecology and evolution. The questions reveal a dynamic science with novel subfields emerging. For example, a group of questions was dedicated to disease and micro-organisms and another on human impacts and global change reflecting the emergence of new subdisciplines that would not have been foreseen a few decades ago. The list also contained a number of questions that have perplexed ecologists for decades and are still seen as crucial to answer, such as the link between population dynamics and life-history evolution. Synthesis. These 100 questions identified reflect the state of ecology today. Using them as an agenda for further research would lead to a substantial enhancement in understanding of the discipline, with practical relevance for the conservation of biodiversity and ecosystem function. <<<
翻译
1014.
颜林林 (2022-06-30 00:17):
#paper doi:10.1038/s41597-022-01450-y Scientific Data, 2022, HunCRC: annotated pathological slides to enhance deep learning applications in colorectal cancer screening. 《Nature》子刊《Scientific Data》确实是宝藏。这篇来自匈牙利的论文,就分享了一组很有用的数据。取材了200张H&E染色的结直肠癌的肿瘤组织切片,使用40倍高分辨率扫描全片,然后由病理医生进行标注,从中切分出多个不同类别的图像块,可用于后续结直肠癌的各类病理图像分析研究。值得夸赞的是,从样本采集到数据处理,整个过程有详细描述,数据处理代码、带标注的原始图像、处理后的带分类信息的图像块,全部都开放供直接下载使用。 代码地址: https://github.com/qbeer/qupath-binarymask-extension https://github.com/patbaa/crc_data_paper 原始图像数据: https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=91357370 处理后数据: https://figshare.com/articles/dataset/patches_and_local_annotations_slide_200_zoom_124x124_um2/19500266
IF:5.800Q1 Scientific data, 2022-06-28. DOI: 10.1038/s41597-022-01450-y PMID: 35764660
Abstract:
Histopathology is the gold standard method for staging and grading human tumors and provides critical information for the oncoteam's decision making. Highly-trained pathologists are needed for careful microscopic analysis of … >>>
Histopathology is the gold standard method for staging and grading human tumors and provides critical information for the oncoteam's decision making. Highly-trained pathologists are needed for careful microscopic analysis of the slides produced from tissue taken from biopsy. This is a time-consuming process. A reliable decision support system would assist healthcare systems that often suffer from a shortage of pathologists. Recent advances in digital pathology allow for high-resolution digitalization of pathological slides. Digital slide scanners combined with modern computer vision models, such as convolutional neural networks, can help pathologists in their everyday work, resulting in shortened diagnosis times. In this study, 200 digital whole-slide images are published which were collected via hematoxylin-eosin stained colorectal biopsy. Alongside the whole-slide images, detailed region level annotations are also provided for ten relevant pathological classes. The 200 digital slides, after pre-processing, resulted in 101,389 patches. A single patch is a 512 × 512 pixel image, covering 248 × 248 μm tissue area. Versions at higher resolution are available as well. Hopefully, HunCRC, this widely accessible dataset will aid future colorectal cancer computer-aided diagnosis and research. <<<
翻译
1015.
颜林林 (2022-06-29 22:30):
#paper doi:10.1002/humu.24424 Human Mutation, 2022, Screening of potential novel candidate genes in schwannomatosis patients. 这篇论文研究的是神经鞘瘤病(Schwannomatosis),是一种由周围神经的神经鞘所形成的肿瘤,该疾病与遗传有很大关系,通常会筛查NF2、SMARCB1和LZTR1这三个基因的胚系突变。然而,仍有相当大比例的患者并不携带这三个基因的突变,提示存在其他致病基因,本文则为寻找这样的基因。研究纳入了来自75个家庭的散发患者,这些患者均经筛查未携带上述三个基因的致病突变,于是采用NGS、MLPA、PCR+Sanger等方法,扩展筛查范围,找到DGCR8、COQ6、CDKN2A和CDKN2B等基因携带致病突变,结合既往文献研究,推断它们与该疾病发生相关,为后续研究该疾病的发病机制提供了证据提示。本文的研究逻辑和方法,也是拓展遗传病致病基因的常规研究套路。
IF:3.300Q2 Human mutation, 2022-10. DOI: 10.1002/humu.24424 PMID: 35723634
Abstract:
Schwannomatosis comprises a group of hereditary tumor predisposition syndromes characterized by, usually benign, multiple nerve sheath tumors, which frequently cause severe pain that does not typically respond to drug treatments. … >>>
Schwannomatosis comprises a group of hereditary tumor predisposition syndromes characterized by, usually benign, multiple nerve sheath tumors, which frequently cause severe pain that does not typically respond to drug treatments. The most common schwannomatosis-associated gene is NF2, but SMARCB1 and LZTR1 are also associated. There are still many cases in which no pathogenic variants (PVs) have been identified, suggesting the existence of as yet unidentified genetic risk factors. In this study, we performed extended genetic screening of 75 unrelated schwannomatosis patients without identified germline PVs in NF2, LZTR1, or SMARCB1. Screening of the coding region of DGCR8, COQ6, CDKN2A, and CDKN2B was carried out, based on previous reports that point to these genes as potential candidate genes for schwannomatosis. Deletions or duplications in CDKN2A, CDKN2B, and adjacent chromosome 9 region were assessed by multiplex ligation-dependent probe amplification analysis. Sequencing analysis of a patient with multiple schwannomas and melanomas identified a novel duplication in the coding region of CDKN2A, disrupting both p14ARF and p16INK4a. Our results suggest that none of these genes are major contributors to schwannomatosis risk but the possibility remains that they may have a role in more complex mechanisms for tumor predisposition. <<<
翻译
1016.
尹志 (2022-06-28 22:16):
#paper doi:10.1093/nar/gkac010 Nucleic Acids Research, Volume 50, Issue 8, 6 May 2022, AggMapNet: enhanced and explainable low-sample omics deep learning with feature-aggregated multi-channel networks 基于组学的生物医学数据的学习,通常依赖于高维特征及小样本,而这对于目前的深度学习主流方法而言则是一项挑战。本文首先提出了一种无监督的特征聚合技术AggMap,其作用是基于组学特征的内在固有关联,将组学特征聚合并映射为多通道的二维空间关联特征图(Fmaps)。AggMap在基准数据集上,相较于现有的算法,具有很强的特征重构能力;接着,文章利用AggMap的多通道Fmap作为输入,通过构建多通道深度学习模型AggMapNet,在18个小样本组学基准数据集上取得超过SOTA的性能。而且AggMapNet在噪声数据和疾病分类的问题上展现了良好的鲁棒性。另外,在可解释性方面,AggMapNet的的解释性模块Simply-explainer可以识别COVID19的检测和严重性预测的关键代谢分子和蛋白。 总体上看,文章提出了一个组学小样本数据建模的pipeline:通过无监督算法AggMap的特征重构能力+基于监督信息的可解释的AggMapNet深度学习模型。 几点启发:这个工作将小样本组学数据通过一个pipeline完成学习,我们可以将这个pipeline理解为特征重表示(AggMap)+DL网络(AggMapNet)。我们看到,这个过程不是端到端的,而是充分利用了对特征的重表示,挖掘新的特征空间的表征能力。有点返璞归真的意思,但又考虑到高维性质,不容易手工构造特征,因此在特征部分,用到了很多无监督聚类的方法,比如利用了基于pairwise关联距离的流形学习方法UMAP将组学数据点嵌入二维空间,同时,通过团聚层级聚类方法将组学数据点团聚为多特征簇。有趣的是,这几类方法是已有的通用的无监督算法。感觉基于流形的这类聚类算法,能很好的在保度规的情况下达到降维的效果,提取有效特征,为下游任务服务。对于小样本而言,这类方法的效果似乎是比较不错的。那么一个想法是,能不能利用生成的方式,合成数据,然后learning的方式去构建这个embedding表示,再去做下游任务?有点想试试看,不过考虑到在18个基准数据集上做pk,多少有点心累
IF:16.600Q1 Nucleic acids research, 2022-05-06. DOI: 10.1093/nar/gkac010 PMID: 35100418
Abstract:
Omics-based biomedical learning frequently relies on data of high-dimensions (up to thousands) and low-sample sizes (dozens to hundreds), which challenges efficient deep learning (DL) algorithms, particularly for low-sample omics investigations. … >>>
Omics-based biomedical learning frequently relies on data of high-dimensions (up to thousands) and low-sample sizes (dozens to hundreds), which challenges efficient deep learning (DL) algorithms, particularly for low-sample omics investigations. Here, an unsupervised novel feature aggregation tool AggMap was developed to Aggregate and Map omics features into multi-channel 2D spatial-correlated image-like feature maps (Fmaps) based on their intrinsic correlations. AggMap exhibits strong feature reconstruction capabilities on a randomized benchmark dataset, outperforming existing methods. With AggMap multi-channel Fmaps as inputs, newly-developed multi-channel DL AggMapNet models outperformed the state-of-the-art machine learning models on 18 low-sample omics benchmark tasks. AggMapNet exhibited better robustness in learning noisy data and disease classification. The AggMapNet explainable module Simply-explainer identified key metabolites and proteins for COVID-19 detections and severity predictions. The unsupervised AggMap algorithm of good feature restructuring abilities combined with supervised explainable AggMapNet architecture establish a pipeline for enhanced learning and interpretability of low-sample omics data. <<<
翻译
1017.
颜林林 (2022-06-28 07:39):
#paper doi:10.1101/2022.06.22.497216 bioRxiv, 2022, Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade. 这篇文章来自西奈山伊坎医学院,其病例队列出自一项用于非小细胞肺癌(NSCLC)、肝细胞癌(HCC)和头颈部鳞癌(HNSCC)的手术前抗PD-1免疫药物(西米普利单抗,Cemiplimab)新辅助治疗的多中心II期临床试验(NCT03916627,该临床试验尚在进行中,始于2019年,预计2024年完成)。本文仅针对其中的肝细胞癌患者,通过对其新辅助治疗后手术取样组织,开展TCR测序、全外显子测序、单细胞转录组测序、多重免疫组化等实验,寻找与新辅助治疗疗效相关的特定细胞类群。通过免疫组化和免疫荧光方法,确认在肿瘤中确实富含T细胞并浸润其中的患者,仍有部分患者对PD-1药物并无响应。对比响应者与无响应者之间的细胞类群组成差异,找到一个细胞类群组合,成熟调节树突状细胞(mregDC,LAMP3+)与 CXCL13+ CD4+ 辅助性T细胞,它们与 PD-1高表达的CD8+ T细胞前体结合,形成三元组,促使后者形成 PD-1高表达的 GZMK+ 效应T细胞。而在没有这两类细胞的情况下,后者将形成耗竭型CD8+ T细胞。这导致了该新辅助治疗的不同预后结局。这项研究也为进一步揭示免疫治疗相关机制提供了新的证据。
Abstract:
Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. … >>>
Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+ CH25H+ IL-21+ PD-1+ CD4 T helper cells (CXCL13+ Th) and Granzyme K+ PD-1+ effector-like CD8 T cells, whereas terminally exhausted CD39hi TOXhi PD-1hi CD8 T cells dominated in non-responders. Strikingly, most T cell receptor (TCR) clones that expanded post-treatment were found in pre-treatment biopsies. Notably, PD-1+ TCF-1+ progenitor-like CD8 T cells were present in tumors of responders and non-responders and shared clones mainly with effector-like cells in responders or terminally differentiated cells in non-responders, suggesting that local CD8 T cell differentiation occurs upon ICB. We found that these progenitor CD8 T cells interact with CXCL13+ Th cells within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". Receptor-ligand analysis revealed unique interactions within these triads that may promote the differentiation of progenitor CD8 T cells into effector-like cells upon ICB. These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ Th cells control the differentiation of tumor-specific progenitor CD8 T cell clones in patients treated with ICB. <<<
翻译
1018.
李翛然 (2022-06-27 18:03):
#paper doi:https://doi.org/10.1038/d41573-022-00052-y Hooking FSH as a potential target for Alzheimer disease 这篇是一个比较新的关于女性老年痴呆的靶点文章,可信度很高,最近我们也在构建这个疾病的小鼠模型。这里面采用的是敲除的手段复现的FSH receptor 作用通路。我们的思路是,通过构建一个基因突变,找到合适的抑制剂。 嘿嘿,这算不算核心技术透露?
1019.
大象城南 (2022-06-27 10:28):
#paper doi: 10.1002/nbm.1579 NMR in Biomedicine, 2022, Mapping brain anatomical connectivity using white matter tractography. 人类大脑中的神经过程的整合是通过存在于不同神经中枢之间的相互连接来实现的。这些相互联系通过白质途径发生。白质纤维束追踪术是目前唯一一种在体内无创重建人脑解剖连接的技术。从神经束的局部方向估计白质通路的轨迹和终止。这些方向是通过测量脑内水扩散得到的。本文综述了利用脑内扩散测量来估计纤维方向的技术。描述了白质束摄影的方法,以及该技术目前的局限性,包括对图像噪声和部分体积的敏感性。讨论了白质束摄影在白质连接的地形表征、特定白质通路的分割以及相应的灰质功能单元等方面的应用。在此背景下,本文描述了白质束成像在绘制人脑功能系统和子系统及其相互关系方面的潜在影响。最后,讨论了白质束成像在脑疾病研究中的应用,包括肿瘤影响的脑纤维束定位和神经和神经精神疾病中连接通路受损的识别。
IF:2.700Q1 NMR in biomedicine, 2010-Aug. DOI: 10.1002/nbm.1579 PMID: 20886567
Abstract:
Integration of the neural processes in the human brain is realized through interconnections that exist between different neural centers. These interconnections take place through white matter pathways. White matter tractography … >>>
Integration of the neural processes in the human brain is realized through interconnections that exist between different neural centers. These interconnections take place through white matter pathways. White matter tractography is currently the only available technique for the reconstruction of the anatomical connectivity in the human brain noninvasively and in vivo. The trajectory and terminations of white matter pathways are estimated from local orientations of nerve bundles. These orientations are obtained using measurements of water diffusion in the brain. In this article, the techniques for estimating fiber directions from diffusion measurements in the human brain are reviewed. Methods of white matter tractography are described, together with the current limitations of the technique, including sensitivity to image noise and partial voluming. The applications of white matter tractography to the topographical characterization of the white matter connections and the segmentation of specific white matter pathways, and corresponding functional units of gray matter, are discussed. In this context, the potential impact of white matter tractography in mapping the functional systems and subsystems in the human brain, and their interrelations, is described. Finally, the applications of white matter tractography to the study of brain disorders, including fiber tract localization in brains affected by tumors and the identification of impaired connectivity routes in neurologic and neuropsychiatric diseases, are discussed. <<<
翻译
1020.
lsj (2022-06-27 10:16):
#Virtual resection predicts surgical outcome for drug-resistant epilepsy. 该研究使用了线性系统稳定性理论与分析方法,提出了一种新的颅内EEG癫痫发作起始区的标记——神经易脆性,并通过多中心的91名患者数据对该方法进行了回顾性验证。
IF:10.600Q1 Brain : a journal of neurology, 2019-12-01. DOI: 10.1093/brain/awz303 PMID: 31599323 PMCID:PMC6885672
Abstract:
Patients with drug-resistant epilepsy often require surgery to become seizure-free. While laser ablation and implantable stimulation devices have lowered the morbidity of these procedures, seizure-free rates have not dramatically improved, … >>>
Patients with drug-resistant epilepsy often require surgery to become seizure-free. While laser ablation and implantable stimulation devices have lowered the morbidity of these procedures, seizure-free rates have not dramatically improved, particularly for patients without focal lesions. This is in part because it is often unclear where to intervene in these cases. To address this clinical need, several research groups have published methods to map epileptic networks but applying them to improve patient care remains a challenge. In this study we advance clinical translation of these methods by: (i) presenting and sharing a robust pipeline to rigorously quantify the boundaries of the resection zone and determining which intracranial EEG electrodes lie within it; (ii) validating a brain network model on a retrospective cohort of 28 patients with drug-resistant epilepsy implanted with intracranial electrodes prior to surgical resection; and (iii) sharing all neuroimaging, annotated electrophysiology, and clinical metadata to facilitate future collaboration. Our network methods accurately forecast whether patients are likely to benefit from surgical intervention based on synchronizability of intracranial EEG (area under the receiver operating characteristic curve of 0.89) and provide novel information that traditional electrographic features do not. We further report that removing synchronizing brain regions is associated with improved clinical outcome, and postulate that sparing desynchronizing regions may further be beneficial. Our findings suggest that data-driven network-based methods can identify patients likely to benefit from resective or ablative therapy, and perhaps prevent invasive interventions in those unlikely to do so. <<<
翻译
回到顶部