来自杂志 Science advances 的文献。
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1.
muton
(2024-01-31 23:04):
# paper:DOI: 10.1126/sciadv.abj4383 Emerged human-like facial expression representation in a deep convolutional neural network 最近的研究发现,经过训练以识别面部身份的深度卷积神经网络(DCNN)自发地学习了支持面部表情识别的特征,反之亦然。作者通过比较pretrain的VGG-Face,untrained VGG-Face以及VGG 16三个模型发现,只有pretrain的VGG-Face最后一层的1.25%的units表现出了和人类类似的面部表情识别以及表情混淆的特征。这些研究结果揭示了特定单元的面孔识别视觉经验对面孔表情知觉发展的必要性。
Abstract:
Recent studies found that the deep convolutional neural networks (DCNNs) trained to recognize facial identities spontaneously learned features that support facial expression recognition, and vice versa. Here, we showed that …
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Recent studies found that the deep convolutional neural networks (DCNNs) trained to recognize facial identities spontaneously learned features that support facial expression recognition, and vice versa. Here, we showed that the self-emerged expression-selective units in a VGG-Face trained for facial identification were tuned to distinct basic expressions and, importantly, exhibited hallmarks of human expression recognition (i.e., facial expression confusion and categorical perception). We then investigated whether the emergence of expression-selective units is attributed to either face-specific experience or domain-general processing by conducting the same analysis on a VGG-16 trained for object classification and an untrained VGG-Face without any visual experience, both having the identical architecture with the pretrained VGG-Face. Although similar expression-selective units were found in both DCNNs, they did not exhibit reliable human-like characteristics of facial expression perception. Together, these findings revealed the necessity of domain-specific visual experience of face identity for the development of facial expression perception, highlighting the contribution of nurture to form human-like facial expression perception.
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2.
muton
(2022-11-30 23:19):
#paper https://science.org/doi/10.1126/ sciadv.abm3829 Science Advances,2022,Higher-dimensional neural representations predict better episodic memory
情景记忆使人类能够编码并随后生动地检索有关我们丰富经历的信息,但怎样的神经表征可以支持这一心理能力?作者让被试学习人脸图片和词语的配对,使用表征维度的分析方法,对由脑成像得到的神经相似性矩阵进行PCA分析,得到每个主成分的eigenvalue,通过对eigenvalue的处理得到RD(representational dimensionality)值,来分析面孔选择区和其他相关脑区的差异,结果发现,面孔选择区保留了高维表征,重要的是,RD值越大,记忆效应就越好。本文提供了新的神经表征分析方法。
Abstract:
Episodic memory enables humans to encode and later vividly retrieve information about our rich experiences, yet the neural representations that support this mental capacity are poorly understood. Using a large …
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Episodic memory enables humans to encode and later vividly retrieve information about our rich experiences, yet the neural representations that support this mental capacity are poorly understood. Using a large fMRI dataset ( = 468) of face-name associative memory tasks and principal component analysis to examine neural representational dimensionality (RD), we found that the human brain maintained a high-dimensional representation of faces through hierarchical representation within and beyond the face-selective regions. Critically, greater RD was associated with better subsequent memory performance both within and across participants, and this association was specific to episodic memory but not general cognitive abilities. Furthermore, the frontoparietal activities could suppress the shared low-dimensional fluctuations and reduce the correlations of local neural responses, resulting in greater RD. RD was not associated with the degree of item-specific pattern similarity, and it made complementary contributions to episodic memory. These results provide a mechanistic understanding of the role of RD in supporting accurate episodic memory.
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3.
笑对人生
(2022-08-31 21:18):
#paper Dynamic patterns of microRNA expression during acute myeloid leukemia state-transition. Sci Adv. 2022 Apr 22;8(16):eabj1664. doi: 10.1126/sciadv.abj1664.
miRNAs是一类长度为21nt的非编码RNA,自1993年首次发现以来,至今已将近30年。在机体内,miRNAs大多数扮演微调的角色。既往的研究已证明miRNAs能作为急性髓系白血病(AML)预后的生物标志物。Inv(16)是与急性髓系白血病密切相关的一种常见染色体易位,携带该变异的患者占总AML患者的5%。该白血病亚型的分子特征是染色体上的CBFB和MYH11基因的相互易位产生CBFB-MYH11融合基因。本研究利用敲入Cbfb-MYH11融合基因小鼠的PBMC,首次绘制AML从疾病开始到进展的动态miRNAs图谱,测序技术使用的是基于PAGE(聚丙烯酰胺凝胶电泳)进行片段筛选的miRNA-seq。研究将每只小鼠的 miRNA 转录组作为准电位中经历布朗运动的粒子,并分成两个稳态,受扰动的造血c1和AMLc2,这两个稳态由不稳定的过渡态(c3)隔开。进一步地将AML疾病由发生到进展划分为四个不同的事件,最终获得四个反映不同疾病进展的miRNAs集。基于先前来自相同小鼠模型PBMC的mRNA测序数据,研究证实了miRNA表达谱在描述疾病进展过程,与mRNA表达相比,具有一定相似性。更为重要的是,该研究发现mmu-miR-126a在疾病发展进程中表达逐渐上调,并与5个AML致病基因(Prkd1、Egfl7、Wt1、Kite和Cbfb-MYH11)的表达高度正相关。此外,还发现了先前未报道的,但与5个致病基因表达高度正相关的miRNAs,分别是mmu-miR-31 和 mmu-miR-340。
Abstract:
MicroRNAs (miRNAs) have been shown to hold prognostic value in acute myeloid leukemia (AML); however, the temporal dynamics of miRNA expression in AML are poorly understood. Using serial samples from …
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MicroRNAs (miRNAs) have been shown to hold prognostic value in acute myeloid leukemia (AML); however, the temporal dynamics of miRNA expression in AML are poorly understood. Using serial samples from a mouse model of AML to generate time-series miRNA sequencing data, we are the first to show that the miRNA transcriptome undergoes state-transition during AML initiation and progression. We modeled AML state-transition as a particle undergoing Brownian motion in a quasi-potential and validated the AML state-space and state-transition model to accurately predict time to AML in an independent cohort of mice. The critical points of the model provided a framework to align samples from mice that developed AML at different rates. Our mathematical approach allowed discovery of dynamic processes involved during AML development and, if translated to humans, has the potential to predict an individual's disease trajectory.
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4.
笑对人生
(2022-03-21 23:28):
#paper Transcriptional census of epithelial-mesenchymal plasticity in cancer. Sci Adv. 2022 Jan 7;8(1):eabi7640. doi: 10.1126/sciadv.abi7640
细胞的上皮间充质可塑性是指细胞具有在上皮细胞和间充质细胞两种细胞形态相互转化的能力,它描述的是细胞对周围复杂微环境做出响应后的一种动态混合形态。EMP包含两种重要的进程,分别为EMT和MET,其中EMT与原发灶肿瘤细胞远端转移和肿瘤细胞干性等相关,而MET与肿瘤细胞在转移病灶定植有关。该篇文章首先对17项已发表研究的单细胞转录组测序数据进行收集,涉及8种类型的癌种,总共266份肿瘤组织样本,223,501个细胞。接着利用这些数据对已报道的328个与EMP相关的基因进行重新定义,最终筛选到含有128个基因的基因集,并以此构建一个肿瘤细胞特异的EMP signature。同时也发现EMP是瘤内异质性发生的来源之一,并有高度的环境依赖性。利用TCGA的泛癌RNAseq数据发现EMP sigature的激活与更短EPI(无进展时间)相关,以及更强免疫抑制微环境相关。最后,作者还探究这个EMP的互作转录因子、MEK抑制剂和TGF-βR1抑制剂的关系。整篇文章属于纯数据挖掘,但没有高深的公式和构建机器学习模型,纯粹是基于生物学原理的逻辑进行推导和探究,具有一定的借鉴意义。
Abstract:
Epithelial-mesenchymal plasticity (EMP) contributes to tumor progression, promoting therapy resistance and immune cell evasion. Definitive molecular features of this plasticity have largely remained elusive due to the limited scale of …
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Epithelial-mesenchymal plasticity (EMP) contributes to tumor progression, promoting therapy resistance and immune cell evasion. Definitive molecular features of this plasticity have largely remained elusive due to the limited scale of most studies. Leveraging single-cell RNA sequencing data from 266 tumors spanning eight different cancer types, we identify expression patterns associated with intratumoral EMP. Integrative analysis of these programs confirmed a high degree of diversity among tumors. These diverse programs are associated with combinations of various common regulatory mechanisms initiated from cues within the tumor microenvironment. We show that inferring regulatory features can inform effective therapeutics to restrict EMP.
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5.
ShanShan
(2022-02-28 18:07):
#paper title: SKP1 drives the prophase I to metaphase I transition during male meiosis
#link:https://pubmed.ncbi.nlm.nih.gov/32232159/
#doi:10.1126/sciadv.aaz2129 Sci Adv, 2020;
作者:该研究由美国宾夕法尼亚大学 Jeremy Wang 教授和武汉大学 罗孟成 教授合作完成(宾夕法尼亚大学博士后关永娟为第一作者)。
导读:研究发现SKP1位于减数分裂染色体联会区域,敲除SKP1导致雌雄小鼠均不育,粗线期染色体提前解离,无法进入减数分裂中期。进一步采用冈田酸处理,粗线期染色体仍然无法进入中期,这表明SKP1是减数分裂染色体获得进入中期能力所必须的一个调控因子。
研究亮点:①利用生殖细胞特异性Ddx4 cre 将SKP1敲除时发现雄性小鼠和雌性小鼠都不育;
②SKP1敲除小鼠模型是目前唯一一个具有提前解联会表型的小鼠模型
Abstract:
The meiotic prophase I to metaphase I (PI/MI) transition requires chromosome desynapsis and metaphase competence acquisition. However, control of these major meiotic events is poorly understood. Here, we identify an …
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The meiotic prophase I to metaphase I (PI/MI) transition requires chromosome desynapsis and metaphase competence acquisition. However, control of these major meiotic events is poorly understood. Here, we identify an essential role for SKP1, a core subunit of the SKP1-Cullin-F-box (SCF) ubiquitin E3 ligase, in the PI/MI transition. SKP1 localizes to synapsed chromosome axes and evicts HORMAD proteins from these regions in meiotic spermatocytes. SKP1-deficient spermatocytes display premature desynapsis, precocious pachytene exit, loss of PLK1 and BUB1 at centromeres, but persistence of HORMAD, γH2AX, RPA2, and MLH1 in diplonema. Strikingly, SKP1-deficient spermatocytes show sharply reduced MPF activity and fail to enter MI despite treatment with okadaic acid. SKP1-deficient oocytes exhibit desynapsis, chromosome misalignment, and progressive postnatal loss. Therefore, SKP1 maintains synapsis in meiosis of both sexes. Furthermore, our results support a model where SKP1 functions as the long-sought intrinsic metaphase competence factor to orchestrate MI entry during male meiosis.
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