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401.
muton (2023-05-31 22:39):
# paper:Challenging the Classical View: Recognition of Identity and Expression as Integrated Processes. https://doi.org/10.3390/ brainsci13020296 最近神经影像学的证据挑战了以往关于人脸信息特征和面部表情由不同神经通路分别加工处理的经典观点,而是认为身份和表情的信息在共同的脑区被编码。作者基于这一背景利用深度卷积神经网络分别对面孔身份和面孔表情的数据集进行了训练,结果发现各自训练后的神经网络不仅可以分别很好的解码身份/表情,同时对于解码未训练过的表情/身份时也有较好的表现。这一结果验证了上述假设。
IF:2.700Q3 Brain sciences, 2023-Feb-10. DOI: 10.3390/brainsci13020296 PMID: 36831839
Abstract:
Recent neuroimaging evidence challenges the classical view that face identity and facial expression are processed by segregated neural pathways, showing that information about identity and expression are encoded within common … >>>
Recent neuroimaging evidence challenges the classical view that face identity and facial expression are processed by segregated neural pathways, showing that information about identity and expression are encoded within common brain regions. This article tests the hypothesis that integrated representations of identity and expression arise spontaneously within deep neural networks. A subset of the CelebA dataset is used to train a deep convolutional neural network (DCNN) to label face identity (chance = 0.06%, accuracy = 26.5%), and the FER2013 dataset is used to train a DCNN to label facial expression (chance = 14.2%, accuracy = 63.5%). The identity-trained and expression-trained networks each successfully transfer to labeling both face identity and facial expression on the Karolinska Directed Emotional Faces dataset. This study demonstrates that DCNNs trained to recognize face identity and DCNNs trained to recognize facial expression spontaneously develop representations of facial expression and face identity, respectively. Furthermore, a congruence coefficient analysis reveals that features distinguishing between identities and features distinguishing between expressions become increasingly orthogonal from layer to layer, suggesting that deep neural networks disentangle representational subspaces corresponding to different sources. <<<
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402.
(2023-05-31 22:30):
#paper Short communication: Dietary bovine milk–derived exosomes improve bone health in an osteoporosis-induced mouse model.DOI: 10.3168/jds.2019-17501. Yun等研究了牛初乳来源的外泌体在体外和体内是否可以促进抗骨质疏松症。抗酒石酸酸性磷酸酶染色的细胞在用外泌体处理过的Raw264.7细胞中受到了显著抑制,这表明破骨细胞的分化减少。口服给予外泌体2个月后,使用糖皮质激素颗粒诱发小鼠的骨质疏松症。与未经外泌体处理的糖皮质激素诱导的骨质疏松实验组相比,外泌体处理的小鼠实验组的骨矿物质密度显著提高。此外,骨质疏松症小鼠的肠道菌群中乳酸杆菌含量降低,但是通过摄入外泌体可以有效地恢复肠道菌群的组成。结果表明,从牛初乳中分离出的外泌体可能是预防骨质疏松症、改善骨重塑和抑制骨吸收的潜在候选物。牛初乳外泌体可以用作预防骨质疏松症的发作。
IF:3.700Q2 Journal of dairy science, 2020-Sep. DOI: 10.3168/jds.2019-17501 PMID: 32622594
Abstract:
Osteoporosis is a systemic skeletal disease characterized by low bone mass and micro-architectural deterioration of bone tissue, with a consequent increase in bone fragility and fracture susceptibility. In an aged … >>>
Osteoporosis is a systemic skeletal disease characterized by low bone mass and micro-architectural deterioration of bone tissue, with a consequent increase in bone fragility and fracture susceptibility. In an aged society with increased life expectancy, the incidence rate of osteoporosis is also rapidly increasing. Inadequate nutrition may negatively influence bone metabolism. Recently, many studies have investigated the functionality of milk-derived exosomes, which play important roles in cell-to-cell communication. However, there are few reports of how milk-derived exosomes influence osteoblast proliferation and differentiation. Here, we determined whether bovine colostrum-derived exosomes promote anti-osteoporosis in vitro and in vivo. Tartrate-resistant acid phosphatase-stained cells were significantly inhibited in Raw264.7 cells treated with exosomes, indicating reduced osteoclast differentiation. We induced osteoporosis in mice using glucocorticoid pellets after orally administering exosomes for 2 mo. Interestingly, the bone mineral density of exosome-fed mouse groups was significantly improved compared with the glucocorticoid-induced osteoporosis group without exosome treatment. In addition, Lactobacillus were decreased in the gut microbiota community of osteoporosis-induced mice, but the gut microbiota community composition was effectively restored by exosome intake. Taken together, we propose that exosomes isolated from bovine colostrum could be a potential candidate for osteoporosis prevention, bone remodeling improvement, and inhibition of bone resorption. To our knowledge, this is the first time that a protective effect of milk exosomes against osteoporosis has been demonstrated in vivo. Our results strongly suggest that bovine colostrum exosomes might be used as a prophylaxis to prevent the onset of osteoporosis. Indeed, our results offer promising alternative strategies in the nutritional management of age-related bone complications. <<<
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403.
周周复始 (2023-05-31 22:29):
#paper doi:https://doi.org/10.48550/arXiv.2201.00308. DiffuseVAE: Efficient, Controllable and High-Fidelity Generation from Low-Dimensional Latents.2022.目前扩散概率模型在几个有竞争性图像合成基准上产生最先进的结果,但缺乏低维、可解释的潜在空间,并且生成速度较慢。而变分自编码器(VAEs)通常具有低维潜在空间,但生成的样本质量较差。基于此本文提出了一种新的生成框架DiffuseVAE,它将VAE集成到扩散模型框架中,并利用它为扩散模型设计新的条件参数化。文章表明,所得到的模型为扩散模型配备了低维VAE推断潜在代码,可用于下游任务,如条件生成。
Abstract:
Diffusion probabilistic models have been shown to generate state-of-the-art results on several competitive image synthesis benchmarks but lack a low-dimensional, interpretable latent space, and are slow at generation. On the … >>>
Diffusion probabilistic models have been shown to generate state-of-the-art results on several competitive image synthesis benchmarks but lack a low-dimensional, interpretable latent space, and are slow at generation. On the other hand, standard Variational Autoencoders (VAEs) typically have access to a low-dimensional latent space but exhibit poor sample quality. We present DiffuseVAE, a novel generative framework that integrates VAE within a diffusion model framework, and leverage this to design novel conditional parameterizations for diffusion models. We show that the resulting model equips diffusion models with a low-dimensional VAE inferred latent code which can be used for downstream tasks like controllable synthesis. The proposed method also improves upon the speed vs quality tradeoff exhibited in standard unconditional DDPM/DDIM models (for instance, FID of 16.47 vs 34.36 using a standard DDIM on the CelebA-HQ-128 benchmark using T=10 reverse process steps) without having explicitly trained for such an objective. Furthermore, the proposed model exhibits synthesis quality comparable to state-of-the-art models on standard image synthesis benchmarks like CIFAR-10 and CelebA-64 while outperforming most existing VAE-based methods. Lastly, we show that the proposed method exhibits inherent generalization to different types of noise in the conditioning signal. For reproducibility, our source code is publicly available at this https URL. <<<
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404.
张贝 (2023-05-31 22:23):
#paper Int J Med Inform. 2019 Oct;130:103940.  doi: 10.1016/j.ijmedinf.2019.07.019.Clinical decision support for therapeutic decision-making in cancer: A systematic review  包括支持性护理在内的癌症管理较为复杂,需要根据已发表的以及患者特异性数据做出适当的治疗决策。临床决策支持(CDS)或许是支持复杂决策的有效实施策略,尽管CDS是否能够改善治疗结局和患者结局尚不明确。因此,本文对CDS进行了系统回顾,以确定CDS用于支持临床癌症治疗决策。令人关注的结果包括CDS对诊疗过程的影响。10项研究符合纳入标准,研究设计、设置和干预存在差异。在衡量过程结局的九项研究中,有五项显示出显著的改善;在衡量患者结局的六项中,有四项显示出显著改善。所有纳入的研究都使用了临床实践指南提及的CDS。总之,CDS用于指导癌症治疗决策是一个尚待研究但很有前景的领域。
Abstract:
Cancer management, including supportive care, is complex and requires availability and synthesis of published and patient-specific data to make appropriate therapeutic decisions. Clinical decision support (CDS) may be an effective … >>>
Cancer management, including supportive care, is complex and requires availability and synthesis of published and patient-specific data to make appropriate therapeutic decisions. Clinical decision support (CDS) may be an effective implementation strategy to support complex decision making although it is unclear whether it improves process outcomes, patient outcomes or both in cancer settings. We therefore conducted a systematic review to identify CDS that have been used to support therapeutic decision making in clinical cancer settings. Outcomes of interest included the effect of CDS on the process, such as clinician's decision making and effect on patient outcomes. Ten studies met inclusion criteria, with variability in the study design, setting, and intervention. Of the nine studies that measured process outcomes, five demonstrated significant improvement; and of the six that measured patient outcomes, four demonstrated significant improvement. All included studies utilized CDS that were informed by clinical practice guidelines. In conclusion, CDS to guide cancer therapeutic decision making is an understudied but promising area. Further research is needed. <<<
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405.
尹志 (2023-05-31 22:12):
#paper doi: https://doi.org/10.1016/j.drudis.2021.05.019 Drug Discovery Today, 2021, De novo molecular design and generative models. 文章是来自业界的Benevolent AI写的,对从头的分子设计进行了综述。主要从颗粒度的角度进行 了分类,讨论了atom based, fragment based, reaction based三种不同的分子表示的视角下分子设计的方法。对于分子设计中的优化方法,文章分为无梯度和基于梯度的方法进行讨论,前者主要集中在演化算法和群体智能算法,而后者则是目前基于深度生成模型的主流。文章还强调了该领域建立合适评价标准和benchmark的重要性,不过考虑到分子设计务实的属性,这里还有非常多亟待解决的问题。文章的总结的思路很清楚,但是这个领域的发展实在是太快太快,因此2021年的综述显然是太老了,最近几年基于各种深度生成模型的分子设计很多已经相当实用化,还是建议大家看最新的文章,当然这篇综述还是可以当做一条不错的线索的。
Abstract:
Molecular design strategies are integral to therapeutic progress in drug discovery. Computational approaches for de novo molecular design have been developed over the past three decades and, recently, thanks in … >>>
Molecular design strategies are integral to therapeutic progress in drug discovery. Computational approaches for de novo molecular design have been developed over the past three decades and, recently, thanks in part to advances in machine learning (ML) and artificial intelligence (AI), the drug discovery field has gained practical experience. Here, we review these learnings and present de novo approaches according to the coarseness of their molecular representation: that is, whether molecular design is modeled on an atom-based, fragment-based, or reaction-based paradigm. Furthermore, we emphasize the value of strong benchmarks, describe the main challenges to using these methods in practice, and provide a viewpoint on further opportunities for exploration and challenges to be tackled in the upcoming years. <<<
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406.
大勇 (2023-05-31 22:11):
#paper doi: https://doi.org/10.1038/s41586-022-05443-0 Kim, R., Hashimoto, A., Markosyan, N. et al. Ferroptosis of tumour neutrophils causes immune suppression in cancer. Nature 612, 338–346 (2022). 该文章主要是对肿瘤相关中性粒,也叫做髓源性抑制细胞(PMN-MDSC)在抗肿瘤免疫中的作用进行了研究,PMN-MDSC中所产生的铁死亡相关脂质代谢产物,可以通过抑制T细胞等的增殖从而抑制肿瘤进展和免疫检查点抑制剂治疗疗效。
IF:50.500Q1 Nature, 2022-12. DOI: 10.1038/s41586-022-05443-0 PMID: 36385526
Abstract:
Ferroptosis is a non-apoptotic form of regulated cell death that is triggered by the discoordination of regulatory redox mechanisms culminating in massive peroxidation of polyunsaturated phospholipids. Ferroptosis inducers have shown … >>>
Ferroptosis is a non-apoptotic form of regulated cell death that is triggered by the discoordination of regulatory redox mechanisms culminating in massive peroxidation of polyunsaturated phospholipids. Ferroptosis inducers have shown considerable effectiveness in killing tumour cells in vitro, yet there has been no obvious success in experimental animal models, with the notable exception of immunodeficient mice. This suggests that the effect of ferroptosis on immune cells remains poorly understood. Pathologically activated neutrophils (PMNs), termed myeloid-derived suppressor cells (PMN-MDSCs), are major negative regulators of anti-tumour immunity. Here we found that PMN-MDSCs in the tumour microenvironment spontaneously die by ferroptosis. Although decreasing the presence of PMN-MDSCs, ferroptosis induces the release of oxygenated lipids and limits the activity of human and mouse T cells. In immunocompetent mice, genetic and pharmacological inhibition of ferroptosis abrogates suppressive activity of PMN-MDSCs, reduces tumour progression and synergizes with immune checkpoint blockade to suppress the tumour growth. By contrast, induction of ferroptosis in immunocompetent mice promotes tumour growth. Thus, ferroptosis is a unique and targetable immunosuppressive mechanism of PMN-MDSCs in the tumour microenvironment that can be pharmacologically modulated to limit tumour progression. <<<
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407.
哪有情可长 (2023-05-31 21:59):
#paper doi.org/10.1007/s42994-023-00095-8 Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development,最近在学习ATAC-seq数据分析,想利用别人已经发表的数据对自己的文章能够更深入。该作者对小麦籽粒5,9,15,20天的小麦籽粒发育阶段的构建了全基因组染色质开放图谱以及基因表达图谱,并对小麦籽粒发育中关键转录因子的调控网络进行了解析,揭示了小麦籽粒发育中亚基因组的分化调控,同时发掘了共调控淀粉与蛋白合成的转录因子。
IF:4.600Q1 aBIOTECH, 2023-Mar. DOI: 10.1007/s42994-023-00095-8 PMID: 37220536
Abstract:
Development of wheat ( L) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network … >>>
Development of wheat ( L) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions, and the proportion of distal ACRs was increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed light on the improvement of wheat yields and qualities. <<<
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408.
庞庞 (2023-05-31 16:12):
#paper doi:https://doi.org/10.1038/s41591-023-02317-4 A shared neural basis underlying psychiatric comorbidity 之前对于精神疾病共病程度,通常使用p因子衡量。但是,这种指标通过临床评分得到,和共病的神经底物、基因都没有关联。对此,作者提出了一种新的神经生物学的跨疾病精神因子:NP因子。作者通过将与多种精神疾病得分显著相关的脑网络连接进行并集,并筛除掉在纵向数据上不稳定的连接,从而获得NP因子。他们同时证明了,NP因子与神经解剖位置、行为以及基因的关系。最后,NP因子可以泛化到其他类型的数据集上,这对以后的精神疾病的干预提供了帮助。
IF:58.700Q1 Nature medicine, 2023-05. DOI: 10.1038/s41591-023-02317-4 PMID: 37095248
Abstract:
Recent studies proposed a general psychopathology factor underlying common comorbidities among psychiatric disorders. However, its neurobiological mechanisms and generalizability remain elusive. In this study, we used a large longitudinal neuroimaging … >>>
Recent studies proposed a general psychopathology factor underlying common comorbidities among psychiatric disorders. However, its neurobiological mechanisms and generalizability remain elusive. In this study, we used a large longitudinal neuroimaging cohort from adolescence to young adulthood (IMAGEN) to define a neuropsychopathological (NP) factor across externalizing and internalizing symptoms using multitask connectomes. We demonstrate that this NP factor might represent a unified, genetically determined, delayed development of the prefrontal cortex that further leads to poor executive function. We also show this NP factor to be reproducible in multiple developmental periods, from preadolescence to early adulthood, and generalizable to the resting-state connectome and clinical samples (the ADHD-200 Sample and the Stratify Project). In conclusion, we identify a reproducible and general neural basis underlying symptoms of multiple mental health disorders, bridging multidimensional evidence from behavioral, neuroimaging and genetic substrates. These findings may help to develop new therapeutic interventions for psychiatric comorbidities. <<<
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409.
Vincent (2023-05-31 13:56):
#paper doi: https://doi.org/10.1111/j.1467-9868.2008.00674.x Journal of he Royal Statistical Society, 2008, Sure independence screening for ultrahighdimensional feature space. 高维数据往往面临着两大难题,参数估计的准确性和计算负担。先前的方法(Dantzig selector)在处理极高维数据(log p > n)时还是不够有效,这篇文章提出了一种基于相关性学习的特征筛选方法,能够将数据从极高维降到的合适的维度(小于n)。文章展示了在十分普遍的渐进框架下,相关性学习有可靠的筛选性能。同时作为该方法的扩展,文章还提出了一种迭代式的特征筛选,能够在有限数据量的情况下,提高筛选的准确性。此外当使用该方法把高维数据降低到低维之后,其他变量选择的方法例如lasso等也可以被运用进来,从而实现更准确和更快速的变量选择。
Abstract:
SummaryVariable selection plays an important role in high dimensional statistical modelling which nowadays appears in many areas and is key to various scientific discoveries. For problems of large scale or … >>>
SummaryVariable selection plays an important role in high dimensional statistical modelling which nowadays appears in many areas and is key to various scientific discoveries. For problems of large scale or dimensionality p, accuracy of estimation and computational cost are two top concerns. Recently, Candes and Tao have proposed the Dantzig selector using L1-regularization and showed that it achieves the ideal risk up to a logarithmic factor log(p). Their innovative procedure and remarkable result are challenged when the dimensionality is ultrahigh as the factor log(p) can be large and their uniform uncertainty principle can fail. Motivated by these concerns, we introduce the concept of sure screening and propose a sure screening method that is based on correlation learning, called sure independence screening, to reduce dimensionality from high to a moderate scale that is below the sample size. In a fairly general asymptotic framework, correlation learning is shown to have the sure screening property for even exponentially growing dimensionality. As a methodological extension, iterative sure independence screening is also proposed to enhance its finite sample performance. With dimension reduced accurately from high to below sample size, variable selection can be improved on both speed and accuracy, and can then be accomplished by a well-developed method such as smoothly clipped absolute deviation, the Dantzig selector, lasso or adaptive lasso. The connections between these penalized least squares methods are also elucidated. <<<
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410.
James (2023-05-30 15:22):
#paper doi: 10.1007/s00125-023-05930-7. Prediabetes, intervening diabetes and subsequent risk of dementia: the Atherosclerosis Risk in Communities (ARIC) study 这项研究主要是评估糖尿病前期与痴呆症的关联是否可以通过干预糖尿病的发作来解释。在社区动脉粥样硬化风险 (ARIC) 研究的参与者中,作者将基线糖尿病前期定义为 HbA1c 39-46 mmol/mol (5.7-6.4%),并将随后发生的糖尿病定义为自我报告的医生诊断或使用糖尿病药物并通过主动监测和确定是否患有痴呆。 作者对糖尿病与痴呆风险之间的关联进行了量化并评估了糖尿病诊断时的年龄是否改变了痴呆症的风险。结果表明糖尿病前期与痴呆症风险相关联,风险可以用随后发生的糖尿病来解释。 较早患糖尿病会大大增加痴呆症的风险。 预防或延缓前驱糖尿病向糖尿病的进展将减轻痴呆负担。
IF:8.400Q1 Diabetologia, 2023-08. DOI: 10.1007/s00125-023-05930-7 PMID: 37221246
Abstract:
AIMS/HYPOTHESIS: The aim of this work was to evaluate whether the association of prediabetes with dementia is explained by the intervening onset of diabetes.METHODS: Among participants of the Atherosclerosis Risk … >>>
AIMS/HYPOTHESIS: The aim of this work was to evaluate whether the association of prediabetes with dementia is explained by the intervening onset of diabetes.METHODS: Among participants of the Atherosclerosis Risk in Communities (ARIC) study we defined baseline prediabetes as HbA1c 39-46 mmol/mol (5.7-6.4%) and subsequent incident diabetes as a self-reported physician diagnosis or use of diabetes medication. Incident dementia was ascertained via active surveillance and adjudicated. We quantified the association of prediabetes with dementia risk before and after accounting for the subsequent development of diabetes among ARIC participants without diabetes at baseline (1990-1992; participants aged 46-70 years). We also evaluated whether age at diabetes diagnosis modified the risk of dementia.RESULTS: Among 11,656 participants without diabetes at baseline, 2330 (20.0%) had prediabetes. Before accounting for incident diabetes, prediabetes was significantly associated with the risk of dementia (HR 1.12 [95% CI 1.01, 1.24]). After accounting for incident diabetes, the association was attenuated and non-significant (HR 1.05 [95% CI 0.94, 1.16]). Earlier age of onset of diabetes had the strongest association with dementia: HR 2.92 (95% CI 2.06, 4.14) for onset before 60 years; HR 1.73 (95% CI 1.47, 2.04) for onset at 60-69 years; and HR 1.23 (95% CI 1.08, 1.40) for onset at 70-79 years.CONCLUSIONS/INTERPRETATION: Prediabetes is associated with dementia risk but this risk is explained by the subsequent development of diabetes. Earlier age of onset of diabetes substantially increases dementia risk. Preventing or delaying progression of prediabetes to diabetes will reduce dementia burden. <<<
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411.
张浩彬 (2023-05-30 11:48):
#paper:doi:10.48550/arXiv.2010.04515 Principal Component Analysis using Frequency Components of Multivariate Time Series 提出了一个新的谱分解方法,使得对多元时间序列(二阶平稳,宽平稳)进行分解,从而使得分解后的子序列在组内是有非零的谱相关,而跨组的子序列则具有零的谱相关性。从写作上,则是典型的问题引入,方法介绍、理论的渐近性质证明,数值模拟,实证研究,其中有大量的推导。
Abstract:
Dimension reduction techniques for multivariate time series decompose the observed series into a few useful independent/orthogonal univariate components. We develop a spectral domain method for multivariate second-order stationary time series … >>>
Dimension reduction techniques for multivariate time series decompose the observed series into a few useful independent/orthogonal univariate components. We develop a spectral domain method for multivariate second-order stationary time series that linearly transforms the observed series into several groups of lower-dimensional multivariate subseries. These multivariate subseries have non-zero spectral coherence among components within a group but have zero spectral coherence among components across groups. The observed series is expressed as a sum of frequency components whose variances are proportional to the spectral matrices at the respective frequencies. The demixing matrix is then estimated using an eigendecomposition on the sum of the variance matrices of these frequency components and its asymptotic properties are derived. Finally, a consistent test on the cross-spectrum of pairs of components is used to find the desired segmentation into the lower-dimensional subseries. The numerical performance of the proposed method is illustrated through simulation examples and an application to modeling and forecasting wind data is presented. <<<
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412.
白鸟 (2023-05-30 09:20):
#paper https://doi.org/10.1093/nar/gkaa1027 Open Targets Platform: supporting systematic drug–target identification and prioritisation 1.靶标-疾病知识库: (1)20 个不同数据源的靶标-疾病关系的证据; (2)关键数据集的新证据:全基因组CRISPR敲除筛选数据, GWAS/UK BioBank统计遗传分析证据; (3)已知药物不良信息:上市后药物不良反应的评估,以及有关靶标成药性和安全性的新精选信息; 2.改进证据评分: 改进了证据评分框架以改进靶标识别 3.Open Targets平台开发: 更新10个版本,开发了用户界面和后端技术以提高性能和可用性
IF:16.600Q1 Nucleic acids research, 2021-01-08. DOI: 10.1093/nar/gkaa1027 PMID: 33196847
Abstract:
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is … >>>
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target-disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive. <<<
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413.
白鸟 (2023-05-30 09:12):
#paper doi:10.1016/j.cell.2022.02.015 Spatial CRISPR genomics identifies regulators of the tumor microenvironment 这篇文章主要包含两个方面: 1.空间CRISPR技术的开发:“Perturb-map”技术,原位CRISPR+多重成像+空间转录组学,该技术是基础作者2018年cell发表的三联体蛋白条形码Pro-Codes单细胞CRISPR技术。三联体蛋白提高并行敲除基因的数目,另外,nPC荧光蛋白标签定位在细胞核中,通过图像分割软件能很好的分割单细胞。 2.空间CRISPR技术的应用:作者通过空间CRISPR技术研究每个基因敲除后如何影响肿瘤生长、组织病理学和免疫组成。并行敲除32个跟免疫治疗相关的靶基因(包括细胞因子,免疫配体和分泌因子),研究肿瘤细胞对免疫细胞招募和排斥的影响。癌细胞的基因如何控制免疫微环境,这有助于开发新的癌症免疫疗法。 文章对于4T1乳腺和KP肺部肿瘤进行研究,他观察到肺癌具有克隆型分布,每个KP肿瘤病变都由单个KP癌细胞形成。敲除单个基因的细胞扎堆分布,也非常适合后续的免疫分析。文章主要对肺癌研究,但是为什么肺癌细胞会克隆型分布,文章没有具体说明。 3.空间CRISPR技术的延伸:很多癌症如4T1乳腺,单基因敲除的肿瘤细胞分布高度不均匀,也不适合空间CRISPR技术的研究。文章2022年发表,后续没有找到相关的研究课题和文章引用。感觉还是有一定的局限性。
IF:45.500Q1 Cell, 2022-03-31. DOI: 10.1016/j.cell.2022.02.015 PMID: 35290801 PMCID:PMC8992964
Abstract:
While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach … >>>
While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomics within the tissue at single-cell resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME. <<<
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414.
Spring (2023-05-30 02:29):
#paperdoi: 10.1038/s41591-023-02324-5 ① 纳入348名原发性癌症患者的新鲜冷冻样本进行全面的基因组分析;② 捕捉到克隆扩增、肿瘤富集的T细胞克隆的存在,并优于传统的预后分子生物标志物,如一致分子亚型和微卫星不稳定性分类;③ 基因免疫编辑的量化,定义为新抗原数量低于预期,进一步提高了其预后价值;④ 瘤内瘤胃球菌2和MBR评分彼此密切相关,发现了由瘤胃球菌驱动的微生物组特征溴化物,与有利结果相关;⑤ 开发并验证了一种复合评分,该评分可确定一组具有良好生存概率的患者。 An integrated tumor, immune and microbiome atlas of colon cancer 05-19
IF:58.700Q1 Nature medicine, 2023-05. DOI: 10.1038/s41591-023-02324-5 PMID: 37202560
Abstract:
The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen … >>>
The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches. <<<
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415.
钟鸣 (2023-05-30 00:39):
#paper doi:10.2147/CCID.S247390 Asian Hair: A Review of Structures, Properties, and Distinctive Disorders 这是一篇讲头发(发质)的综述,重点是亚洲人的发质。作者首先对比了亚欧非人种头发的各项指标特性,包括生长速度、头发密度、硬度刚性韧性等。随后简单介绍了头发的物理结构,为后文的介绍做了铺垫。后文中大致介绍了亚洲人发质特性的成因,主要归结于正选择下的基因变异,即EDAR基因。最后作者还介绍了在亚洲人中更高发的毛发疾病,包括困扰当下年轻人的脱发和毛囊炎等疾病。
Abstract:
Asian hair is known for its straightness, dark pigmentation, and large diameter. The cuticle layer in Asians is thicker with more compact cuticle cells than that in Caucasians. Asian hair … >>>
Asian hair is known for its straightness, dark pigmentation, and large diameter. The cuticle layer in Asians is thicker with more compact cuticle cells than that in Caucasians. Asian hair generally exhibits the strongest mechanical properties, and its cross-sectional area is determined greatly by genetic variations, particularly from the gene. However, knowledge on Asian hair remains unclear with limited studies. This article aimed to review and summarize the characteristics and properties of Asian hair. It also aimed to discuss hair disorders including linear lupus panniculitis and pseudocyst of the scalp that occur distinctively in Asian populations. <<<
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416.
李翛然 (2023-05-29 22:06):
#paper doi:https://doi.org/10.1016/j.eng.2023.01.014 Artificial Intelligence in Pharmaceutical Sciences 这篇文章是国内几个大学发表在 engineer的综述文章,我的评价就是对于想进入AI制药领域的来说,是一个对于历史的很好总结,不过对于未来的展望,明显还是功力不足。 是一个纯外行的角度,在看制药行业的发展,明显没有深入制药领域并结合AI来进行分析。 这篇文章大家可以作为一个入门文章看一看。
IF:10.100Q1 Engineering, 2023. DOI: 10.1016/j.eng.2023.01.014
Abstract:
Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market. However, investments in a new drug often go unrewarded due to the long and … >>>
Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market. However, investments in a new drug often go unrewarded due to the long and complex process of drug research and development (R&D). With the advancement of experimental technology and computer hardware, artificial intelligence (AI) has recently emerged as a leading tool in analyzing abundant and high-dimensional data. Explosive growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&D. Driven by big data in biomedicine, AI has led to a revolution in drug R&D, due to its ability to discover new drugs more efficiently and at lower cost. This review begins with a brief overview of common AI models in the field of drug discovery; then, it summarizes and discusses in depth their specific applications in various stages of drug R&D, such as target discovery, drug discovery and design, preclinical research, automated drug synthesis, and influences in the pharmaceutical market. Finally, the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed. <<<
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417.
惊鸿 (2023-05-29 09:56):
#paper Date  : 2023-05-05 DOI : 10.1021/acssynbio.3c00216 Immortalized Bovine Satellite Cells for Cultured Meat Applications该论文提到,为了使培养肉在规模上成功,食用相关物种的肌肉细胞必须在体外快速可靠地扩展,从而每年生产数百万吨的生物量。基因不老化的细胞比原代细胞具有显着的优势,包括快速增长、逃避细胞衰老和始终一致的起始细胞群体生产。因此,研究人员通过持续表达牛端粒酶逆转录酶(TERT)和Cyclin-dependent kinase 4(CDK4)开发了基因不老化的牛卫星细胞(iBSCs)。这些细胞在发布时已经实现了超过120倍增殖,并保持了其肌肉分化能力。因此,它们为这一领域提供了有价值的工具,可以进一步推动培养肉的研究和开发。
IF:3.700Q1 ACS synthetic biology, 2023-05-19. DOI: 10.1021/acssynbio.3c00216 PMID: 37146268
Abstract:
For cultured meat to succeed at scale, muscle cells from food-relevant species must be expanded in vitro in a rapid and reliable manner to produce millions of metric tons of … >>>
For cultured meat to succeed at scale, muscle cells from food-relevant species must be expanded in vitro in a rapid and reliable manner to produce millions of metric tons of biomass annually. Toward this goal, genetically immortalized cells offer substantial benefits over primary cells, including rapid growth, escape from cellular senescence, and consistent starting cell populations for production. Here, we develop genetically immortalized bovine satellite cells (iBSCs) via constitutive expression of bovine Telomerase reverse transcriptase (TERT) and Cyclin-dependent kinase 4 (CDK4). These cells achieve over 120 doublings at the time of publication and maintain their capacity for myogenic differentiation. They therefore offer a valuable tool to the field, enabling further research and development to advance cultured meat. <<<
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418.
DeDe宝 (2023-05-29 09:31):
#paper doi: 10.1371/journal.pbio.3002056 PLOS Biology, 2023, Feature-specific reactivations of pastinformation shift current neural encoding thereby mediating serial bias behaviors。serial bias是知觉领域的一个重要现象,该现象表明当前实验试次的感知决策受到前几个试次的影响并产生系统偏差。但是,当前感知决策是受到之前试次的什么信息影响,是之前的刺激、之前的类别决策还是之前的运动反应?这一直处于长期争论中。本研究的行为分析和脑电信号分析揭示了序列依赖效应的动态神经机制。首先,当前试次的脑电活动中能解码当前试次的信息(预料之中)。但最为有趣的是,当前的事件发生会自动激发过去试次的相应特征信息:音调信息激发过去试次的音调,类别信息激发过去试次的类别,运动响应激活过去试次的运动反应(图2)。值得注意的是,过去试次包含的信息因为已经发生,理论上是可以一直处于激活状态的,然而研究结果表明,它们会潜入记忆的“静默态”,直到被当前试次的相应事件所重新激活。
IF:7.800Q1 PLoS biology, 2023-03. DOI: 10.1371/journal.pbio.3002056 PMID: 36961821
Abstract:
The regularities of the world render an intricate interplay between past and present. Even across independent trials, current-trial perception can be automatically shifted by preceding trials, namely the "serial bias." … >>>
The regularities of the world render an intricate interplay between past and present. Even across independent trials, current-trial perception can be automatically shifted by preceding trials, namely the "serial bias." Meanwhile, the neural implementation of the spontaneous shift of present by past that operates on multiple features remains unknown. In two auditory categorization experiments with human electrophysiological recordings, we demonstrate that serial bias arises from the co-occurrence of past-trial neural reactivation and the neural encoding of current-trial features. The meeting of past and present shifts the neural representation of current-trial features and modulates serial bias behavior. Critically, past-trial features (i.e., pitch, category choice, motor response) keep their respective identities in memory and are only reactivated by the corresponding features in the current trial, giving rise to dissociated feature-specific serial biases. The feature-specific automatic reactivation might constitute a fundamental mechanism for adaptive past-to-present generalizations over multiple features. <<<
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419.
徐炳祥 (2023-05-29 09:11):
#paper doi: 10.1073/pnas.2023347118 PNAS, 2021, DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis。DNA甲基化是重要的表观遗传调控维度,CpG岛甲基化水平的改变对基因表达起了重要的调控作用。然而DNA甲基化和表观遗传的其他维度之间的关系研究尚十分缺乏。本文通过对具有不同DNA甲基转移酶活性的拟南芥品系进行染色质开放性图谱和染色质空间构象图谱的测定和比较,对此问题进行了研究。结果显示,低DNA甲基化确实与染色质开放和染色质区室从B向A的转换有关。该研究是目前仅有的几项DNA甲基化与染色质空间构象直接关联的研究,但不同品系的相互比较仍不能说明二者之间是否以及具有何种因果关系。
Abstract:
DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains … >>>
DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. Here, we present genome-wide chromatin accessibility profiles of 18 mutants that are deficient in CG, CHG, or CHH DNA methylation. We find that DNA methylation in all three sequence contexts impacts chromatin accessibility in heterochromatin. Many chromatin regions maintain inaccessibility when DNA methylation is lost in only one or two sequence contexts, and signatures of accessibility are particularly affected when DNA methylation is reduced in all contexts, suggesting an interplay between different types of DNA methylation. In addition, we found that increased chromatin accessibility was not always accompanied by increased transcription, suggesting that DNA methylation can directly impact chromatin structure by other mechanisms. We also observed that an increase in chromatin accessibility was accompanied by enhanced long-range chromatin interactions. Together, these results provide a valuable resource for chromatin architecture and DNA methylation analyses and uncover a pivotal role for methylation in the maintenance of heterochromatin inaccessibility. <<<
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420.
龙海晨 (2023-05-23 02:52):
#paper Sun M, Ji H, Xu N, Jiang P, Qu T, Li Y. Real-world data analysis of immune checkpoint inhibitors in stage III-IV adenocarcinoma and squamous cell carcinoma. BMC Cancer. 2022 Jul 13;22(1):762. doi: 10.1186/s12885-022-09843-3. PMID: 35831785; PMCID: PMC9277844. 文章对肺癌的鳞癌和腺癌患者接受免疫检查抑制治疗immune checkpoint inhibitors (ICIs)进行回顾性研究,评估ICIs的疗效和安全性。发现,ICIs对癌症患者有良好的疗效,并显著改善ORR和PFS。objective response rate (ORR) ,客观缓解率,是一种直接衡量药物抗肿瘤活性的指标,ORR反应了肿瘤药物治疗后,肿瘤缩小或被消灭的概率。无进展生存期(progression free survival,PFS)这个名词通常用在中晚期癌症,肿瘤侵犯范围比较大,或是发生转移的病人。病人的治疗目的是控制癌细胞生长不要继续恶化,改善病人的生活品质及延长生命。例如,4期肺癌病人接受标靶药物治疗,一年无进展生存期几率是30%,表示开始治疗追踪一年后,有3成的病人能够控制住肺癌。
IF:3.400Q2 BMC cancer, 2022-Jul-13. DOI: 10.1186/s12885-022-09843-3 PMID: 35831785
Abstract:
BACKGROUND: This study was designed to investigate the clinical application, efficacy, and safety of immune checkpoint inhibitors (ICIs) in the treatment of lung cancer in the real world.METHODS: A retrospective, … >>>
BACKGROUND: This study was designed to investigate the clinical application, efficacy, and safety of immune checkpoint inhibitors (ICIs) in the treatment of lung cancer in the real world.METHODS: A retrospective, observational analysis was conducted on patients treated with ICIs in four tertiary hospitals in the region from January 2015 to March 2021, to evaluate the clinical efficacy of ICIs single-agent or combined chemotherapy and anti-vascular drugs in the first-line or second-line treatment of patients with lung cancer.RESULTS: Three hundred and fifteen patients were enrolled in this study. In patients with stage III-IV adenocarcinoma and Squamous cell carcinoma, the objective response rate (ORR) and disease control rate (DCR) were 35.5% (87/245) and 93.5% (229/245), respectively, the median progression-free survival (PFS) was 10.8 months, and the median overall survival (OS) was not reached. A total of 132 patients received ICIs as the first-line treatment, the median treatment cycle was 8 cycles (2-20 cycles), the short-term efficacy ORR was 38.6%, DCR was 93.9%, and the median PFS was 11.4 months. One hundred thirteen patients received ICIs treatment as second-line treatment, the median treatment cycle was five cycles (2-10 cycles), the short-term efficacy ORR was 31.9%, DCR was 92.9%, and the median PFS was 10.0 months. There were no statistically significant differences in ORR, DCR, or median PFS with ICIs as the first-line treatment compared with the second-line treatment(P > 0.05). The results of subgroup analysis showed that Eastern Cooperative Oncology Group performance status (ECOG PS), epidermal growth factor receptor (EGFR) mutation status, pathological type and number of treatment lines were not correlated with median PFS(P > 0.05). However, there were statistically significant differences in programmed death-ligand 1(PD-L1) expression, corticosteroid interference, and antibiotic (Abx) treatment among all groups (P < 0.05). In terms of safety, the overall incidence of adverse reactions in 315 patients was 62.5%, and the incidence of immune-related adverse events (irAEs) was 13.7%. Grade 1-2 and 3-4 incidence of adverse events were 34.9 and 27.65%, respectively. There were four patients who experienced fatal irAEs, two cases were liver damage leading to liver failure, one case was immune related pneumonia, and one case was immune related myocarditis.CONCLUSION: In the real world, ICIs has a good effect on patients with lung cancer and significantly improves ORR and PFS. <<<
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