当前共找到 1276 篇文献分享,本页显示第 601 - 620 篇。
601.
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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602.
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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603.
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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604.
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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605.
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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606.
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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607.
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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608.
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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609.
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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610.
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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611.
张德祥 (2023-05-16 08:14):
#paper https://doi.org/10.48550/arXiv.2203.11740 我们可以把我们的大脑想象成是地球,地心熔岩的产生如同在海马体的短期记忆的发生,过程是量子的;地表的地震因为势能释放,选出强的短期记忆成为长期记忆存储在不同皮层的记忆印记细胞能被释放。 AI+脑科学+量子力学的结合。我们提出了PNN,但它不仅仅是简单的时间序列模型。 除了突触连接的共享权重,我们提出了新的神经网络包括突触有效范围权重也会进行前向和反向计算。而且很多仿真是RNN无法实现的。 正向和负向记忆的大脑塑性是量子的并产生短期记忆,并且波函数展现出在一段时间表现出指数衰减,在海马体里产生。而指数衰减是因为壁垒,壁垒可能和星形胶质细胞有关。工作记忆的大脑塑性在大脑流动从海马体到不同皮层通过方向导数。强的工作记忆的大脑塑性转变成长期记忆也就是最大的方向导数,而最大的方向导数就是梯度。这样长期记忆是工作记忆的大脑塑性的梯度。短期记忆变成长期记忆的过程,也就是非经典力学变成经典力学的过程。 PNN的仿真符合了6篇正刊、6篇子刊和1篇物理顶刊的脑科学实验和假设。 更多可以参考: https://mp.weixin.qq.com/s/k-KD1KcQo9FiYcQvSypBjQ
Abstract:
In addition to the shared weights of the synaptic connections, we proposed a new neural network that includes the synaptic effective range weights for both the forward and back propagation. … >>>
In addition to the shared weights of the synaptic connections, we proposed a new neural network that includes the synaptic effective range weights for both the forward and back propagation. And lots of simulations were used which RNN cannot be achieved. The simulations of PNN fit very well in experiments and hypotheses of 6 papers CNS Journals, 6 papers of CNS family Journals and 1 paper top Physics Journal [14-26]. The brain plasticity in positive or negative memory may be quantum and produce short-term memory, and exhibits an exponential decay in the wave function over a period of time, produced in the hippocampus. And exponential decay occurs due to barriers, and barriers can refer to astrocytes. Brain plasticity in working memory flows through the brain, from the hippocampus to the cortex, through directional derivatives. The strong working memory brain plasticity turns to long-term memory means maximum of directional derivatives, and maximum of directional derivatives is gradient. Thus, long-term memory signifies the gradient of brain plasticity in working memory. The process of short-term memory turns to long-term memory is the process of non-classically turns to classically. Astrocytic cortex memory persistence factor also inhibits local synaptic accumulation, and the model inspires experiments. This could be the process of astrocytes phagocytose synapses is driven by both positive and negative memories of plasticity in the brain. In simulation, it is possible that thicker cortices and more diverse individuals within the brain could have high IQ, but thickest cortices and most diverse individuals may have low IQ in simulation. PSO considers global solution or best previous solution, but also considers relatively good and relatively inferior solution. And PNN modified ResNet to consider memory gradient. The simple PNN only considers astrocytes phagocytosed synapses. <<<
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612.
姗姗来迟 (2023-05-14 19:34):
#paper Multimodal Graph Transformer for Multimodal Question Answering https://arxiv.org/abs/2305.00581 这项工作从这两个世界中受益,并提出了一种新的多模态图转换器,用于需要跨多模态执行推理的问答任务。引入了一种涉及图形的即插即用类注意机制,将从文本和视觉数据中获得的多模态图形信息作为有效的先验信息整合到vanilla自注意力中。 具体来说,文章构建文本图、密集区域图和语义图来生成邻接矩阵,然后将它们与输入的视觉和语言特征组合在一起进行下游推理。 学习笔记链接:https://blog.csdn.net/weixin_44845357/article/details/130577459?csdn_share_tail=%7B%22type%22%3A%22blog%22%2C%22rType%22%3A%22article%22%2C%22rId%22%3A%22130577459%22%2C%22source%22%3A%22weixin_44845357%22%7D
Abstract:
Despite the success of Transformer models in vision and language tasks, they often learn knowledge from enormous data implicitly and cannot utilize structured input data directly. On the other hand, … >>>
Despite the success of Transformer models in vision and language tasks, they often learn knowledge from enormous data implicitly and cannot utilize structured input data directly. On the other hand, structured learning approaches such as graph neural networks (GNNs) that integrate prior information can barely compete with Transformer models. In this work, we aim to benefit from both worlds and propose a novel Multimodal Graph Transformer for question answering tasks that requires performing reasoning across multiple modalities. We introduce a graph-involved plug-and-play quasi-attention mechanism to incorporate multimodal graph information, acquired from text and visual data, to the vanilla self-attention as effective prior. In particular, we construct the text graph, dense region graph, and semantic graph to generate adjacency matrices, and then compose them with input vision and language features to perform downstream reasoning. Such a way of regularizing self-attention with graph information significantly improves the inferring ability and helps align features from different modalities. We validate the effectiveness of Multimodal Graph Transformer over its Transformer baselines on GQA, VQAv2, and MultiModalQA datasets. <<<
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613.
颜林林 (2023-05-11 22:05):
#paper doi:10.3389/fneur.2023.1036453 Frontiers in Neurology, 2023, Mechanism of Qihuang needle therapy in the management of tic disorders: a clinical trial protocol. 这是一篇关于针灸治疗方法开展注册临床试验的文章(在中国临床试验注册中心注册,编号:ChiCTR2200057723,网址:https://www.chictr.org.cn/showproj.html?proj=161252)。该临床试验于2022年3月至2023年9月期间开展,通过岐黄针对抽动障碍的儿童进行干预性治疗(预计入组干预组和对照组各20例),并随访患儿12周,除相关临床量表评估外,还采集外周血并通过质谱和ELISA实验测定其血浆中的代谢物和蛋白,以及采集粪便进行16S rRNA的微生物组分析,以期通过这些多组学数据来探索针灸治疗的作用机制。临床试验尚未结束,本文的投稿时间为2022年9月(历经半年至2023年4月接收),为提前公开详细披露其临床试验具体操作流程,因此仅有方法描述,而无结果数据。虽然很难想象代谢物、蛋白及肠道菌群等信息,要与针灸对神经类疾病治疗的作用机制该如何关联,但中医讲究整体系统论,万事万物皆有联系,既然在肉眼可见的解剖学水平难以建立直接联系,那间接通过不同多组学的尝试来观察和早期探索,或许也是一种不错的尝试。先期待下临床试验完成后的数据分析结果的公开发表吧。
Abstract:
Background: Qihuang needle therapy is a newly developed acupuncture therapy to treat tic disorders in clinical practice. However, the mechanism to reduce tic severity remains unknown. Changes in intestinal flora … >>>
Background: Qihuang needle therapy is a newly developed acupuncture therapy to treat tic disorders in clinical practice. However, the mechanism to reduce tic severity remains unknown. Changes in intestinal flora and circulation metabolites are perhaps the potential pathogenesis of tic disorders. As a result, we present a protocol for a controlled clinical trial using multi-omics analysis to probe the mechanism of the Qihuang needle in managing tic disorders.Methods: This is a matched-pairs design, controlled, clinical trial for patients with tic disorders. Participants will be allocated to either an experimental group or a healthy control group. The main acupoints are Baihui (GV20), Yintang (EX-HN3), and Jueyinshu (BL14). The experimental group will receive Qihuang needle therapy for a month, while the control group will receive no interventions.Expected outcomes: The change in the severity of the tic disorder is set as the main outcome. Secondary outcomes include gastrointestinal severity index and recurrence rate, which will be calculated after a 12-week follow-up. Gut microbiota, measured by 16S rRNA gene sequencing; serum metabolomics, assessed via LC/MS; and serum zonulin, assessed by enzyme-linked immunosorbent assay (ELISA), will be used as biological specimen analysis outcomes. The present study will investigate the possible interactions between intestinal flora and serum metabolites and the improvement of clinical profiles, which may elucidate the mechanism of Qihuang needle therapy for tic disorders.Trial registration: This trial is registered at the Chinese Clinical Trial Registry (http://www.chictr.org.cn/). Registration number: ChiCTR2200057723, Date: 2022-04-14. <<<
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614.
AI 5.0.3 (2023-05-08 17:03):
#paper Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex,https://doi.org/10.1016/j.neuron.2020.01.040,本文借助bmtk建模工具对视觉皮层v1区进行建模计算提出了生物学模型和计算机拓扑模型,主要分为生物学成分模型和整合发射点神经元模型,有较好的迁移性可以使用在其他脑区建模上。
IF:14.700Q1 Neuron, 2020-05-06. DOI: 10.1016/j.neuron.2020.01.040 PMID: 32142648
Abstract:
Structural rules underlying functional properties of cortical circuits are poorly understood. To explore these rules systematically, we integrated information from extensive literature curation and large-scale experimental surveys into a data-driven, … >>>
Structural rules underlying functional properties of cortical circuits are poorly understood. To explore these rules systematically, we integrated information from extensive literature curation and large-scale experimental surveys into a data-driven, biologically realistic simulation of the awake mouse primary visual cortex. The model was constructed at two levels of granularity, using either biophysically detailed or point neurons. Both variants have identical network connectivity and were compared to each other and to experimental recordings of visual-driven neural activity. While tuning these networks to recapitulate experimental data, we identified rules governing cell-class-specific connectivity and synaptic strengths. These structural constraints constitute hypotheses that can be tested experimentally. Despite their distinct single-cell abstraction, both spatially extended and point models perform similarly at the level of firing rate distributions for the questions we investigated. All data and models are freely available as a resource for the community. <<<
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颜林林 (2023-05-06 00:47):
#paper doi:10.1056/NEJMoa2212856 The New England Journal of Medicine, 2023, Interrupting Endocrine Therapy to Attempt Pregnancy after Breast Cancer. 乳腺癌患者在接受手术后,若为HR阳性,则会继续开展数年的内分泌辅助治疗,以巩固和改善疗效,避免和降低疾病复发。在辅助治疗期间,患者若打算怀孕生娃,则需要停止原定的内分泌治疗,这是否会导致严重的负面影响,尚无明确结论。这篇研究就是针对此情况开展的注册临床试验(NCT02308085),入组了2014至2019年期间符合条件的518位患者,她们都因怀孕计划中断了内分泌治疗,对她们进行持续随访,分析其乳腺癌复发事件及生育情况。目前已达到次要终点,复发事件数未超过预定安全阈值,数据进行锁定和分析。与外部一个1499例的未中断内分泌治疗的乳腺癌队列进行对比,复发事件的发生率并无明显区别。初步支持为尝试怀孕而暂停治疗不会产生明显的短期负面影响。对这些患者的随访还在继续,以便未来对相应产生的长期影响做出评估和结论。
Abstract:
BACKGROUND: Prospective data on the risk of recurrence among women with hormone receptor-positive early breast cancer who temporarily discontinue endocrine therapy to attempt pregnancy are lacking.METHODS: We conducted a single-group … >>>
BACKGROUND: Prospective data on the risk of recurrence among women with hormone receptor-positive early breast cancer who temporarily discontinue endocrine therapy to attempt pregnancy are lacking.METHODS: We conducted a single-group trial in which we evaluated the temporary interruption of adjuvant endocrine therapy to attempt pregnancy in young women with previous breast cancer. Eligible women were 42 years of age or younger; had had stage I, II, or III disease; had received adjuvant endocrine therapy for 18 to 30 months; and desired pregnancy. The primary end point was the number of breast cancer events (defined as local, regional, or distant recurrence of invasive breast cancer or new contralateral invasive breast cancer) during follow-up. The primary analysis was planned to be performed after 1600 patient-years of follow-up. The prespecified safety threshold was the occurrence of 46 breast cancer events during this period. Breast cancer outcomes in this treatment-interruption group were compared with those in an external control cohort consisting of women who would have met the entry criteria for the current trial.RESULTS: Among 516 women, the median age was 37 years, the median time from breast cancer diagnosis to enrollment was 29 months, and 93.4% had stage I or II disease. Among 497 women who were followed for pregnancy status, 368 (74.0%) had at least one pregnancy and 317 (63.8%) had at least one live birth. In total, 365 babies were born. At 1638 patient-years of follow-up (median follow-up, 41 months), 44 patients had a breast cancer event, a result that did not exceed the safety threshold. The 3-year incidence of breast cancer events was 8.9% (95% confidence interval [CI], 6.3 to 11.6) in the treatment-interruption group and 9.2% (95% CI, 7.6 to 10.8) in the control cohort.CONCLUSIONS: Among select women with previous hormone receptor-positive early breast cancer, temporary interruption of endocrine therapy to attempt pregnancy did not confer a greater short-term risk of breast cancer events, including distant recurrence, than that in the external control cohort. Further follow-up is critical to inform longer-term safety. (Funded by ETOP IBCSG Partners Foundation and others; POSITIVE ClinicalTrials.gov number, NCT02308085.). <<<
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616.
AI 5.0.3 (2023-04-30 23:59):
#paper A distributed and efficient population code of mixed selectivity neurons for flexible navigation decisions https://doi.org/10.1038/s41467-023-37804-2 这篇文章研究了虚拟导航背后皮层区域和神经活动模式,根据不同线索匹配切换不同导航策略,通过编码电流和记忆视觉提示混合介导导航开关,提供导航决策灵活性。
IF:14.700Q1 Nature communications, 2023-04-14. DOI: 10.1038/s41467-023-37804-2 PMID: 37055431
Abstract:
Decision-making requires flexibility to rapidly switch one's actions in response to sensory stimuli depending on information stored in memory. We identified cortical areas and neural activity patterns underlying this flexibility … >>>
Decision-making requires flexibility to rapidly switch one's actions in response to sensory stimuli depending on information stored in memory. We identified cortical areas and neural activity patterns underlying this flexibility during virtual navigation, where mice switched navigation toward or away from a visual cue depending on its match to a remembered cue. Optogenetics screening identified V1, posterior parietal cortex (PPC), and retrosplenial cortex (RSC) as necessary for accurate decisions. Calcium imaging revealed neurons that can mediate rapid navigation switches by encoding a mixture of a current and remembered visual cue. These mixed selectivity neurons emerged through task learning and predicted the mouse's choices by forming efficient population codes before correct, but not incorrect, choices. They were distributed across posterior cortex, even V1, and were densest in RSC and sparsest in PPC. We propose flexibility in navigation decisions arises from neurons that mix visual and memory information within a visual-parietal-retrosplenial network. <<<
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半面阳光 (2023-04-30 23:55):
#paper DOI: 10.1038/s41436-019-0467-4, Genet Med. 2019, Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes. 这篇文章研究了无创产前检测(NIPT)用于拷贝数变异检测的检测能力。这一研究征集了9万多名孕妇外周血样本,进行了拓展性NIPT检测。研究结果显示,拓展性NIPT在检测常见的染色体非整体时的检出效果更佳,对于拷贝数变异具有一定的检出能力。总体上看,拓展性NIPT对产前染色体异常检测的检出效果由于常规的NIPT。
Abstract:
PURPOSE: To assess the clinical performance of an expanded noninvasive prenatal screening (NIPS) test ("NIPS-Plus") for detection of both aneuploidy and genome-wide microdeletion/microduplication syndromes (MMS).METHODS: A total of 94,085 women … >>>
PURPOSE: To assess the clinical performance of an expanded noninvasive prenatal screening (NIPS) test ("NIPS-Plus") for detection of both aneuploidy and genome-wide microdeletion/microduplication syndromes (MMS).METHODS: A total of 94,085 women with a singleton pregnancy were prospectively enrolled in the study. The cell-free plasma DNA was directly sequenced without intermediate amplification and fetal abnormalities identified using an improved copy-number variation (CNV) calling algorithm.RESULTS: A total of 1128 pregnancies (1.2%) were scored positive for clinically significant fetal chromosome abnormalities. This comprised 965 aneuploidies (1.026%) and 163 (0.174%) MMS. From follow-up tests, the positive predictive values (PPVs) for T21, T18, T13, rare trisomies, and sex chromosome aneuploidies were calculated as 95%, 82%, 46%, 29%, and 47%, respectively. For known MMS (n = 32), PPVs were 93% (DiGeorge), 68% (22q11.22 microduplication), 75% (Prader-Willi/Angleman), and 50% (Cri du Chat). For the remaining genome-wide MMS (n = 88), combined PPVs were 32% (CNVs ≥10 Mb) and 19% (CNVs <10 Mb).CONCLUSION: NIPS-Plus yielded high PPVs for common aneuploidies and DiGeorge syndrome, and moderate PPVs for other MMS. Our results present compelling evidence that NIPS-Plus can be used as a first-tier pregnancy screening method to improve detection rates of clinically significant fetal chromosome abnormalities. <<<
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Ricardo (2023-04-30 23:45):
#paper Pancreatic Cancer Detection on CT Scans with Deep Learning: A Nationwide Population-based Study https://doi.org/10.1148/radiol.220152 正好最近要写一篇和医院合作的腹腔影像的论文,所以最近看了一些这方面的论文。这篇论文的合作者回顾性收集了2006年1月至2018年7月期间诊断为胰腺癌的患者的对比增强CT研究与2004年1月至2019年12月期间获得的正常胰腺个体(对照组)的CT研究进行了比较。开发了包含分割卷积神经网络(CNN)和集成五个CNN的分类器的端到端工具,并在内部测试集和全国范围内的验证集中进行了验证。546例胰腺癌患者(平均年龄65岁6 12岁[SD],男性297例)和733例对照者随机分为训练组、验证组和测试组。在内部测试集中,DL工具达到89.9% (98 / 109;95% CI: 82.7, 94.9)敏感性95.9% (141 / 147;95% CI: 91.3, 98.5)特异性(受试者工作特征曲线下面积[AUC], 0.96;95% CI: 0.94, 0.99),敏感性与原始放射科医生报告相比无显著差异(P = 0.11) (96.1% [98 / 102];95% ci: 90.3, 98.9)。在台湾各机构的1473个真实CT研究(669个恶性研究,804个对照研究)的测试集中,DL工具区分CT恶性研究和对照研究的准确率为89.7%(669个中的600个;95% CI: 87.1, 91.9)敏感性和92.8%特异性(746 / 804;95% ci: 90.8, 94.5) (auc, 0.95;95% CI: 0.94, 0.96), 74.7% (68 / 91;95% CI: 64.5, 83.3)对小于2cm的恶性肿瘤的敏感性。
IF:12.100Q1 Radiology, 2023-01. DOI: 10.1148/radiol.220152 PMID: 36098642
Abstract:
Background Approximately 40% of pancreatic tumors smaller than 2 cm are missed at abdominal CT. Purpose To develop and to validate a deep learning (DL)-based tool able to detect pancreatic … >>>
Background Approximately 40% of pancreatic tumors smaller than 2 cm are missed at abdominal CT. Purpose To develop and to validate a deep learning (DL)-based tool able to detect pancreatic cancer at CT. Materials and Methods Retrospectively collected contrast-enhanced CT studies in patients diagnosed with pancreatic cancer between January 2006 and July 2018 were compared with CT studies of individuals with a normal pancreas (control group) obtained between January 2004 and December 2019. An end-to-end tool comprising a segmentation convolutional neural network (CNN) and a classifier ensembling five CNNs was developed and validated in the internal test set and a nationwide real-world validation set. The sensitivities of the computer-aided detection (CAD) tool and radiologist interpretation were compared using the McNemar test. Results A total of 546 patients with pancreatic cancer (mean age, 65 years ± 12 [SD], 297 men) and 733 control subjects were randomly divided into training, validation, and test sets. In the internal test set, the DL tool achieved 89.9% (98 of 109; 95% CI: 82.7, 94.9) sensitivity and 95.9% (141 of 147; 95% CI: 91.3, 98.5) specificity (area under the receiver operating characteristic curve [AUC], 0.96; 95% CI: 0.94, 0.99), without a significant difference ( = .11) in sensitivity compared with the original radiologist report (96.1% [98 of 102]; 95% CI: 90.3, 98.9). In a test set of 1473 real-world CT studies (669 malignant, 804 control) from institutions throughout Taiwan, the DL tool distinguished between CT malignant and control studies with 89.7% (600 of 669; 95% CI: 87.1, 91.9) sensitivity and 92.8% specificity (746 of 804; 95% CI: 90.8, 94.5) (AUC, 0.95; 95% CI: 0.94, 0.96), with 74.7% (68 of 91; 95% CI: 64.5, 83.3) sensitivity for malignancies smaller than 2 cm. Conclusion The deep learning-based tool enabled accurate detection of pancreatic cancer on CT scans, with reasonable sensitivity for tumors smaller than 2 cm. © RSNA, 2022 See also the editorial by Aisen and Rodrigues in this issue. <<<
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(2023-04-30 23:36):
#paper Fractionation of κ-casein from caprine micellar caseins using differential precipitation. https://doi.org/10.1016/j.idairyj.2023.105677. 江南大学食品科学与技术国家重点实验室等的Luo Guixin, Liu Xiaoming, Liu Dasong*, Zhou Peng等系统研究从山羊乳胶束酪蛋白浓缩物(micellar casein concentrate,MCC)中差异沉淀获得κ-酪蛋白的主要步骤中潜在关键加工条件的影响,还研究了酪蛋白浓度对κ-酪蛋白分馏的影响,旨在提高扩大条件下的加工能力。使用差异沉淀法对κ-酪蛋白进行分馏是基于单个酪蛋白在碱性pH值条件下对过量添加Ca的不同亲和力,然后进行中和,以促进αs-酪蛋白和β-酪蛋白的选择性沉淀。为提高从山羊乳MCC中分离的κ-酪蛋白产量和纯度,对每个主要步骤中的主要加工变量条件依次进行优化,得到最佳条件为:在pH 11.0条件下,使用匀浆再水合MCC(含3%酪蛋白),然后解离胶束;添加45 mmol/L Ca在25 ℃条件下络合酪蛋白60 min,然后使用2 mol/L乙酸在pH 7.0、25 ℃条件下再次沉淀β-/αs-酪蛋白60 min;使用2 个分馏循环,在第2个循环中添加50 mmol/L Ca,然后在pH 3.8、50 ℃条件下沉淀κ-酪蛋白。为提高扩大条件下的加工能力,将酪蛋白浓度提高4%~7%,同时添加60 mmol/L Ca,可获得与最佳条件下相当的κ-酪蛋白产量和纯度。在酪蛋白含量为4%时,MCC分散体中κ-酪蛋白的最大产量和纯度分别为84.6%和84.4%。
Abstract:
The effects of potentially important processing conditions at each step of differential precipitation on the yield and purity of κ-casein fractionated from caprine micellar casein concentrate (MCC) were investigated. The … >>>
The effects of potentially important processing conditions at each step of differential precipitation on the yield and purity of κ-casein fractionated from caprine micellar casein concentrate (MCC) were investigated. The optimal conditions were: rehydrating (3% casein) MCC using homogenisation followed by dissociating micelles at pH 11.0; complexing caseins using 45 mm added Ca at 25 °C for 60 min, followed by precipitating β-/αS-caseins using 2 m acetic acid at pH 7.0 again at 25 °C for 60 min. Two fractionation cycles were used with 50 mm added Ca for the second cycle, followed by precipitating κ-casein at pH 3.8 and 50 °C. To increase processing capacity for scale-up, increased casein concentrations of 4–7% along with 60 mm added Ca resulted in comparable yields and purity of the κ-casein. Maximum yield and purity of 84.6% and 84.4%, respectively, were achieved for κ-casein from the MCC dispersions at 4% casein. <<<
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林海onrush (2023-04-30 23:31):
#paper,Tensor Decompositions and Applications∗,DOI: 10.1137/07070111X,张量分解在诸多领域都有深入的尝试,高阶张量(即N≥3的N路数组)在心理测量学、化学计量学、信号处理、数值线性代数、计算机视觉、数值分析、数据挖掘、神经科学、图分析和其他方面均有应用。这篇paper讲述了张量运算的基础,对张量的运算基础进行了详细的探讨,我认为非常有学习价值,未来会在很多行业的发展上具有重大贡献。
IF:10.800Q1 SIAM Review, 2009. DOI: 10.1137/07070111X
Abstract:
This survey provides an overview of higher-order tensor decompositions, their applications, and available software. A tensor is a multidimensional or N-way array. Decompositions of higher-order tensors (i.e., N-way arrays with … >>>
This survey provides an overview of higher-order tensor decompositions, their applications, and available software. A tensor is a multidimensional or N-way array. Decompositions of higher-order tensors (i.e., N-way arrays with N≥3) have applications in psycho-metrics, chemometrics, signal processing, numerical linear algebra, computer vision, numerical analysis, data mining, neuroscience, graph analysis, and elsewhere. Two particular tensor decompositions can be considered to be higher-order extensions of the matrix singular value decomposition: CANDECOMP/PARAFAC (CP) decomposes a tensor as a sum of rank-one tensors, and the Tucker decomposition is a higher-order form of principal component analysis. There are many other tensor decompositions, including INDSCAL, PARAFAC2, CANDELINC, DEDICOM, and PARATUCK2 as well as nonnegative variants of all of the above. The N-way Toolbox, Tensor Toolbox, and Multilinear Engine are examples of software packages for working with tensors. <<<
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