当前共找到 1317 篇文献分享,本页显示第 1181 - 1200 篇。
1181.
颜林林
(2022-06-05 06:41):
#paper doi:10.1186/s12864-022-08435-6 BMC Genomics, Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance. 在基因组和分子演化的研究中,我们通常认为(非3整倍长度的)移码突变会造成蛋白功能的完全丧失,而关于密码子表的容错能力通常也局限在第三个碱基上。这篇文章从方法上看,是一项非常经典的纯生物信息学研究,它基于公共数据和序列分析方法,对移码突变的特性进行分析,发现并验证了移码突变后的蛋白,与突变前野生型的蛋白,在序列和氨基酸理化性质等各方面,是保留有一定相似性的。这种保留,与完全随机的突变相比,是存在显著差异的。从而证明了各物种的基因组序列,以及密码子表,在对移码突变的容错方面,是“经过优化”的。这为密码子表的演化形成提供了新的角度及思路。在拥有大量公开生物序列数据的今天,充分利用这些数据,基于少量简单合理的假设前提,辅以诸如序列分析这样的生信基础技术和相应的统计检验过程,来回答一些基础生物学问题,做得比较认真和扎实,我个人很喜欢这样的研究工作。
Abstract:
Frameshift mutations have been considered of significant importance for the molecular evolution of proteins and their coding genes, while frameshift protein sequences encoded in the alternative reading frames of coding …
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Frameshift mutations have been considered of significant importance for the molecular evolution of proteins and their coding genes, while frameshift protein sequences encoded in the alternative reading frames of coding genes have been considered to be meaningless. However, functional frameshifts have been found widely existing. It was puzzling how a frameshift protein kept its structure and functionality while substantial changes occurred in its primary amino-acid sequence. This study shows that the similarities among frameshifts and wild types are higher than random similarities and are determined at different levels. Frameshift substitutions are more conservative than random substitutions in the standard genetic code (SGC). The frameshift substitutions score of SGC ranks in the top 2.0-3.5% of alternative genetic codes, showing that SGC is nearly optimal for frameshift tolerance. In many genes and certain genomes, frameshift-resistant codons and codon pairs appear more frequently than expected, suggesting that frameshift tolerance is achieved through not only the optimality of the genetic code but, more importantly, the further optimization of a specific gene or genome through the usages of codons/codon pairs, which sheds light on the role of frameshift mutations in molecular and genomic evolution.
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1182.
颜林林
(2022-06-04 07:46):
#paper doi:10.3322/caac.21727 CA: A Cancer Journal for Clinicians, 2022, Oncologic emergencies and urgencies: A comprehensive review. 这是一篇关于肿瘤急诊的综述。虽然这些年来,得益于肿瘤诊治相关研究的快速进步,肿瘤整体上越来越趋近于慢性病,但其死亡率和危害仍然位居前列。急诊诊断肿瘤往往属晚期,占所有新发肿瘤的11%至29%,且预后都较差。本文对这类紧急情况,包括其潜在病因和临床处置路径等,进行了全面的综述。包括肿瘤发展过程中常见的发热性中性粒细胞减少症、高钙血症、肿瘤溶解综合征、恶性脊髓压迫、机械性肠梗阻和突发性疼痛等症状,也包括其他特定癌种伴发的抗利尿激素分泌不当综合征、静脉血栓栓塞和恶性积液等。此外,对于因为肿瘤治疗,包括小分子靶向药物、免疫检查点抑制剂、CAR-T治疗等导致的不良反应和紧急并发症,也都做了详细介绍。记得在一次学术交流中,有临床医生提及其自己的经验,那些免疫治疗过程中出现不良反应的患者,如果能及时处理和控制好并发症,经常其对药物的响应和疗效是更明显。因此,了解肿瘤急诊各类情况及其处置,对于探明肿瘤危害及病因,以及发展完善各类诊治方法,都是有重要意义的。
Abstract:
Patients with advanced cancer generate 4 million visits annually to emergency departments (EDs) and other dedicated, high-acuity oncology urgent care centers. Because of both the increasing complexity of systemic treatments …
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Patients with advanced cancer generate 4 million visits annually to emergency departments (EDs) and other dedicated, high-acuity oncology urgent care centers. Because of both the increasing complexity of systemic treatments overall and the higher rates of active therapy in the geriatric population, many patients experiencing acute decompensations are frail and acutely ill. This article comprehensively reviews the spectrum of oncologic emergencies and urgencies typically encountered in acute care settings. Presentation, underlying etiology, and up-to-date clinical pathways are discussed. Criteria for either a safe discharge to home or a transition of care to the inpatient oncology hospitalist team are emphasized. This review extends beyond familiar conditions such as febrile neutropenia, hypercalcemia, tumor lysis syndrome, malignant spinal cord compression, mechanical bowel obstruction, and breakthrough pain crises to include a broader spectrum of topics encompassing the syndrome of inappropriate antidiuretic hormone secretion, venous thromboembolism and malignant effusions, as well as chemotherapy-induced mucositis, cardiomyopathy, nausea, vomiting, and diarrhea. Emergent and urgent complications associated with targeted therapeutics, including small molecules, naked and drug-conjugated monoclonal antibodies, as well as immune checkpoint inhibitors and chimeric antigen receptor T-cells, are summarized. Finally, strategies for facilitating same-day direct admission to hospice from the ED are discussed. This article not only can serve as a point-of-care reference for the ED physician but also can assist outpatient oncologists as well as inpatient hospitalists in coordinating care around the ED visit.
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1183.
颜林林
(2022-06-03 12:22):
#paper doi:10.1038/s41586-022-04759-1 Nature 2022, Fast and efficient DNA replication with purified human proteins. 这篇新发表的Nature文章,是还原论研究方法的典范。通过人工合成的方法,用43个多肽,从头构建了体外的多个DNA合成因子,并组装成具有生物活性的复合物,重现了快速高效的DNA合成过程。由于是完全人工合成,所以通过这个体系,可以研究各个组分在DNA复制过程中的必要性,以及组分之间的相互关系,并确认可以不需要其他更多额外分子。这项研究重点研究了人体DNA合成中的PCNA、CLASPIN、TIMELESS-TIPIN、AND-1等组分在相应合成步骤中的作用。
Abstract:
Chromosome replication is performed by a complex and intricate ensemble of proteins termed the replisome, where the DNA polymerases Polδ and Polε, DNA polymerase α-primase (Polα) and accessory proteins including …
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Chromosome replication is performed by a complex and intricate ensemble of proteins termed the replisome, where the DNA polymerases Polδ and Polε, DNA polymerase α-primase (Polα) and accessory proteins including AND-1, CLASPIN and TIMELESS-TIPIN (respectively known as Ctf4, Mrc1 and Tof1-Csm3 in Saccharomyces cerevisiae) are organized around the CDC45-MCM-GINS (CMG) replicative helicase. Because a functional human replisome has not been reconstituted from purified proteins, how these factors contribute to human DNA replication and whether additional proteins are required for optimal DNA synthesis are poorly understood. Here we report the biochemical reconstitution of human replisomes that perform fast and efficient DNA replication using 11 purified human replication factors made from 43 polypeptides. Polε, but not Polδ, is crucial for optimal leading-strand synthesis. Unexpectedly, Polε-mediated leading-strand replication is highly dependent on the sliding-clamp processivity factor PCNA and the alternative clamp loader complex CTF18-RFC. We show how CLASPIN and TIMELESS-TIPIN contribute to replisome progression and demonstrate that, in contrast to the budding yeast replisome, AND-1 directly augments leading-strand replication. Moreover, although AND-1 binds to Polα, the interaction is dispensable for lagging-strand replication, indicating that Polα is functionally recruited via an AND-1-independent mechanism for priming in the human replisome. Collectively, our work reveals how the human replisome achieves fast and efficient leading-strand and lagging-strand DNA replication, and provides a powerful system for future studies of the human replisome and its interactions with other DNA metabolic processes.
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1184.
颜林林
(2022-06-02 07:08):
#paper doi:10.1101/gr.276193.121 Genome Research 2022, Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression. 二倍体生物的每个基因都有两个等位基因拷贝,等位基因的表达并非随机发生,哪些因素决定了到底开启哪条等位基因进行表达,是个值得研究的问题。本文通过杂交两个品系的小鼠,构建出在大多数基因上都呈现杂合型的F1代,并用这个模型进行等位基因特异性表达(Allele-Specific Expression,ASE)的研究,使得通过测序方法可以很容易大批量识别出所表达基因的来源等位基因(来自父方或母方)。由于是动物模型实验,可以很容易进行是否高脂饮食等对照实验,以及可以进行不同器官组织类型的样本采集,研究在不同组别、不同组织中的ASE事件。通过这套体系,本文发现了几千个存在ASE的基因,并研究了基因序列、基因表观状态、饮食习惯以及不同器官组织等因素对ASE的影响。
Abstract:
Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's …
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Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases. Male and female mice from a F reciprocal cross of the LG/J and SM/J strains were fed a high or low fat diet. We harnessed strain-specific variants to distinguish between two ASE classes: parent-of-origin-dependent (unequal expression based on parental origin) and sequence-dependent (unequal expression based on nucleotide identity). We present a comprehensive map of ASE patterns in 2853 genes across three tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue and environmental context. They vary across metabolically relevant tissues, between males and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific expression, which is an essential step toward deciphering the genotype-to-phenotype map.
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1185.
颜林林
(2022-06-01 07:41):
#paper doi:10.1101/2022.05.29.493900 bioRxiv 2022, Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform. 这是来自MIT的一家创业公司Ultima Genomics的新作品,它从设计原理上对当前“边合成边测序”的方法进行突破创新。通过在圆形大晶片上设计流控和光学系统,使相应的试剂耗材更加便宜。相对于Illumina测序在每个cycle进行可逆阻断的碱基追加方法,本文通过使用非阻断的方法,使碱基追加过程更加快速,同时配合一套CNN算法,来实现准确的base calling。实测下来,该测序方法可以做到在20小时以内、300bp长读长、Q30>85%高质量的高通量测序,且每Gb数据成本低于1美元。本文还使用GIAB及千人基因组的样本进行了基准测试,验证了测序结果的准确度。我们很多人天天都在围绕高通量测序做研究,早已把Illumina测序原理当做习以为常且理所当然的技术,默认了它的垄断和天花板地位,很少去考虑它还有什么可以进一步改善的地方。这篇文章是个拓展这方面眼界的机会。
bioRxiv,
2022.
DOI: 10.1101/2022.05.29.493900
Abstract:
We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow …
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We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions of reads with longer read length (~300bp) and fast runs times (<20hrs) with high base accuracy (Q30 > 85%), at a low cost of $1/Gb. We establish system performance by whole-genome sequencing of the Genome-In-A-Bottle reference samples HG001-7, demonstrating high accuracy for SNPs (99.6%) and Indels in homopolymers up to length 10 (96.4%) across the vast majority (>98%) of the defined high-confidence regions of these samples. We demonstrate scalability of the whole-genome sequencing workflow by sequencing an additional 224 selected samples from the 1000 Genomes project achieving high concordance with reference data.
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1186.
Ricardo
(2022-06-01 00:59):
#paper 10.1109/TMI.2021.3116879. SynthMorph: Learning Contrast-Invariant Registration Without Acquired Images. 这篇文章很漂亮的展现了如何用神经网络直接暴力学习度量。多模态配准一直是一个领域难题,各路大佬们提出了大量的方法度量两个不同模态图像之间的相似性。这篇文章作者想了一个很直接的点子,就是我直接根据分割的label构造具有不同contrast的图像对网络进行训练就好了呀,至于loss怎么设计就直接测量配准前后两个label的相似性就好了,这样网络自己就学习到了如何测量不同模态间图像的相似性。这篇文章我感觉像是自监督,毕竟就是自己通过设计某种规则寻找数据自己内蕴的规律,进一步我在想配准任务是否能够作为医学影像任务的预训练模型呢,毕竟既然两个图像能够很好的对齐的话,那说明网络能够检测到两张图像之间需要对齐的解剖结构,本质上也就是学习到更general的图像特征表征图像自身的结构了。
IF:8.900Q1
IEEE transactions on medical imaging,
2022-03.
DOI: 10.1109/TMI.2021.3116879
PMID: 34587005
PMCID:PMC8891043
Abstract:
We introduce a strategy for learning image registration without acquired imaging data, producing powerful networks agnostic to contrast introduced by magnetic resonance imaging (MRI). While classical registration methods accurately estimate …
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We introduce a strategy for learning image registration without acquired imaging data, producing powerful networks agnostic to contrast introduced by magnetic resonance imaging (MRI). While classical registration methods accurately estimate the spatial correspondence between images, they solve an optimization problem for every new image pair. Learning-based techniques are fast at test time but limited to registering images with contrasts and geometric content similar to those seen during training. We propose to remove this dependency on training data by leveraging a generative strategy for diverse synthetic label maps and images that exposes networks to a wide range of variability, forcing them to learn more invariant features. This approach results in powerful networks that accurately generalize to a broad array of MRI contrasts. We present extensive experiments with a focus on 3D neuroimaging, showing that this strategy enables robust and accurate registration of arbitrary MRI contrasts even if the target contrast is not seen by the networks during training. We demonstrate registration accuracy surpassing the state of the art both within and across contrasts, using a single model. Critically, training on arbitrary shapes synthesized from noise distributions results in competitive performance, removing the dependency on acquired data of any kind. Additionally, since anatomical label maps are often available for the anatomy of interest, we show that synthesizing images from these dramatically boosts performance, while still avoiding the need for real intensity images. Our code is available at doic https://w3id.org/synthmorph.
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1187.
Ricardo
(2022-06-01 00:51):
#paper https://doi.org/10.1016/j.neuroimage.2021.118799. Longitudinal brain atlases of early developing cynomolgus macaques from birth to 48 months of age. 2022年发表于neuroimage。这篇研究和《A 4D infant brain volumetric atlas based on the UNC/UMN baby connectome project (BCP) cohort》这篇研究差不多,用的方法基本上是一样的。只不过研究对象换成了48月龄以前的食蟹猴。这里面强调了一个问题,就是在做纵向配准的时候,不能直接将年龄跨度差异较大的两个大脑直接进行配准,应当一步一步地在相邻年龄上的图像进行配准,这样能够最大程度的保证解剖结构在整个发育轨迹上的一致性。
Abstract:
Longitudinal brain imaging atlases with densely sampled time-points and ancillary anatomical information are of fundamental importance in studying early developmental characteristics of human and non-human primate brains during infancy, which …
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Longitudinal brain imaging atlases with densely sampled time-points and ancillary anatomical information are of fundamental importance in studying early developmental characteristics of human and non-human primate brains during infancy, which feature extremely dynamic imaging appearance, brain shape and size. However, for non-human primates, which are highly valuable animal models for understanding human brains, the existing brain atlases are mainly developed based on adults or adolescents, denoting a notable lack of temporally densely-sampled atlases covering the dynamic early brain development. To fill this critical gap, in this paper, we construct a comprehensive set of longitudinal brain atlases and associated tissue probability maps (gray matter, white matter, and cerebrospinal fluid) with totally 12 time-points from birth to 4 years of age (i.e., 1, 2, 3, 4, 5, 6, 9, 12, 18, 24, 36, and 48 months of age) based on 175 longitudinal structural MRI scans from 39 typically-developing cynomolgus macaques, by leveraging state-of-the-art computational techniques tailored for early developing brains. Furthermore, to facilitate region-based analysis using our atlases, we also provide two popular hierarchy parcellations, i.e., cortical hierarchy maps (6 levels) and subcortical hierarchy maps (6 levels), on our longitudinal macaque brain atlases. These early developing atlases, which have the densest time-points during infancy (to the best of our knowledge), will greatly facilitate the studies of macaque brain development.
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1188.
Ricardo
(2022-06-01 00:45):
#paper https://doi.org/10.1016/j.neuroimage.2022.119097 A 4D infant brain volumetric atlas based on the UNC/UMN baby connectome project (BCP) cohort. 2022年发表于neuroimage。由于人类大脑在出生后的头两年处于快速发育的过程,随着年龄的增长,其MRI影像的图像appearance和contrast呈现动态的变化。因此,为婴幼儿早期发育研究构建高精度的时空脑图谱是一件非常重要的事情。这篇研究从240名26月龄以前的婴幼儿被试中采集了542例T1和T2的纵向影像数据用于图谱的构建。出乎我意料的是,他们没有采用他们实验室之前开发的一系列针对于婴幼儿脑影像数据特点的配准技术,而是通过结合强度图像和分割图像并利用基于成人大脑开发的配准算法构建的图谱。他们对0-24个月的婴幼儿分年龄段的构建了17个时间点的图谱,其中前12个月每一个月构建一个图谱,后12个月每3个月构建一个图谱。当然这篇文章存在一些技术问题,我的博士课题也正在考虑做相似的工作,可能会根据里面出现的问题做一些改进。
Abstract:
Spatiotemporal (four-dimensional) infant-dedicated brain atlases are essential for neuroimaging analysis of early dynamic brain development. However, due to the substantial technical challenges in the acquisition and processing of infant brain …
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Spatiotemporal (four-dimensional) infant-dedicated brain atlases are essential for neuroimaging analysis of early dynamic brain development. However, due to the substantial technical challenges in the acquisition and processing of infant brain MR images, 4D atlases densely covering the dynamic brain development during infancy are still scarce. Few existing ones generally have fuzzy tissue contrast and low spatiotemporal resolution, leading to degraded accuracy of atlas-based normalization and subsequent analyses. To address this issue, in this paper, we construct a 4D structural MRI atlas for infant brains based on the UNC/UMN Baby Connectome Project (BCP) dataset, which features a high spatial resolution, extensive age-range coverage, and densely sampled time points. Specifically, 542 longitudinal T1w and T2w scans from 240 typically developing infants up to 26-month of age were utilized for our atlas construction. To improve the co-registration accuracy of the infant brain images, which typically exhibit dynamic appearance with low tissue contrast, we employed the state-of-the-art registration method and leveraged our generated reliable brain tissue probability maps in addition to the intensity images to improve the alignment of individual images. To achieve consistent region labeling on both infant and adult brain images for facilitating region-based analysis across ages, we mapped the widely used Desikan cortical parcellation onto our atlas by following an age-decreasing mapping manner. Meanwhile, the typical subcortical structures were manually delineated to facilitate the studies related to the subcortex. Compared with the existing infant brain atlases, our 4D atlas has much higher spatiotemporal resolution and preserves more structural details, and thus can boost accuracy in neurodevelopmental analysis during infancy.
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1189.
李翛然
(2022-05-31 23:45):
#paper doi:10.1038/s41586-022-04463-0 nature FSH blockade improves cognition in mice with Alzheimer’s disease FSH,2022年3月发表在Nature正刊,用于治疗老年痴呆症,调控 beta蛋白和Tau蛋白.本文是多个描述AZ疾病的论文中比较肯定的这个荷尔蒙作用。目前是一个潜在的重要靶点
Abstract:
Alzheimer's disease has a higher incidence in older women, with a spike in cognitive decline that tracks with visceral adiposity, dysregulated energy homeostasis and bone loss during the menopausal transition. …
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Alzheimer's disease has a higher incidence in older women, with a spike in cognitive decline that tracks with visceral adiposity, dysregulated energy homeostasis and bone loss during the menopausal transition. Inhibiting the action of follicle-stimulating hormone (FSH) reduces body fat, enhances thermogenesis, increases bone mass and lowers serum cholesterol in mice. Here we show that FSH acts directly on hippocampal and cortical neurons to accelerate amyloid-β and Tau deposition and impair cognition in mice displaying features of Alzheimer's disease. Blocking FSH action in these mice abrogates the Alzheimer's disease-like phenotype by inhibiting the neuronal C/EBPβ-δ-secretase pathway. These data not only suggest a causal role for rising serum FSH levels in the exaggerated Alzheimer's disease pathophysiology during menopause, but also reveal an opportunity for treating Alzheimer's disease, obesity, osteoporosis and dyslipidaemia with a single FSH-blocking agent.
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1190.
小W
(2022-05-31 23:44):
doi:DOI: 10.1126/science.abl5197 Cross-tissue immune cell analysis reveals
tissue-specific features in humans
Human Cell Atlas (HCA) 五月发布的泛组织单细胞文章中一篇。这几篇文章对单细胞技术,细胞特异性的RNA剪接方式,细胞与人类疾病关联分析,免疫细胞组织特异性特征进行了论述。本文分析了来自12名成年器官捐献者16个组织的33万个免疫细胞的scrna-seq数据,通过随机梯度下降优化的逻辑回归分类器训练免疫细胞类型注释工具,对主要免疫细胞和细胞亚型(101种)注释。研究了单核吞噬细胞共有的和组织受限的标志物,B细胞亚群间标志物、免疫球蛋白偏好性和不同克隆分布,T细胞亚型的组织分布。其提供的免疫细胞参考图集,有助于了解感染组织特征,免疫药物设计和递送。
Abstract:
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors …
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Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
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1191.
小擎子
(2022-05-31 23:21):
#paper doi:10.1038/nbt.2579 Nat Biotechnol., 2013, Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes。用新的差异覆盖分箱方法从环境宏基因组中恢复多个低丰度的物种基因组,为从宏基因组中恢复质量好的MAG提供方法,数据和方法资料齐全,值得参考。
Abstract:
Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach …
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Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.
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1192.
张贝
(2022-05-31 22:51):
#paper DOI: 10.1038/s41392-021-00501-x Signal Transduct Target Ther. 2021. Targeting Erbin in B cells for therapy of lung metastasis of colorectal cancer. 结直肠癌是全球致死率最高的癌症之一,其中肺是结直肠癌转移的第二大器官,但目前关于结直肠癌肺转移的机制以及涉及到的肿瘤环境中的关键因子还尚不明确。本文作者发现结直肠癌肺转移中lgA产生的肠道免疫网络明显失调。单细胞RNA测序发现Erbin(富含亮氨酸重复序列和PDZ域(LAP)家族的一员)阳性的B细胞亚型参与了肺转移。敲除B细胞的Erbin抑制体内结直肠癌的肺转移。从机制上讲,Erbin基因敲除减弱了TGFβ介导的CXCR5 + IgA +细胞迁移和STAT6介导的PD1表达的抑制。该研究揭示了Erbin在CRC肺转移中调节PD1 + IgA + B细胞的关键作用。靶向Erbin以及联合使用中和B细胞和中和PD1的抗体可抑制小鼠结直肠癌的肺转移,该研究为治疗结直肠癌肺转移提供潜在的选择。
IF:40.800Q1
Signal transduction and targeted therapy,
2021-03-12.
DOI: 10.1038/s41392-021-00501-x
PMID: 33707428
PMCID:PMC7952714
Abstract:
The mechanisms and key factors involved in tumor environments for lung metastasis of CRC are still unclear. Here, using clinical samples from lung metastases of CRC patients, we found that …
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The mechanisms and key factors involved in tumor environments for lung metastasis of CRC are still unclear. Here, using clinical samples from lung metastases of CRC patients, we found that intestinal immune network for IgA production was significantly dysregulated in lung metastases of CRC. Single-cell RNA sequencing discovered a subtype of B cells positive for Erbin, one member of the leucine-rich repeat and PDZ domain (LAP) family, was involved in the lung metastases. Erbin deletion in B cells suppressed lung metastasis of CRC in vivo. And, deletion of Erbin in B cells enhanced the killing effects of CD8 T cells on tumor cells. Mechanistically, Erbin knockout attenuated TGFβ-mediated suppression of migration of CXCR5 IgA cells and STAT6-mediated PD1 expression. Our study uncovered a key role of Erbin in regulating PD1 IgA B cells in lung metastasis of CRC. Targeting Erbin as well as combined use of neutralizing B cells and antibodies neutralizing PD1 suppresses lung metastasis of CRC in mice, suggesting the potential option for treatment of lung metastasis of CRC.
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1193.
June
(2022-05-31 22:42):
#paper:doi: 10.1038/s41556-021-00818-3.该研究通过独立的全基因组 CRISPR-Cas9 和激酶抑制剂文库筛选将 PKCβII 鉴定为铁死亡的关键贡献者。研究结果表明,PKCβII 可感知初始脂质过氧化物,并通过 ACSL4 的磷酸化和激活来放大与铁死亡相关的脂质过氧化。脂质组学分析表明,活化的 ACSL4 催化含多不饱和脂肪酸的脂质生物合成并促进脂质过氧化产物的积累,导致铁死亡。PKCβII-ACSL4 通路的减弱在体外有效地阻断了铁死亡,并在体内削弱了与铁死亡相关的癌症免疫治疗。总之,该研究结果将 PKCβII 确定为脂质过氧化的感应器,脂质过氧化-PKCβII-ACSL4 正反馈轴可能为铁死亡相关疾病治疗提供潜在的靶点。
Abstract:
The accumulation of lipid peroxides is recognized as a determinant of the occurrence of ferroptosis. However, the sensors and amplifying process of lipid peroxidation linked to ferroptosis remain obscure. Here …
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The accumulation of lipid peroxides is recognized as a determinant of the occurrence of ferroptosis. However, the sensors and amplifying process of lipid peroxidation linked to ferroptosis remain obscure. Here we identify PKCβII as a critical contributor of ferroptosis through independent genome-wide CRISPR-Cas9 and kinase inhibitor library screening. Our results show that PKCβII senses the initial lipid peroxides and amplifies lipid peroxidation linked to ferroptosis through phosphorylation and activation of ACSL4. Lipidomics analysis shows that activated ACSL4 catalyses polyunsaturated fatty acid-containing lipid biosynthesis and promotes the accumulation of lipid peroxidation products, leading to ferroptosis. Attenuation of the PKCβII-ACSL4 pathway effectively blocks ferroptosis in vitro and impairs ferroptosis-associated cancer immunotherapy in vivo. Our results identify PKCβII as a sensor of lipid peroxidation, and the lipid peroxidation-PKCβII-ACSL4 positive-feedback axis may provide potential targets for ferroptosis-associated disease treatment.
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1194.
大象城南
(2022-05-31 22:41):
#paper: doi.org/10.1016/j.neuroimage.2012.10.022 扩散加权 (DW) MRI 有助于对组织微观结构进行无创量化,并结合适当的信号处理,对纤维方向进行三维估计。近年来,人们的注意力已经从扩散张量模型转移到更复杂的高角分辨率扩散成像 (HARDI) 分析技术,该模型假设单峰高斯扩散位移分布来恢复纤维取向(具有各种有据可查的限制)。 球面反卷积 (SD) 方法假设体素内的纤维取向密度函数 (fODF) 可以通过从观察到的 DW 信号集中对“普通”单纤维响应函数进行反卷积来获得。在实践中,这种常见的响应函数是先验未知的,因此必须使用估计的纤维响应。在这里,这种单纤维响应函数的建立被称为“校准”。这项工作检查了两种不同的 SD 方法对不适当的响应函数校准的脆弱性:(1) 约束球谐反卷积 (CSHD) - 一种利用球谐基组的技术和 (2) 阻尼 Richardson-Lucy (dRL) 反卷积 - 一种技术基于标准的 Richardson-Lucy 反卷积。 通过模拟,研究了在单光纤和交叉光纤配置中校准的扩散剖面与观察到的(“目标”)DW 信号之间的差异的影响。结果表明,随着校准和目标响应之间的差异增加,CSHD 会产生虚假 fODF 峰(与众所周知的振铃伪影一致),而 dRL 对误校准表现出较低的整体敏感性(对于高度各向异性光纤的校准响应函数为最佳)。然而,与 CSHD 相比,dRL 显示出解决低各向异性交叉纤维的能力降低。得出的结论是,必须仔细考虑图像中预期单纤维各向异性的范围和空间分布,以确保选择适当的算法、参数和校准。未能仔细选择校准响应函数可能会严重影响任何最终纤维束成像的质量。
IF:4.700Q1
NeuroImage,
2013-Jan-15.
DOI: 10.1016/j.neuroimage.2012.10.022
PMID: 23085109
PMCID:PMC3580290
Abstract:
Diffusion weighted (DW) MRI facilitates non-invasive quantification of tissue microstructure and, in combination with appropriate signal processing, three-dimensional estimates of fibrous orientation. In recent years, attention has shifted from the …
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Diffusion weighted (DW) MRI facilitates non-invasive quantification of tissue microstructure and, in combination with appropriate signal processing, three-dimensional estimates of fibrous orientation. In recent years, attention has shifted from the diffusion tensor model, which assumes a unimodal Gaussian diffusion displacement profile to recover fibre orientation (with various well-documented limitations), towards more complex high angular resolution diffusion imaging (HARDI) analysis techniques. Spherical deconvolution (SD) approaches assume that the fibre orientation density function (fODF) within a voxel can be obtained by deconvolving a 'common' single fibre response function from the observed set of DW signals. In practice, this common response function is not known a priori and thus an estimated fibre response must be used. Here the establishment of this single-fibre response function is referred to as 'calibration'. This work examines the vulnerability of two different SD approaches to inappropriate response function calibration: (1) constrained spherical harmonic deconvolution (CSHD)--a technique that exploits spherical harmonic basis sets and (2) damped Richardson-Lucy (dRL) deconvolution--a technique based on the standard Richardson-Lucy deconvolution. Through simulations, the impact of a discrepancy between the calibrated diffusion profiles and the observed ('Target') DW-signals in both single and crossing-fibre configurations was investigated. The results show that CSHD produces spurious fODF peaks (consistent with well known ringing artefacts) as the discrepancy between calibration and target response increases, while dRL demonstrates a lower over-all sensitivity to miscalibration (with a calibration response function for a highly anisotropic fibre being optimal). However, dRL demonstrates a reduced ability to resolve low anisotropy crossing-fibres compared to CSHD. It is concluded that the range and spatial-distribution of expected single-fibre anisotropies within an image must be carefully considered to ensure selection of the appropriate algorithm, parameters and calibration. Failure to choose the calibration response function carefully may severely impact the quality of any resultant tractography.
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1195.
lsj
(2022-05-31 22:29):
#paper:https://doi.org/10.1371/journal.pcbi.1003588
几千年来,哲学家们一直在争论意识的本质,以及它能否存在于其他物种中。而现在,随着人工智能技术越发成熟,人们对揭开意识的谜底更迫切——仅仅通过交互,即经典的图灵测试,可能已无法判断你是在和机器打交道,还是在和人打交道了,伴随而来的人工智能伦理挑战越发不容忽视。本文提出了一种定量刻画意识的理论,整合信息论,来探索意识的机制。主要有几部分关键内容,整合信息论简介、关于意识的公理、对意识的物理基质的假定、机制的系统与概念结构、整合信息论的局限性。
Abstract:
This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific--it is …
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This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific--it is what it is by how it differs from alternative experiences; integration says that it is unified--irreducible to non-interdependent components; exclusion says that it has unique borders and a particular spatio-temporal grain. These axioms are formalized into postulates that prescribe how physical mechanisms, such as neurons or logic gates, must be configured to generate experience (phenomenology). The postulates are used to define intrinsic information as "differences that make a difference" within a system, and integrated information as information specified by a whole that cannot be reduced to that specified by its parts. By applying the postulates both at the level of individual mechanisms and at the level of systems of mechanisms, IIT arrives at an identity: an experience is a maximally irreducible conceptual structure (MICS, a constellation of concepts in qualia space), and the set of elements that generates it constitutes a complex. According to IIT, a MICS specifies the quality of an experience and integrated information ΦMax its quantity. From the theory follow several results, including: a system of mechanisms may condense into a major complex and non-overlapping minor complexes; the concepts that specify the quality of an experience are always about the complex itself and relate only indirectly to the external environment; anatomical connectivity influences complexes and associated MICS; a complex can generate a MICS even if its elements are inactive; simple systems can be minimally conscious; complicated systems can be unconscious; there can be true "zombies"--unconscious feed-forward systems that are functionally equivalent to conscious complexes.
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1196.
笑对人生
(2022-05-31 22:11):
#paper doi: 10.1038/s41592-022-01481-8. Benchmarking spatial and single-cell transcriptomics integration methods. Nat Methods. 2022 May 16. 空间转录组(spatial transcriptomics)的发展极大提高了我们对组织RNA转录本的空间定位的认知。然而,目前空间转录组的技术并不能获取单个细胞的转录组特征。为了突破这个局限,人们往往将单细胞转录组测序(single-cell transcriptomics)和空间转录组测序进行整合分析。本文利用45对公开数据(空转和单细胞)和32份模拟数据,分别就两个整合需考虑的问题,对16种整合工具(有些工具两种功能都有)进行了基准测试(benchmark)。第一个问题是预测RNA转录本在组织空间分布(复位),共测试了8种整合方法。第二个问题是对组织的spot进行正确的单细胞类型区分和注释,共测试了12种整合方法。结果表明,解决第一个问题优势明显的有Tangram、gimVI、SpaGE。解决第二问题优势明显的是Cell2location、SpatialDWLS和RCTD。如果综合效率和准确性的话,推荐使用Tangram和Seurat。
Abstract:
No abstract available.
1197.
旺旺小小酥
(2022-05-31 21:30):
#paper 网络结构与银行效率:基于时变“银行—股东”网络的研究[J].经济研究,2021,56(12):60-76. 文章截取04年至17年间商业银行作为数据源构建时变“银行-股东”网络,探究社会网络结构对银行效率的关系,也从微观层面探求社会网络对金融领域发挥的作用。研究结果当然表现出明显的积极性,和文中所作的假设结论一致,但影响程度会在风险加权资产后有所降低,类似的,银行的交叉持股结构、产权性质和银行类型存在异质性。在这种时变“银行-股东”网络机制中,有两个值得注意的机制传导路径:①提升银行间的资源共享 ②银行竞争性扭曲的降低。针对第一个路径,近年来很多银行也在积极地寻求变革,包括银行的数字化专项、金融科技等道路的探索,第二条路径,有两个方面,一个是银行自身要考虑表内外风险因素的影响,第二个则是需要政策进行引导,促进银行间的协同带动效应。
经济研究,
2021.
Abstract:
高效健全的银行体系是实体经济高质量发展的基石,本文基于2004—2017年105家商业银行数据构建时变"银行—股东"网络,从社会网络这一非正式制度视角考察网络结构对银行效率的影响和微观机制。研究发现:时变"银行—股东"网络中心度提升对银行效率具有积极影响,网络位置越中心,网络广度、中介程度越高,银行效率相对越高;在纳入表内外风险资产作为非期望产出进行效率估算后,网络中心度与银行效率的这一正向关系依然成立,但作用幅度有所降低;在传导机制上,网络中心度的提升通过"竞争机制"和"资源共享机制"改善银行整体效率。同时,银行的交叉持股水平、产权性质及银行类型会对网络结构与银行效率间的关系产生异质性影响。本研究为商业银行进行效率管理提供了来自非正式制度的全新分析视角,也为有关部门制定银行体系的发展战略提供了一定参考。
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高效健全的银行体系是实体经济高质量发展的基石,本文基于2004—2017年105家商业银行数据构建时变"银行—股东"网络,从社会网络这一非正式制度视角考察网络结构对银行效率的影响和微观机制。研究发现:时变"银行—股东"网络中心度提升对银行效率具有积极影响,网络位置越中心,网络广度、中介程度越高,银行效率相对越高;在纳入表内外风险资产作为非期望产出进行效率估算后,网络中心度与银行效率的这一正向关系依然成立,但作用幅度有所降低;在传导机制上,网络中心度的提升通过"竞争机制"和"资源共享机制"改善银行整体效率。同时,银行的交叉持股水平、产权性质及银行类型会对网络结构与银行效率间的关系产生异质性影响。本研究为商业银行进行效率管理提供了来自非正式制度的全新分析视角,也为有关部门制定银行体系的发展战略提供了一定参考。
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1198.
颜林林
(2022-05-31 07:28):
#paper doi:10.1038/s41586-021-03583-3 Nature 2021, Swarm Learning for decentralized and confidential clinical machine learning. 精准医学的发展得益于数据的快速积累,然而数据共享却始终是数据充分使用的重大障碍。本文提出一种群体学习方法,它结合了边缘计算、区块链等技术,使数据拥有者可以在不违反隐私法规的情况下,让数据可以在全球范围被集成使用,从而解决药物靶标发现、诊断标志物发现等精准医学研究目标所亟需的大规模数据整合需求。为验证该方法的可行性,本文选取了四种疾病,新冠、结核、白血病和肺病,包括血液转录组和胸部X光片数据,且这些数据存在普遍的异质性和对照分布不均匀等问题,对这些数据进行此群体学习的分析。通过将数据分散到不同网络节点,并让这些节点动态加入计算,最终实现对这些疾病的识别或亚型鉴定,并与传统机器学习方法结果进行对比。本文最近在Nature Reviews Immunology的一篇comment上被再次提及,并介绍了其白血病临床诊断已被欧盟成功标准化并随后商业化,进一步验证了该方法的实际价值。同时,由于它以“共享见解而非共享数据(sharing insights, not data)”的方式进行协作,对于当下诸如医学免疫学等复杂研究,也将起到更大作用。
Abstract:
Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine. Patients with leukaemia can be identified using machine learning on the basis …
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Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning-a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.
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1199.
Ricardo
(2022-05-30 23:39):
#paper https://arxiv.org/abs/2102.04159v3 Deep Residual Learning in Spiking Neural Networks. 2021年发表于NIPS。基于人工神经网络的现代深度学习技术在各个领域上都取得了相当大的进展,但是由于其数学上的黑箱不可解释性、功耗高的问题,有一部分研究开始关注于基于生物脉冲神经元的脉冲神经网络上(SNN)。SNN有较高的生物解释性、事件驱动性和低功耗等特点,被视为人工神经网络的潜在竞争对手。但是SNN仍然面临许多理论和工程问题,在一些复杂任务上的表现仍然比ANN差。基于残差学习在ANN上取得的巨大成功,自然会去研究如何利用残差学习去训练SNN。之前的一些研究仿照ANN中标准的残差模块,简单地将relu激活函数替换成脉冲神经元,但是这样的网络伴随着深度的增加会出现退化问题,从而难以实现残差学习。在这篇论文里,作者证明了之前在SNN上的残差学习方法会导致梯度爆炸/消失问题,从而难以实现identity mapping。因此,他们提出了一个方法用来解决这么一个梯度爆炸/消失问题。实验结果也挺漂亮的,在多个数据集上都比之前的snn方法更好,当然不如ann的结果啦。并且能够通过加深网络深度提高snn的performance。而且,也首次实现了能够直接训练超过100层的snn。
arXiv,
2022.
DOI: 10.48550/arXiv.2102.04159
Abstract:
Deep Spiking Neural Networks (SNNs) present optimization difficulties for gradient-based approaches due to discrete binary activation and complex spatial-temporal dynamics. Considering the huge success of ResNet in deep learning, it …
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Deep Spiking Neural Networks (SNNs) present optimization difficulties for gradient-based approaches due to discrete binary activation and complex spatial-temporal dynamics. Considering the huge success of ResNet in deep learning, it would be natural to train deep SNNs with residual learning. Previous Spiking ResNet mimics the standard residual block in ANNs and simply replaces ReLU activation layers with spiking neurons, which suffers the degradation problem and can hardly implement residual learning. In this paper, we propose the spike-element-wise (SEW) ResNet to realize residual learning in deep SNNs. We prove that the SEW ResNet can easily implement identity mapping and overcome the vanishing/exploding gradient problems of Spiking ResNet. We evaluate our SEW ResNet on ImageNet, DVS Gesture, and CIFAR10-DVS datasets, and show that SEW ResNet outperforms the state-of-the-art directly trained SNNs in both accuracy and time-steps. Moreover, SEW ResNet can achieve higher performance by simply adding more layers, providing a simple method to train deep SNNs. To our best knowledge, this is the first time that directly training deep SNNs with more than 100 layers becomes possible.
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1200.
魏魏魏
(2022-05-30 23:07):
#paper doi:10.1016/j.paid.2015.01.017 Personality and Individual Differences, (2015), The impact of self-determined motivation on volunteer role identities: A cross-lagged panel study. 志愿者的工作在很多领域都被探讨,那么这种有计划且持久的亲社会行为的动机基础是什么?本研究探讨的就是这个问题,即志愿者是如何认同自己角色的。自我决定理论认为,动机的品质会极大影响人们在各种情况下的行为表现和幸福感等。当前研究采用了交叉滞后研究设计,探讨了自我决定及控制性动机与整体角色认同和组织特异性角色认同两种不同志愿者角色类型之间的交叉之后效应,这个交叉之后的时间间隔是16个月。最终的分析结果表明,自我决定的动机对两种不同志愿者角色类型都存在积极影响。只有组织特异性角色认同对随后的自我决定动机有积极影响。组织特异性角色认同对随后的控制性动机有积极的交叉之后效应。整体来讲,该研究支持了自我决定动机是志愿者角色认同的观点。
Abstract:
Volunteer role identity is regarded the direct and proximal cause of sustained volunteerism. Self-determination theory suggests that the quality of motivation greatly affects performance and well-being in various contexts. Therefore, …
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Volunteer role identity is regarded the direct and proximal cause of sustained volunteerism. Self-determination theory suggests that the quality of motivation greatly affects performance and well-being in various contexts. Therefore, this study investigated cross-lagged effects (over a time period of 16 months) between self-determined and controlled motivation, on the one hand, and two types of volunteer role identities, on the other hand: general role identity (GRI) and organization-specific role identity (OSRI). Analyses confirmed positive time-lagged effects of self-determined motivation on both GRI and OSRI. Time-lagged effects in opposite direction were significantly weaker; only OSRI showed a positive impact on subsequent self-determined motivation. OSRI (but not GRI) also had a positive lagged effect on controlled motivation. Overall, this study supported the idea that self-determined motivation represents a causal antecedent of volunteer role identities.
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