当前共找到 1194 篇文献分享,本页显示第 401 - 420 篇。
401.
朵朵 (2023-09-30 22:00):
#paper Ivanov, Iskren. "Reshaping U.S. Smart Power: Towards a Post-Pandemic Security Architecture." Journal of Strategic Security 13, no. 3 (2020) : 46-74. DOI: https://doi.org/10.5038/1944-0472.13.3.1829 这篇论文的主题是后疫情时代,美国应运用“巧实力”塑造世界安全架构。论文先对“巧实力”的概念进行分析,对比了约瑟夫·奈等三人对于“巧实力”的不同定义,提出了自己的一个关于“巧实力”的理论框架,包括5个层次: ·hard power ·soft power ·smart goal ·smart strategy ·smart face 并用这个框架分析了美国在后疫情时代应该重点关注的四个领域,包括美中、美俄、美国与中东、美国与亚太。关于如何在美中关系中运用“巧实力”,照实抄录可能发不出来,反正挺狠。可以看看关于美俄: ·hard power:经济制裁俄罗斯 ·soft power :对俄罗斯侵犯人权行为进行媒体报道 ·smart goal:通过美欧能源会议限制俄罗斯对欧盟及北约成员对能源影响力 ·smart strategy:对欧洲盟友进行人道主义、金融、军事支持 ·smart face :通过在北约东线重新部署美国军队来防御俄罗斯 我读这篇文章,有几个体会:第一,“巧实力”这个概念,我不是很认同,更像是卖弄词汇,其根基还没有软实力深,软实力大家还能说上几句,巧实力是什么,谁也说不清,感觉就是软硬兼施而已。第二,这篇论文写作是面向实际问题的,提出一个理论框架分析现实,甭管你认同不认同,至少这点做得不错。不喜欢纯理论探讨的。第三,文章发表在2020年,那个时候疫情刚刚开始,俄乌冲突还没发生,当时发表估计作者觉得很有前瞻性,但俄乌冲突是世界安全架构的一个巨大变量,所以当时前瞻的分析,现在有点过时。
Abstract:
COVID19 turned out to be one of the deadliest diseases in history. The United States faced a series of new challenges after the Coronavirus spread throughout the world. China is … >>>
COVID19 turned out to be one of the deadliest diseases in history. The United States faced a series of new challenges after the Coronavirus spread throughout the world. China is taking advantage of the pandemic to challenge the U.S. global dominance. The main purpose of this article is to analyze the role of the United States in the postpandemic security architecture at a global level. The basic claim of the article is that Washington should reshape U.S. smart power in order to preserve the American global dominance. The article’s claim rests on the assumption that smart power is the most effective instrument of U.S. Foreign Policy in the post-Cold War era. It was U.S. smart power that allowed Washington to maintain its global leadership after the 9/11 attacks. The Coronacrisis will have longterm consequences for the global security architecture. However, this article argues that the Coronavirus pandemic will not change the global order. <<<
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402.
惊鸿 (2023-09-30 19:52):
#paper Fear of the dark The invisible enemy. 27 September 2023 https://doi.org/10.1038/d41586-023-03002-9 这篇文章描述了一个军官与一位教授的对话,讨论了关于暗物质中的生物存在和潜在威胁的问题。故事中,教授向军官解释了暗物质的存在和性质,并透露他们已经发现了一些暗物质的聚集体,里面有活动的“事物”。这些事物不仅仅是无生命的物质,它们还拥有技术,并且暗物质的力量比我们所知的力量更为强大。教授担心这些暗物质生物可能会利用他们的技术建造引力武器,对人类构成威胁。因此,他建议采取行动,并使用一个小型黑洞来消灭他们。最后,军官同意了这个建议,并表示将动用军队来执行任务。
IF:50.500Q1 Nature, 2023-Sep-27. DOI: 10.1038/d41586-023-03002-9 PMID: 37759111
Abstract: No abstract available.
403.
大勇 (2023-09-30 19:42):
#paper A membrane-associated MHC-I inhibitory axis for cancer immune evasion Cell August 08, 2023DOI:https://doi.org/10.1016/j.cell.2023.07.016 这篇文献使用CRISPR的文库筛选方法,通过构建特异性抗原提呈模型筛选与MHCI特异性调控相关的因子,并通过机制分析和表型探索,发现了STW复合物对其的自噬降解调控作用
IF:45.500Q1 Cell, 2023-08-31. DOI: 10.1016/j.cell.2023.07.016 PMID: 37557169
Abstract:
Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of … >>>
Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of resistance, we identified key MHC-I regulators using specific peptide-MHC-I-guided CRISPR-Cas9 screens in AML. The top-ranked negative regulators were surface protein sushi domain containing 6 (SUSD6), transmembrane protein 127 (TMEM127), and the E3 ubiquitin ligase WWP2. SUSD6 is abundantly expressed in AML and multiple solid cancers, and its ablation enhanced MHC-I AP and reduced tumor growth in a CD8 T cell-dependent manner. Mechanistically, SUSD6 forms a trimolecular complex with TMEM127 and MHC-I, which recruits WWP2 for MHC-I ubiquitination and lysosomal degradation. Together with the SUSD6/TMEM127/WWP2 gene signature, which negatively correlates with cancer survival, our findings define a membrane-associated MHC-I inhibitory axis as a potential therapeutic target for both leukemia and solid cancers. <<<
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404.
半面阳光 (2023-09-30 19:16):
#paper DOI:https://doi.org/10.3390/genes12040478,Genes,2021,Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities:A Prospective Study from a Less Developed Autonomous Region in Mainland China. 拓展的NIPT检测,即除了检测21,18和13三条常见染色体三体异常之外,拓展到检测性染色体、其他常染色体的检测,乃至一些拷贝数异常的检测。这篇文章收集了86262例单胎妊娠的NIPT受检样本,其中86193例样本能够获得检测结果。这篇文章最主要的意义是将这8万例受检样本按照人群特征进行分类,并统计计算了不同人群中,NIPT检测检出常见三种染色体三体、不常见的常染色体三体、性染色体异常以及CNV的PPV、NPV、检测的敏感性特异性等统计数据。这给临床检测中应用拓展性NIPT技术提供了参考依据。
IF:2.800Q2 Genes, 2021-03-25. DOI: 10.3390/genes12040478 PMID: 33806256
Abstract:
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively … >>>
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information. <<<
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405.
周周复始 (2023-09-30 15:59):
#paper Sample sizes and population differences in brain template construction.November 2019NeuroImage 206:116318.DOI: 10.1016/j.neuroimage.2019.116318.在磁共振成像(MRI)数据处理的各种pipeline中,通常使用空间归一化或对标准脑模板的形变作为关键模块。大脑模板通常是使用有限数量的受试者的MRI数据构建的,个体大脑在形态上表现出显著的差异。因此,样本量和群体差异是影响脑模板构建的两个关键因素。为了解决这些影响,本文用HCP和CHCP的两个数据来量化样本量和人口对大脑模板构建的影响。首先使用来自HCP和CHCP的数据子集评估样本量对体积脑模板构建的影响。应用了变形变异性的体素指数和对数变换的雅可比行列式来评估与模板构建相关的变异性,并将大脑模板变异性建模为样本量的幂函数。在系统水平上,额顶叶控制网络和背侧注意网络表现出较高的变形变异性,而其他主要网络表现出较低的变异性。为了研究人群差异,还构建了高加索人和中国人的标准脑图谱(即US200和CN200)。两个人口统计学上匹配的模板,特别是语言相关区域,在边缘上回和额下回的变形变异性和记录的雅可比行列式上表现出显著的双边差异。使用HCP和CHCP的独立数据,检验了分割和配准的准确性,发现在空间归一化中使用人口不匹配模板显著降低了大脑的分割和配准性能。研究结果为支持在人脑图谱研究中使用人口匹配模板提供了证据。
IF:4.700Q1 NeuroImage, 2020-02-01. DOI: 10.1016/j.neuroimage.2019.116318 PMID: 31689538
Abstract:
Spatial normalization or deformation to a standard brain template is routinely used as a key module in various pipelines for the processing of magnetic resonance imaging (MRI) data. Brain templates … >>>
Spatial normalization or deformation to a standard brain template is routinely used as a key module in various pipelines for the processing of magnetic resonance imaging (MRI) data. Brain templates are often constructed using MRI data from a limited number of subjects. Individual brains show significant variabilities in their morphology; thus, sample sizes and population differences are two key factors that influence brain template construction. To address these influences, we employed two independent groups from the Human Connectome Project (HCP) and the Chinese Human Connectome Project (CHCP) to quantify the impacts of sample sizes and population on brain template construction. We first assessed the effect of sample size on the construction of volumetric brain templates using data subsets from the HCP and CHCP datasets. We applied a voxel-wise index of the deformation variability and a logarithmically transformed Jacobian determinant to quantify the variability associated with the template construction and modeled the brain template variability as a power function of the sample size. At the system level, the frontoparietal control network and dorsal attention network demonstrated higher deformation variability and logged Jacobian determinants, whereas other primary networks showed lower variability. To investigate the population differences, we constructed Caucasian and Chinese standard brain atlases (namely, US200 and CN200). The two demographically matched templates, particularly the language-related areas, exhibited dramatic bilaterally in supramarginal gyri and inferior frontal gyri differences in their deformation variability and logged Jacobian determinant. Using independent data from the HCP and CHCP, we examined the segmentation and registration accuracy and observed significant reduction in the performance of the brain segmentation and registration when the population-mismatched templates were used in the spatial normalization. Our findings provide evidence to support the use of population-matched templates in human brain mapping studies. The US200 and CN200 templates have been released on the Neuroimage Informatics Tools and Resources Clearinghouse (NITRC) website (https://www.nitrc.org/projects/us200_cn200/). <<<
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406.
张贝 (2023-09-30 13:45):
#paper Serial assessment of measurable residual disease in medulloblastoma liquid biopsies Cancer Cell. 2021 Nov 8;39(11):1519-1530.e4.髓母细胞瘤(Medulloblastoma,MB)是一种恶性的儿童胚胎中枢神经系统肿瘤,近三分之一的MB儿童死于这种疾病。通过影像学和脑脊液(CSF)细胞学进行常规反应监测仍然具有挑战性,并且缺乏可检测MRD的标志物。本文使用来自CSF的cfDNA作为MRD生物标志物,前瞻性验证从MB儿童(123名患者,476个样本)收集的CSF样本中的临床效用。使用低深度全基因组测序,研究了来自CSF的cfDNA中肿瘤相关拷贝数的变化。在基线时分别在85%和54%的转移性和局限性疾病患者中检测到MRD。MRD阳性患者的数量随着治疗的进行而下降,但那些持续性MRD阳性的患者有更高的进展风险。该研究阐释了cfDNA检测的疾病预测价值和诊断价值。
IF:48.800Q1 Cancer cell, 2021-11-08. DOI: 10.1016/j.ccell.2021.09.012 PMID: 34678152 PMCID:PMC9620970
Abstract:
Nearly one-third of children with medulloblastoma, a malignant embryonal tumor of the cerebellum, succumb to their disease. Conventional response monitoring by imaging and cerebrospinal fluid (CSF) cytology remains challenging, and … >>>
Nearly one-third of children with medulloblastoma, a malignant embryonal tumor of the cerebellum, succumb to their disease. Conventional response monitoring by imaging and cerebrospinal fluid (CSF) cytology remains challenging, and a marker for measurable residual disease (MRD) is lacking. Here, we show the clinical utility of CSF-derived cell-free DNA (cfDNA) as a biomarker of MRD in serial samples collected from children with medulloblastoma (123 patients, 476 samples) enrolled on a prospective trial. Using low-coverage whole-genome sequencing, tumor-associated copy-number variations in CSF-derived cfDNA are investigated as an MRD surrogate. MRD is detected at baseline in 85% and 54% of patients with metastatic and localized disease, respectively. The number of MRD-positive patients declines with therapy, yet those with persistent MRD have significantly higher risk of progression. Importantly, MRD detection precedes radiographic progression in half who relapse. Our findings advocate for the prospective assessment of CSF-derived liquid biopsies in future trials for medulloblastoma. <<<
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407.
笑对人生 (2023-09-30 11:38):
#paper doi: 10.1038/s41467-023-41452-x. Belliveau NM, et al. Whole-genome screens reveal regulators of differentiation state and context-dependent migration in human neutrophils. Nat Commun. 2023 Sep 18;14(1):5770. 中性粒细胞是人类数量最多的淋巴细胞,主要通过迁移到组织损伤和感染发生部位为机体提供早期的先天性免疫应答。在分子信号的刺激下,中性粒细胞的迁移速度能达5-20 um/min。那么,在迁移过程,中性粒细胞分化和出现表型多样性的机制是什么?它们是如何适应和改变目的环境?本研究通过全基因组CRISPR敲低筛选技术(CRISPRi screen),首先发现mTORC1信号通路是人HL-60分化的类中性细胞系分化向迁移状态转化的关键通路。接着通过定向敲低该通路的基因,定位到ATIC基因。ATIC基因主要通过影响中性粒细胞能量代谢驱动迁移。此外,作者发现中性粒细胞直接的趋化作用和间接的化学动力学行为具有非常强的基因表达相关性。以及黏附依赖和非黏附依赖迁移行为之间存在数百个差异基因。总之,本研究为CRISPRi screen应用于细胞时序行为提供了很好的研究范式。有趣的是,本研究对活细胞示踪图像数据提供了一个定量细胞迁移持久性的算法模型(贝叶斯推断)。
IF:14.700Q1 Nature communications, 2023-09-18. DOI: 10.1038/s41467-023-41452-x PMID: 37723145
Abstract:
Neutrophils are the most abundant leukocyte in humans and provide a critical early line of defense as part of our innate immune system. We perform a comprehensive, genome-wide assessment of … >>>
Neutrophils are the most abundant leukocyte in humans and provide a critical early line of defense as part of our innate immune system. We perform a comprehensive, genome-wide assessment of the molecular factors critical to proliferation, differentiation, and cell migration in a neutrophil-like cell line. Through the development of multiple migration screen strategies, we specifically probe directed (chemotaxis), undirected (chemokinesis), and 3D amoeboid cell migration in these fast-moving cells. We identify a role for mTORC1 signaling in cell differentiation, which influences neutrophil abundance, survival, and migratory behavior. Across our individual migration screens, we identify genes involved in adhesion-dependent and adhesion-independent cell migration, protein trafficking, and regulation of the actomyosin cytoskeleton. This genome-wide screening strategy, therefore, provides an invaluable approach to the study of neutrophils and provides a resource that will inform future studies of cell migration in these and other rapidly migrating cells. <<<
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408.
符毓 Yu (2023-09-30 10:07):
#paper doi:10.1038/171737a0 International Conference on Industrial Engineering and Systems Management (IESM), 2019, AMHS Vehicle Management Policies in Semiconductor Manufacturing: A Short Review. AMHS(Automated Material Handling Systems)在半导体晶圆厂里属于较为重要的设备系统,主要解决不同加工工序间物料的等待和运输效率问题。国内有少数企业正在努力做此环节的国产替代故而关注到这个方向。本文较为基础,介绍了AMHS的背景、特征和构成,以及主流调度方法的各自优缺点
409.
小年 (2023-09-30 08:20):
#paper draft human pangenome reference, Nature, 10 May 2023. doi.org/10.1038/s41586-023-05896-x. 这篇文章中人类泛基因组参考联盟(Human Pangenome Reference Consortium)首次呈现了人类泛基因组参考图谱的初步版本。该泛基因组参考图谱由来自遗传多样性人群的47个单倍体定相的二倍体组装基因组序列构成。这些组装序列覆盖了每个基因组中超过99%的序列,并且在结构和碱基水平上的准确性也超过99%。基于这些组装序列的比对,本篇文章作者生成了一个初步版本的泛基因组参考图谱,其中包含已知变异和单倍型,并揭示了在结构复杂位点上的新等位基因。此外,相对于现有的GRCh38参考基因组,泛基因组参考图谱添加了11,900万个常染色体多态位点和1,115个基因重复,其中约有9,000万个额外的碱基对来自结构变异。基于初步版本泛基因组参考图谱分析短读长测序数据,相对于基于GRCh38的工作流程,小突变的检测误差降低了34%,每个单倍型序列检测到的结构变异数量增加了104%,并且实现了对大多数样本的结构变异等位基因的分型。 思考:目前通用的人类参考基因组(GRCh38)是基于多个捐献者的DNA组装成而成线性参考基因组,捐献者主要以非裔和欧裔为主,亚裔成分较少。由于世界各地区人群中存在大量的遗传多态性,GRCh38并不能代表各个群体内所有的遗传多态性。本篇文章生成了来自世界各地区人群的47个单倍型定相的组装基因组,从而构建了人类泛基因组的初步版本。通过对短读长测序数据进行分析,发现相较于GRCh38的检测流程,对各类型的遗传突变都有了更好的检测效果。不过本篇文章构建的泛基因组主要是基于美洲和非洲人群,亚洲人群的比例只有13%,可能并不能很好的代表亚洲人群的遗传多样性。
IF:50.500Q1 Nature, 2023-05. DOI: 10.1038/s41586-023-05896-x PMID: 37165242 PMCID:PMC10172123
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K Lucas, Jean Monlong, Haley J Abel, Silvia Buonaiuto, Xian H Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M Eizenga, Xiaowen Feng, Christian Fischer, Robert S Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J Martin, Matthew W Mitchell, Katherine M Munson, Moses Njagi Mwaniki, Adam M Novak, Hugh E Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R Vollger, Lucinda L Antonacci-Fulton, Gunjan Baid, Carl A Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E Cook, Robert M Cook-Deegan, Omar E Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa' A Garrison, Carlos Garcia Giron, Richard E Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P Ji, Eimear E Kenny, Barbara A Koenig, Alexey Kolesnikov, Jan O Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D Olson, Alice B Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A Regier, Arang Rhie, Samuel Sacco, Ashley D Sanders, Valerie A Schneider, Baergen I Schultz, Kishwar Shafin, Michael W Smith, Heidi J Sofia, Ahmad N Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M D Wood, Aleksey V Zimin, Guillaume Bourque, Mark J P Chaisson, Paul Flicek, Adam M Phillippy, Justin M Zook, Evan E Eichler, David Haussler, Ting Wang, Erich D Jarvis, Karen H Miga, Erik Garrison, Tobias Marschall, Ira M Hall, Heng Li, Benedict Paten <<<
Abstract:
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These … >>>
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample. <<<
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410.
钟鸣 (2023-09-29 22:03):
#paper doi:10.1128/iai.00252-23 Protection against lethal sepsis following immunization with Candida species varies by isolate and inversely correlates with bone marrow tissue damage 文章通过攻毒保护实验探讨了不同念珠菌接种小鼠后引发的免疫保护能力。结果认为,不同毒力表型的分离株提供的保护作用各不相同,不提供交叉保护。第二,股骨组织的铁死亡和结构完整性可作为定量指标衡量分离株的毒力强弱。此外还有一个意料之外的现象:毒力最强的分离株提供的免疫保护作用却最弱。
IF:2.900Q2 Infection and immunity, 2023-10-17. DOI: 10.1128/iai.00252-23 PMID: 37702509
Abstract:
Protection against lethal ()/ () intra-abdominal infection (IAI)-mediated sepsis can be achieved by a novel form of trained innate immunity (TII) involving Gr-1+ myeloid-derived suppressor cells (MDSCs) that are induced … >>>
Protection against lethal ()/ () intra-abdominal infection (IAI)-mediated sepsis can be achieved by a novel form of trained innate immunity (TII) involving Gr-1+ myeloid-derived suppressor cells (MDSCs) that are induced by inoculation (immunization) with low virulence species [i.e., ()] that infiltrate the bone marrow (BM). In contrast, more virulent species (i.e., ), even at sub-lethal inocula, fail to induce similar levels of protection. The purpose of the present study was to test the hypothesis that the level of TII-mediated protection induced by strains inversely correlates with damage in the BM as a reflection of virulence. Mice were immunized by intraperitoneal inoculation with several parental and mutant strains of deficient in virulence factors (hyphal formation and candidalysin production), followed by an intraperitoneal challenge 14 d later and monitored for sepsis and mortality. Whole femur bones were collected 24 h and 13 d after immunization and assessed for BM tissue/cellular damage via ferroptosis and histology. While immunization with standard but not sub-lethal inocula of most wild-type strains resulted in considerable mortality, protection against lethal / IAI challenge varied by strain was usually less than that for , with no differences observed between parental and corresponding mutants. Finally, levels of protection afforded by the strains were inversely correlated with BM tissue damage ( = -0.773). TII-mediated protection against lethal sepsis induced by strain immunization inversely correlates with BM tissue/cellular damage as a reflection of localized virulence. <<<
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哪有情可长 (2023-09-28 21:40):
#paper A de novo evolved gene contributes to rice grain shape difference between indica and japonica, Nature Communications, 22 September 2023. doi.org/10.1038/s41467-023-41669-w. 该论文首先对粳稻和梗稻亚群组成的群体对籽粒长度和籽粒重量分别进行全基因组关联分析,关联分析的结果表型在9号染色体上都具有GSE9这个位点。其中在这个基因附近具有15个基因,对粳稻和梗稻亚群分别进行转录组鉴定其基因表达量后,最终缺点给一个ORF家族的基因,认为该基因是GSE9。后续实验验证发现该基因在粳稻中花11和日本晴背景下,敲除GSE9导致粒长显著增加、粒宽减小、长宽比增大;而过表达该基因导致粒长和粒宽均显著增加,表明水稻GSE9基因参与水稻粒型的调控。GSE9在稻属物种O. sativa、O. rufipogon、O. barthii、O. glumaepatula和O. longistaminata中存在高度同源的DNA序列,且仅在大部分粳稻品种和少数普通野生稻(O. rufipogon)中具有编码序列特征,而在其它稻属物种中的起始密码子位点为GTG,并非真核生物的起始密码子ATG,表明该基因可能通过de novo起源方式最早起源于普通野生稻的原非编码区,并传递到绝大部分粳稻品种中。对GSE9基因区段的序列分析,发现绝大部分粳稻品种具有起始密码子ATG,而绝大部分籼稻品种则不具备起始密码子(起始密码子位点为GTG,gse9),且序列变异表现出明显的籼粳亚种间分化特征。进一步结合系统进化树和单倍型网络分析,发现gse9型籼稻和GSE9型粳稻独立起源于Or-I和Or-III型普通野生稻。关于de novo origination在小麦重的研究还没有人有一个完整的基因list出来,也查看该专业祖师爷龙漫远的文章,拟南芥重从头起源的基因讲解的也很精彩。
IF:14.700Q1 Nature communications, 2023-09-22. DOI: 10.1038/s41467-023-41669-w PMID: 37737275
Abstract:
The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes … >>>
The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape. <<<
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前进 (2023-09-27 10:56):
#paper doi:10.1109/cvpr.2019.00223  2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR).  Noise2Void - Learning Denoising From Single Noisy Images. 基于深度学习的图像去噪一般是通过干净图像和噪声图像组成的图相对来进行训练的。目前也有一些做法可以无需干净图像,仅需多张噪声图像来完成模型的训练(N2N)。而本文提出了一种基于单张噪声图像的去噪方法。基于Patch去噪的观点认为,结果图像中的每一个像素点由于感受野的限制只取决于输入图像中的一部分区域。基于这个观点衍生出许多去噪的方法,例如Noise2Noise的方法,它不再需要干净的图像作为target。而本文提出了一种只需要单张噪声图像就能完成去噪的方法。作者认为,如果对于单张图像,以其中的一个patch作为网络的input,以这个patch中心位置的像素作为target,那么网络将会学习到直接将输入patch中心的像素映射到网络的输出这这种identity map。因此,作者设计了有一种特殊的感受野,将感受野中心的像素“抹去”,再要求网络去预测中心位置的信息。这种做法基于两个假设:1、不同位置的噪声像素之间是相互独立的 2、噪声的均值为0 。因此预测出来的中心像素点更有可能是信号而非噪声。
413.
龙海晨 (2023-09-27 10:40):
#paper Falahi S, Zamanian MH, Feizollahi P, Rezaiemanesh A, Salari F, Mahmoudi Z, Gorgin Karaji A. Evaluation of the relationship between IL-6 gene single nucleotide polymorphisms and the severity of COVID-19 in an Iranian population. Cytokine. 2022 Jun;154:155889. doi: 10.1016/j.cyto.2022.155889. Epub 2022 Apr 19. PMID: 35461173; PMCID: PMC9015956. 这是一篇2022年发表的新冠研究的文章。这个杂志影响因子3.8,对于这个杂志我真是感情复杂,当初我2022年投稿该杂志,他们说我不适合在他们这发表,然后给我推荐了另一个杂志,是杂志内部推荐,我的文章自动过去,然后他推荐的那个杂志把我拒稿了。现在,我很感谢他们当初的不发之恩,最后我的文章在4.6的杂志上发表还是中科院的Top期刊。这是一篇阴性结果的研究,估计就因为蹭了当时新冠的热点得以发表。做的实验不多研究的也简单,就是SNP位点的,研究的伊朗克尔曼沙赫库尔德人,共346人(175名重度新冠肺炎患者和171名轻度新冠肺炎患者)分析白细胞介素-6(IL-6)基因多态性,从患者外周血白细胞中提取基因组DNA以确定三个选择的SNPs的基因型(rs1800795(−174 G>C)、rs1800796(−572 G>C,和rs1800797(−597 G>A)),结果表明这些SNP与伊朗克尔曼沙赫库尔德人口中新冠肺炎的严重程度无关。SNP,阴性结果,如果不是当初新冠的热度,估计发不了这么高分的杂志。
IF:3.700Q2 Cytokine, 2022-06. DOI: 10.1016/j.cyto.2022.155889 PMID: 35461173
Abstract:
BACKGROUND: Emerged coronavirus disease 2019 (COVID-19) is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). Disease severity is associated with elevated levels of proinflammatory cytokines, such … >>>
BACKGROUND: Emerged coronavirus disease 2019 (COVID-19) is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). Disease severity is associated with elevated levels of proinflammatory cytokines, such as interleukin-6 (IL-6). Genetic polymorphisms in the regulatory regions of cytokine genes may be associated with differential cytokine production in COVID-19 patients. This study aimed to investigate the association between three potentially functional single-nucleotide polymorphisms (SNPs) in the promoter region of IL-6 and the severity of susceptibility to COVID-19 in an Iranian population.METHODS: In total, 346 individuals (175 patients with severe COVID-19 and 171 patients with mild COVID-19) were recruited for this cohort study. Genomic DNA was extracted from peripheral blood leukocytes of patients to determine the genotypes of three selected SNPs (rs1800795 (-174 G > C), rs1800796 (-572 G > C), and rs1800797 (-597 G > A)) in the promoter region of the IL-6 gene using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.RESULTS: There were no significant differences in the genotype or allele distribution of selected SNPs (rs1800795 (-174 G > C), rs1800796 (-572 G > C), and rs1800797 (-597 G > A)) in the promoter region of the IL-6 gene in patients with severe COVID-19 and patients with mild COVID-19.DISCUSSION: Our study indicated that these SNPs are not associated with COVID-19 severity in the Kurdish population from Kermanshah, Iran. <<<
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颜林林 (2023-09-27 09:43):
#paper doi:10.1038/s41467-023-41690-z. 2023, Nature Communications, Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk. 这篇文章使用了一种名为 Activity-by-Contact (ABC) 的计算方法,在20个癌种的已发表的多组学测序数据中进行分析,识别出54万多个“增强子-基因调控(Enhancer-gene regulation)”关系对,为解释这其中的非编码区突变功能提供了基础。此后又入组10例结直肠癌(CRC)临床样本,也进行多组学检测和上述调控关系对的鉴别,并将发现结果放到数万例的大规模人群中进行验证。此外,还进一步对其中发现的与CRC风险相关的调控区突变位点rs4810856,使用细胞系、小鼠模型等,在基因表达、蛋白表达等层面,分别进行了功能上的验证。整篇文章从逻辑上看并不特别连贯,但工作量比较大,更像是一开始入组了10例癌症患者的临床样本,做了多组学测序,之后在分析数据结果基础上不断扩展完善,最后拼凑出来的故事。
IF:14.700Q1 Nature communications, 2023-09-25. DOI: 10.1038/s41467-023-41690-z PMID: 37749132
Abstract:
Genome-wide association studies have identified numerous variants associated with human complex traits, most of which reside in the non-coding regions, but biological mechanisms remain unclear. However, assigning function to the … >>>
Genome-wide association studies have identified numerous variants associated with human complex traits, most of which reside in the non-coding regions, but biological mechanisms remain unclear. However, assigning function to the non-coding elements is still challenging. Here we apply Activity-by-Contact (ABC) model to evaluate enhancer-gene regulation effect by integrating multi-omics data and identified 544,849 connections across 20 cancer types. ABC model outperforms previous approaches in linking regulatory variants to target genes. Furthermore, we identify over 30,000 enhancer-gene connections in colorectal cancer (CRC) tissues. By integrating large-scale population cohorts (23,813 cases and 29,973 controls) and multipronged functional assays, we demonstrate an ABC regulatory variant rs4810856 associated with CRC risk (Odds Ratio = 1.11, 95%CI = 1.05-1.16, P = 4.02 × 10) by acting as an allele-specific enhancer to distally facilitate PREX1, CSE1L and STAU1 expression, which synergistically activate p-AKT signaling. Our study provides comprehensive regulation maps and illuminates a single variant regulating multiple genes, providing insights into cancer etiology. <<<
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李翛然 (2023-09-26 17:25):
#paper Cell2Sentence: Teaching Large Language Models the Language of Biology doi:10.1101/2023.09.11.557287; 该论文提出了一种称为Cell2Sentence的新方法,以便使大规模语言模型能够在单细胞转录组数据上进行训练。 该方法将基因表达配置文件表示为文本序列,作者称之为“细胞句子”。 这些细胞句子由基因名称组成,这些基因名称根据表达水平排序,从而创造了一个稳健且可逆的生物数据编码。作者的研究表明,细胞句子以语言模型易于理解的格式正确编码了基因表达数据。 在这些细胞句子上微调的语言模型不仅稳健收敛,而且与从零开始训练的模型或其他专门用于处理单细胞RNA测序数据的前沿深度学习模型相比,在与细胞句子相关的任务上的表现显著提高。 细胞句子可以与文本注释无缝集成,以执行生成和总结任务,这两种任务都从自然语言预训练中受益。 事实上,在使用Cell2Sentence生成的细胞句子上应用任何基于文本的体系结构没有理论限制。 作者的发现强调了迁移学习在这一交叉学科设置中的好处。 总之,该方法提供了一种简单、可适应的框架,利用现有的语言模型和库将自然语言和转录组学相结合。 作者证明了语言模型可以被进一步微调以生成和理解转录组学数据,同时保留其生成文本的能力。这为分析、解释和生成单细胞RNA测序数据开辟了新的途径。 关键贡献包括: 引入Cell2Sentence,一种有效的方法,可以将单细胞数据表示为文本序列。 证明了大规模语言模型可以在细胞句子上进行微调,以生成准确的细胞类型并理解转录组数据,从而预测细胞标签。 提供了一个简单且模块化的框架,利用流行的LLM库将LLM适配到转录组学。 Cell2Sentence模型的关键思想是将单个细胞的基因表达谱转换成基因名称的文本序列,这些基因名称按表达水平排序。具体来说:对单细胞RNA测序数据进行标准预处理,包括过滤低质量细胞,归一化计数矩阵等。对每个细胞的基因表达式进行排序,排序根据每个基因的表达量从高到低进行。将排序后的基因名称序列作为该细胞对应的文本,称为“细胞句子”。可以在细胞句子中加入元数据,如细胞类型等 biological annotations。现有的预训练语言模型可以在这些细胞句子上进一步微调,学习细胞句子的分布。微调后的模型可以用于下游任务,如根据细胞类型提示生成细胞句子,或者根据细胞句子预测细胞类型等。生成的细胞句子可以转换回基因表达空间,用于后续分析。整个框架提供了一种直接运用现有语言模型处理转录组学数据的灵活方法。 Cell2Sentence的关键创新在于提出了一种可逆的细胞表达至文本序列的转换,将单细胞数据表示成语言模型可以处理的格式。研究表明,该转换可以高效地在两个模态之间传递信息,为应用自然语言模型提供了可能。 这是我看到的第一个大模型的方法在基因和单细胞分析上,一看就是一个学生作品,比如关于转录中,上下游的调控,和基因的异质性的问题都没有考虑。 不过把,我倒觉得是个进步,随着AI的深度介入,如果真的在 DNA-RNA-蛋白质建立起来了一个庞大的对应关系库。 那么人类的再生医学会有质的飞跃,而且我觉得这个时间不会太久。
Abstract:
AbstractLarge language models like GPT have shown impressive performance on natural language tasks. Here, we present a novel method to directly adapt these pretrained models to a biological context, specifically … >>>
AbstractLarge language models like GPT have shown impressive performance on natural language tasks. Here, we present a novel method to directly adapt these pretrained models to a biological context, specifically single-cell transcriptomics, by representing gene expression data as text. Our Cell2Sentence approach converts each cell’s gene expression profile into a sequence of gene names ordered by expression level. We show that these gene sequences, which we term “cell sentences”, can be used to fine-tune causal language models like GPT-2. Critically, we find that natural language pretraining boosts model performance on cell sentence tasks. When fine-tuned on cell sentences, GPT-2 generates biologically valid cells when prompted with a cell type. Conversely, it can also accurately predict cell type labels when prompted with cell sentences. This demonstrates that language models fine-tuned using Cell2Sentence can gain a biological understanding of single-cell data, while retaining their ability to generate text. Our approach provides a simple, adaptable framework to combine natural language and transcriptomics using existing models and libraries. Our code is available at:https://github.com/vandijklab/cell2sentence-ft. <<<
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徐炳祥 (2023-09-24 14:05):
#paper doi: 10.1186/s13059-023-03019-3 Genome Biology, 2023, The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees。对灵长类动物进行比较基因组学研究受限于伦理因素和材料获取的困难而一直进展缓慢。由iPSC细胞诱导获得的胚胎样团(EB)是进行此类研究的好材料。本文作者使用人类和大猩猩的iPSC细胞分别诱导获得了EB,并使用单细胞RNA-seq进行了基因表达的比较分析。结果显示,胚胎样团中已包含大量已知细胞类型。对不同类型的细胞进行人-猩猩的基因差异表达分析鉴定了一系列差异表达基因。与序列保守性和基因功能注释进行比对发现在多个细胞类型中存在差异的基因与更低的序列保守性和人与猩猩的差异有关,而在各细胞类型中表达保守的基因集中于基础生命过程。进一步,作者使用人-猩猩融合细胞构建了EB并借此将表达差异分解为顺式和反式两类,证明了反式差异与两个物种的基因表达调控网络差异有关。作为一项干湿结合的研究,本文仅有3位作者。新产出数据量也不大。是资源/规模有限的研究组通过发挥专长和优化的实验设计在避免堆砌数据的前提下解决重大生物问题的良好范例。
IF:10.100Q1 Genome biology, 2023-09-11. DOI: 10.1186/s13059-023-03019-3 PMID: 37697401
Abstract:
BACKGROUND: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect … >>>
BACKGROUND: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees.RESULTS: We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes.CONCLUSIONS: Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences. <<<
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DeDe宝 (2023-09-23 08:50):
#paper https://www.nature.com/articles/s41598-022-18245-1: A comparison of reinforcement learning models of human spatial navigation , Scientific Reports, 2022,强化学习Reinforcement Learning, RL是机器学习的一个子领域,通过最大化长期的奖励的方式更新状态和行为进行学习。强化学习被广泛应用于决策、价值学习等领域,但用于描述人类空间导航的研究比较少,尤其是量化描述导航策略以及使用策略的一致性的研究就更少。本文比较了三类(共五个)强化学习模型对人类空间导航学习策略的量化描述,结果表明Model-Based RL和Model-Free RL线性加权所得的混合模型表现最好。
IF:3.800Q1 Scientific reports, 2022-08-17. DOI: 10.1038/s41598-022-18245-1 PMID: 35978035
Abstract:
Reinforcement learning (RL) models have been influential in characterizing human learning and decision making, but few studies apply them to characterizing human spatial navigation and even fewer systematically compare RL … >>>
Reinforcement learning (RL) models have been influential in characterizing human learning and decision making, but few studies apply them to characterizing human spatial navigation and even fewer systematically compare RL models under different navigation requirements. Because RL can characterize one's learning strategies quantitatively and in a continuous manner, and one's consistency of using such strategies, it can provide a novel and important perspective for understanding the marked individual differences in human navigation and disentangle navigation strategies from navigation performance. One-hundred and fourteen participants completed wayfinding tasks in a virtual environment where different phases manipulated navigation requirements. We compared performance of five RL models (3 model-free, 1 model-based and 1 "hybrid") at fitting navigation behaviors in different phases. Supporting implications from prior literature, the hybrid model provided the best fit regardless of navigation requirements, suggesting the majority of participants rely on a blend of model-free (route-following) and model-based (cognitive mapping) learning in such navigation scenarios. Furthermore, consistent with a key prediction, there was a correlation in the hybrid model between the weight on model-based learning (i.e., navigation strategy) and the navigator's exploration vs. exploitation tendency (i.e., consistency of using such navigation strategy), which was modulated by navigation task requirements. Together, we not only show how computational findings from RL align with the spatial navigation literature, but also reveal how the relationship between navigation strategy and a person's consistency using such strategies changes as navigation requirements change. <<<
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Ricardo (2023-09-21 17:32):
#paper https://www.biorxiv.org/content/10.1101/2023.09.15.557874v1.full SACNet: A Multiscale Diffeomorphic Convolutional Registration Network with Prior Neuroanatomical Constraints for Flexible Susceptibility Artifact Correction in Echo Planar Imaging 这是我最近released的一个工作。由于回波平面成像技术成像(EPI)速度较快,因此弥散磁共振成像和功能磁共振成像大都会采用EPI技术进行影像采集工作。但是EPI图像中一般会存在磁敏感性伪影(Susceptibility Artifacts, SAs),从而会导致采集的影像存在几何和信号上的扭曲。目前的伪影校正算法一般是针对特定采集序列的图像开发专门的方法,并且存在处理时间较长且校正质量有限等问题。因此,在这个研究中,我提出了一个基于无监督学习的卷积配准网络的伪影校正框架,该框架有以下几点技术创新:1. 我们建立了一个统一的数学框架,通过修正模型超参数,从而可以灵活地用于多相位编码和单相位编码数据的校正;2. 我们通过修改核物理领域内用于模拟无限深势阱的Woods-Saxon势函数,从而提出了一个微分同胚保持函数,用于生成微分同胚形变场;3. 我们设计了一个先验解剖学信息约束函数,从而将没有伪影的T1w/T2w图像中的先验结构信息纳入模型中;4. 我们最后针对该问题设计了一套多尺度的训练及推理协议用于网络的快速训练并优化模型收敛。通过在涵盖新生儿、儿童以及健康成年人的2000个脑影像扫描数据上实验证明,我们的方法比现有的方法表现出更加优异的性能。
Abstract:
AbstractSusceptibility artifacts (SAs), which are inevitable for modern diffusion brain MR images with single-shot echo planar imaging (EPI) protocols in wide large-scale neuroimaging datasets, severely hamper the accurate detection of … >>>
AbstractSusceptibility artifacts (SAs), which are inevitable for modern diffusion brain MR images with single-shot echo planar imaging (EPI) protocols in wide large-scale neuroimaging datasets, severely hamper the accurate detection of the human brain white matter structure. While several conventional and deep-learning based distortion correction methods have been proposed, the correction quality and model generality of these approaches are still limited. Here, we proposed the SACNet, a flexible SAs correction (SAC) framework for brain diffusion MR images of various phase-encoding EPI protocols based on an unsupervised learning-based registration convolutional neural network. This method could generate smooth diffeomorphic warps with optional neuroanatomy guidance to correct both geometric and intensity distortions of SAs. By employing near 2000 brain scans covering neonatal, child, adult and traveling participants, our SACNet consistently demonstrates state-of-the-art correction performance and effectively eliminates SAs-related multicenter effects compared with existing SAC methods. To facilitate the development of standard SAC tools for future neuroimaging studies, we also created easy-to-use command lines incorporating containerization techniques for quick user deployment. <<<
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芝麻 (2023-09-21 13:34):
#paper https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216877 Multi-modal characterization and simulation of human epileptic circuitry 颞叶癫痫是第四常见的神经系统疾病,大约有40%的患者对药物治疗无效。文章根据海马硬化严重程度将四个样本颞叶癫痫进行分级,然后进行单细胞核测序对比,发现了海马颗粒细胞在疾病进展中发生的改变,并将这些变化归因于三种电导通道:BK、Cav2.2和Kir2.1,最后作者在一个网络模型中通过调试以上三种电导通路的活性,达到了将疾病进展有关的变化逆转成一个较不易兴奋的“早期疾病样”状态
IF:7.500Q1 Cell reports, 2022-12-27. DOI: 10.1016/j.celrep.2022.111873 PMID: 36577383
Abstract:
Temporal lobe epilepsy is the fourth most common neurological disorder, with about 40% of patients not responding to pharmacological treatment. Increased cellular loss is linked to disease severity and pathological … >>>
Temporal lobe epilepsy is the fourth most common neurological disorder, with about 40% of patients not responding to pharmacological treatment. Increased cellular loss is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions, the impact of the disease at the cellular level remains unclear. Here, we show that hippocampal granule cells change with disease progression as measured in living, resected hippocampal tissue excised from patients with epilepsy. We show that granule cells increase excitability and shorten response latency while also enlarging in cellular volume and spine density. Single-nucleus RNA sequencing combined with simulations ascribes the changes to three conductances: BK, Cav2.2, and Kir2.1. In a network model, we show that these changes related to disease progression bring the circuit into a more excitable state, while reversing them produces a less excitable, "early-disease-like" state. <<<
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小年 (2023-09-01 00:00):
#paper https://doi.org/10.1038/sdata.2018.157 A tissue-based draft map of the murine MHC class I immunopeptidome 文章介绍了一个关于小鼠MHC I类免疫肽组的组织图谱,其中包含了19种正常组织中呈现给CD8+ T细胞的肽段的全面概述。方法总结如下: 1. 得到质谱下机数据。 2. 使用Msconvert将原始质谱数据转换为mzML格式。 3. 使用Comet、MS-GF+和XTandem等数据库搜索引擎,将mzML格式的数据与小鼠蛋白质数据库进行比对,以鉴定肽段。 4. 使用Prophets进行统计验证,以确定鉴定的肽段的置信度。 5. 使用GibbsCluster v.1对鉴定的肽段进行聚类分析,以确定具有相似质谱特征的肽段。 6. 使用NetMHC v.4对鉴定的肽段进行注释分析,以确定其长度和预测MHC结合亲和力。 7. 根据统计验证和注释分析的结果,筛选出高置信度的MHC相关肽段。 8. 使用高置信度的MHC相关肽段,构建高质量的H2D b/K b特异性肽段光谱和测定库。 9. 将构建的肽段光谱和测定库共享到SysteMHC Atlas和SWATH Atlas中,以便其他研究人员可以使用和分析这些数据。 10. 最终的结果呈现,包括肽段光谱和测定库的构建、MHC相关肽段的注释和筛选等。
IF:5.800Q1 Scientific data, 2018-08-07. DOI: 10.1038/sdata.2018.157 PMID: 30084848
Abstract:
The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC … >>>
The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo. We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I immunopeptidome in health. Peptides were extracted from 19 normal tissues from C57BL/6 mice and prepared for MS injections, resulting in a total number of 28,448 high-confidence H2D/K-associated peptides identified and annotated in the atlas. This atlas provides initial qualitative data to explore the tissue-specificity of the immunopeptidome and serves as a guide to identify potential tumor-associated antigens from various cancer models. Our data were shared via PRIDE (PXD008733), SysteMHC Atlas (SYSMHC00018) and SWATH Atlas. We anticipate that this unique dataset will be expanded in the future and will find wide applications in basic and translational immunology. <<<
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