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561.
龙海晨 (2023-04-10 13:25):
#paper Toama W, Wiederin J, Shanley R, Jewett P, Gu C, Shenoy C, Nijjar PS, Blaes AH. Impact of pectoralis muscle loss on cardiac outcome and survival in Cancer patients who received anthracycline based chemotherapy: retrospective study. BMC Cancer. 2022 Jul 13;22(1):763. doi: 10.1186/s12885-022-09882-w. PMID: 35831837; PMCID: PMC9281070. 文章回顾研究了几种癌症患者用蒽环类药物化疗后胸肌质量指数(pectoralis muscle mass index,PMI)与总体死亡率,主要心脏事件(Major Adverse Cardiovascular Events,MACE)生存率间的关系。(这里给大家解释几个专业名词MACE通俗讲解就是与心脏相关的不好的事情,例如,1,心脏原因引起的死亡;2,发生非致命的心肌梗死;3;发生非致命的心血管事件。具体点来说,日常遇到的,复发心绞痛、急性心肌梗死、严重心律失常、心力衰竭、冠心病死亡,心血管疾病事件,心衰,缺血性心血管事件,心源性死亡。PMI是计算胸肌的一个指标,有点类似于我们日常生活中的BMI,PMI:胸大肌面积 [cm 2 ]/身高2 [m 2 ])文章对474名癌症患者进行了回顾性分析,发现,接受蒽环类药物治疗的患者治疗前胸肌指数越高,发生 MACE 的风险越低。认为对化疗前检测PMI,尤其是对肌肉减少症患者化疗前进行干预预防能有效减少患者的MACE风险。
IF:3.400Q2 BMC cancer, 2022-Jul-13. DOI: 10.1186/s12885-022-09882-w PMID: 35831837
Abstract:
INTRODUCTION: The impact of pectoralis muscle mass index (PMI) on cardiac events is not well studied in cancer patients, especially in those who have received chemotherapy with high potential cardiac … >>>
INTRODUCTION: The impact of pectoralis muscle mass index (PMI) on cardiac events is not well studied in cancer patients, especially in those who have received chemotherapy with high potential cardiac toxicity such as anthracyclines.METHODS: Individuals aged ≥18 years with a diagnosis of breast cancer, sarcoma, or lymphoma who received anthracycline-based chemotherapy at the University of Minnesota MHealth Fairview between 2009 and 2014. Eligible patients had to have two CT scans: a baseline CT scan within 6 months prior to chemotherapy and a follow-up CT scan within 2 years after treatment. The PMI was calculated as the right pectoralis muscle area indexed to height squared. Multivariable linear regression was used to analyze factors associated with PMI at follow-up, overall mortality, and major cardiac events (MACE).RESULTS: A total of 474 patients (breast cancer 192; lymphoma 184; sarcoma 98) participated with a median age of 61 years at the time of baseline CT scan; 161 (34%) were male. Almost all patients received anthracyclines except 12% who received trastuzumab only. The median baseline PMI was 5.8 cm2/m2 (4.9, 7.7) which decreased 10.5% after chemotherapy, to 5.2 cm2/m2 (4.4, 6.4). Baseline PMI was not significantly associated with OS, but we detected lower risks of MACE with larger PMI at baseline. Greater baseline PMI was associated with greater follow-up PMI, but also with greater relative PMI loss. Female gender, older age, and history of smoking were also associated with greater PMI losses.CONCLUSION: Greater pre-treatment pectoralis muscle index in patients treated with anthracyclines have a lower risk of MACE. Early identification of sarcopenia using PMI could trigger proactive engagement for intervention and risk-stratified therapies. <<<
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562.
DeDe宝 (2023-04-10 11:47):
#paper doi:/10.1371/journal.pone.0000943.Causal Inference in Multisensory Perception,2007,Plos One(发表在Plos One,但是引用高) 神经系统不断地将来自不同感觉方式的不确定信息组合成对感觉刺激原因的综合理解。这些信息可能有相同的来源,也可能来自不同的来源,因此,线索的组合必须根据线索的因果关系。多模式感知整合的方法之一是线索整合概率模型,线索整合概率模型的基础是假定原因是统一的,但是后来的实验发现,当视觉和听觉刺激差异很大时,这种整合就会失效。信息之间的差异称为disparity(分离度)。当两个线索之间的disparity(分离度)增大,那么线索A对于另一个线索B的影响就会减小,反之亦然。disparity(分离度)的存在说明强制融合(无条件假定原因统一)是不成立的,因此还需要对线索之间的因果关系进行推断,需要在模型中增加一个检验交互性的先验(一个联合先验分布),用来分析两个线索同源的可能性高,还是不同源的可能性高。本研究提出了一个因果推断模型,该模型准确地预测了人类受试者在两个听觉-视觉定位任务中对线索的非线性整合。结果表明,人类确实可以有效地推断因果结构以及线索源的位置。推断因果结构的能力不仅限于有意识的、高层次的认知;它也在感知中不断地、毫不费力地进行。
IF:2.900Q1 PLoS ONE, 2007. DOI: 10.1371/journal.pone.0000943
Abstract:
Perceptual events derive their significance to an animal from their meaning about the world, that is from the information they carry about their causes. The brain should thus be able … >>>
Perceptual events derive their significance to an animal from their meaning about the world, that is from the information they carry about their causes. The brain should thus be able to efficiently infer the causes underlying our sensory events. Here we use multisensory cue combination to study causal inference in perception. We formulate an ideal-observer model that infers whether two sensory cues originate from the same location and that also estimates their location(s). This model accurately predicts the nonlinear integration of cues by human subjects in two auditory-visual localization tasks. The results show that indeed humans can efficiently infer the causal structure as well as the location of causes. By combining insights from the study of causal inference with the ideal-observer approach to sensory cue combination, we show that the capacity to infer causal structure is not limited to conscious, high-level cognition; it is also performed continually and effortlessly in perception. <<<
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563.
笑对人生 (2023-03-31 23:57):
#paper doi: 10.1016/j.cell.2018.03.027.Chen H, et al. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 Apr 5;173(2):386-399.e12. 增强子(enhancer)通常位于结构基因的附近,是一类非编码DNA调节元件,在癌症的发展过程中起到越来越重要的作用。本研究利用TCGA数据库33癌种,总共8928肿瘤患者的RNA-seq数据,从全基因组范围识别和鉴定出大量表达的增强子。通过与正常组织进行比较,发现大多数癌种的增强子处在激活状态,且与非整倍体改变正相关,但与突变负荷无关,由此提出增强子与基因互作的染色体状态假说。为了建立因果关系的增强子-基因调控网络模型,作者通过整合eQTL分析、mRNA共表达分析以及Hi-C数据分析的结果,最终发现65个增强子-基因互作对。这些互作对经过CGC注释,总共包含22个原癌基因和8个肿瘤抑制基因。文章的最后,作者还通过CRISPR/Cas9 RNAs技术证实了存在于PD-L1基因上游140kb的一个增强子。
IF:45.500Q1 Cell, 2018-04-05. DOI: 10.1016/j.cell.2018.03.027 PMID: 29625054
Abstract:
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number … >>>
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers. <<<
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564.
(2023-03-31 23:30):
#paper 2023-Structural changes induced by pasteurisation and/or high-pressure treatment of skim caprine milk。https://doi.org/10.1016/j.idairyj.2022.105528。该研究结果表明脱脂山羊乳的巴氏杀菌和高压(HP)组合(PHP)过程可以改变蛋白质的二级结构,导致表面疏水性增加。HP处理前的巴氏杀菌降低了α-螺旋结构含量,同时增加了β-折叠结构含量,这与脱脂山羊乳样品表面疏水性和固有荧光的变化有关。对于PHP和HP处理组样品,随着压力水平的增加和处理时间的延长,α-螺旋和β-转角结构含量降低,而β-折叠和无规卷曲结构含量增加。PHP处理可作为乳制品行业的一种良好替代技术,以提高脱脂山羊乳的功能特性。
Abstract:
The effects of pasteurisation, high-pressure (HP), and a combination of pasteurisation and high-pressure (PHP) on the physicochemical properties and protein structure of caprine skim milk was investigated. Samples treated by … >>>
The effects of pasteurisation, high-pressure (HP), and a combination of pasteurisation and high-pressure (PHP) on the physicochemical properties and protein structure of caprine skim milk was investigated. Samples treated by PHP generally had a higher pH, whey protein denaturation, surface hydrophobicity, and intrinsic fluorescence than those treated only with heat or pressure. In contrast, the size of skim milk casein micelles decreased significantly with an increase in pressure level and time; however, the effect was less marked when heat and pressure treatments were combined. For the PHP and HP samples, as the level and time of pressure increased, the α-helix and β-turn content reduced, whereas β-sheet and random coil were induced. Thus, PHP treatment could be used as a good alternative technology in the dairy industry to promote the functional properties of skim caprine milk. <<<
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565.
林海onrush (2023-03-31 23:17):
#paper, BloombergGPT: A Large Language Model for Finance, doi:10.48550/arXiv.2303.17564, ChatGPT引爆的AI热潮也“烧到了”金融圈,彭博社重磅发布为金融界打造的大型语言模型(LLM)——BloombergGPT。3月30日,根据彭博社最新发布的报告显示,其构建迄今为止最大的特定领域数据集,并训练了专门用于金融领域的LLM,开发了拥有500亿参数的语言模型——BloombergGPT。报告显示,该模型依托彭博社的大量金融数据源,构建了一个3630亿个标签的数据集,支持金融行业内的各类任务。该模型在金融任务上的表现远超过现有模型,且在通用场景上的表现与现有模型也能一较高下。报告指出,从测试来看,BloombergGPT在五项任务中的四项(ConvFinQA,FiQA SA,FPB和Headline)表现最佳,在NER(Named Entity Recognition)中排名第二。因此,BloombergGPT有其优势性。
Abstract:
The use of NLP in the realm of financial technology is broad and complex, with applications ranging from sentiment analysis and named entity recognition to question answering. Large Language Models … >>>
The use of NLP in the realm of financial technology is broad and complex, with applications ranging from sentiment analysis and named entity recognition to question answering. Large Language Models (LLMs) have been shown to be effective on a variety of tasks; however, no LLM specialized for the financial domain has been reported in literature. In this work, we present BloombergGPT, a 50 billion parameter language model that is trained on a wide range of financial data. We construct a 363 billion token dataset based on Bloomberg's extensive data sources, perhaps the largest domain-specific dataset yet, augmented with 345 billion tokens from general purpose datasets. We validate BloombergGPT on standard LLM benchmarks, open financial benchmarks, and a suite of internal benchmarks that most accurately reflect our intended usage. Our mixed dataset training leads to a model that outperforms existing models on financial tasks by significant margins without sacrificing performance on general LLM benchmarks. Additionally, we explain our modeling choices, training process, and evaluation methodology. As a next step, we plan to release training logs (Chronicles) detailing our experience in training BloombergGPT. <<<
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566.
小擎子 (2023-03-31 23:05):
#paper doi:10.1136/gutjnl-2018-317178 Gut, 2019, Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer 结直肠癌的肠道真菌失调和生态改变。一般研究癌症里的微生物多是细菌,病毒和真菌的少。这篇文献主要分析了结直肠癌患者样本的真菌。真菌一般在采样中的序列占比也少,但仍有分析价值。研究分析了香港的184名CRC患者、197名腺瘤患者和204名对照受试者。分析的粪便样本,分为发现队列和验证队列。主成分分析显示结直肠癌和对照组可以分为两个簇,早期和晚期的结直肠癌也有不同的真菌群。与健康人相比,结直肠癌患者粪便内的担子菌(Basidiomycota):子囊菌(Ascomycota)的比值增加。在CRC中真菌纲马拉色纲(Malasseziomycetes)富集,Saccharomycetes和Pneumocystidomycetes减少。研究找了14种真菌标志物其丰度可以将CRC和对照组分开,AUC为0.74~0.93。研究还采用了SparCC算法做了生态学分析,与对照组相比,CRC中的真菌会有界内共存的联系,而真菌与细菌会有排斥现象。研究发现了真菌粪便标志物在诊断CRC上有潜在潜力。真菌一般分析较少,研究主要用了Kraken注释reads,并且用Jellyfish程序利用公开数据做了一个自定义数据库。
IF:23.000Q1 Gut, 2019-04. DOI: 10.1136/gutjnl-2018-317178 PMID: 30472682
Abstract:
OBJECTIVES: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC.DESIGN: Faecal … >>>
OBJECTIVES: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC.DESIGN: Faecal shotgun metagenomic sequences of 184 patients with CRC, 197 patients with adenoma and 204 control subjects from Hong Kong were analysed (discovery cohort: 73 patients with CRC and 92 control subjects; validation cohort: 111 patients with CRC, 197 patients with adenoma and 112 controls from Hong Kong). CRC-associated fungal markers and ecological changes were also validated in additional independent cohorts of 90 patients with CRC, 42 patients with adenoma and 66 control subjects of published repository sequences from Germany and France. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.RESULTS: Principal component analysis revealed separate clusters for CRC and control (p<0.0001), with distinct mycobiomes in early-stage and late-stage CRC (p=0.0048). Basidiomycota:Ascomycota ratio was higher in CRC (p=0.0042), with increase in Malasseziomycetes (p<0.0001) and decrease in Saccharomycetes (p<0.0001) and Pneumocystidomycetes (p=0.0017). Abundances of 14 fungal biomarkers distinguished CRC from controls with an area under the receiver-operating characteristic curve (AUC) of 0.93 and validated AUCs of 0.82 and 0.74 in independent Chinese cohort V1 and European cohort V2, respectively. Further ecological analysis revealed higher numbers of co-occurring fungal intrakingdom and co-exclusive bacterial-fungal correlations in CRC (p<0.0001). Moreover, co-occurrence interactions between fungi and bacteria, mostly contributed by fungal Ascomycota and bacterial Proteobacteria in control, were reverted to co-exclusive interplay in CRC (p=0.00045).CONCLUSIONS: This study revealed CRC-associated mycobiome dysbiosis characterised by altered fungal composition and ecology, signifying that the gut mycobiome might play a role in CRC. <<<
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567.
钟鸣 (2023-03-31 22:47):
#paper doi:10.1128/iai.00529-22 Hyperglycemia Increases Severity of Staphylococcus aureus Osteomyelitis and Influences Bacterial Genes Required for Survival in Bone 过去的研究中发现高血糖患者更容易发生严重的金黄色葡萄球菌感染,这是一种广泛存在于环境中且具有重要公共卫生意义的细菌。为了这种现象的原因,研究者使用小鼠作为实验动物,构建了高血糖模型,同时使用转座子测序技术对金黄色葡萄球菌随机插入突变,随后攻毒检验毒力。实验结果是得到一个基因,sodA ,编码超氧化物歧化酶 A,与该菌在高糖环境下的毒力增加有关。从技术和研究方案来说很成熟很简单,但是得到的结论很有价值且深远。但该基因如何影响金黄色葡萄球菌在特定环境下的表型,以及这种调控是否具有种属特异性、该基因是否具有未探明的功能,仍然未知。当然还需要更多的实验从不同角度验证本文的结论。
IF:2.900Q2 Infection and immunity, 2023-04-18. DOI: 10.1128/iai.00529-22 PMID: 36877063
Abstract:
Hyperglycemia, or elevated blood glucose, renders individuals more prone to developing severe Staphylococcus aureus infections. S. aureus is the most common etiological agent of musculoskeletal infection, which is a common … >>>
Hyperglycemia, or elevated blood glucose, renders individuals more prone to developing severe Staphylococcus aureus infections. S. aureus is the most common etiological agent of musculoskeletal infection, which is a common manifestation of disease in hyperglycemic patients. However, the mechanisms by which S. aureus causes severe musculoskeletal infection during hyperglycemia are incompletely characterized. To examine the influence of hyperglycemia on S. aureus virulence during invasive infection, we used a murine model of osteomyelitis and induced hyperglycemia with streptozotocin. We discovered that hyperglycemic mice exhibited increased bacterial burdens in bone and enhanced dissemination compared to control mice. Furthermore, infected hyperglycemic mice sustained increased bone destruction relative to euglycemic controls, suggesting that hyperglycemia exacerbates infection-associated bone loss. To identify genes contributing to S. aureus pathogenesis during osteomyelitis in hyperglycemic animals relative to euglycemic controls, we used transposon sequencing (TnSeq). We identified 71 genes uniquely essential for S. aureus survival in osteomyelitis in hyperglycemic mice and another 61 mutants with compromised fitness. Among the genes essential for S. aureus survival in hyperglycemic mice was the gene encoding superoxide dismutase A (), one of two S. aureus superoxide dismutases involved in detoxifying reactive oxygen species (ROS). We determined that a mutant exhibits attenuated survival in high glucose and during osteomyelitis in hyperglycemic mice. SodA therefore plays an important role during growth in high glucose and promotes S. aureus survival in bone. Collectively, these studies demonstrate that hyperglycemia increases the severity of osteomyelitis and identify genes contributing to S. aureus survival during hyperglycemic infection. <<<
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568.
muton (2023-03-31 22:44):
#paper https://doi.org/10.7554/eLife.82250 Extra-hippocampal contributions to pattern separation 模式分离,或记忆中高度相似的刺激或经验由不重叠的神经组合代表的过程,通常被归结为由海马体支持的过程。然而,广泛研究的证据表明,模式分离是一个由大脑区域网络支持的多阶段过程。基于这些证据,再加上文献中的相关发现,作者提出了 "皮质-海马模式分离"(CHiPS)框架,认为参与认知控制的大脑区域在模式分离中发挥了重要作用。特别是,这些区域可能通过以下方式对模式分离做出贡献:(1)解决投射到海马的感觉区域的干扰,从而调节其皮质输入;或(2)根据任务要求直接调节海马的过程。本文创新之处是作者认为模式分离也同样受到新皮层-海马而不仅仅是海马的支持。
IF:6.400Q1 eLife, 2023-03-27. DOI: 10.7554/eLife.82250 PMID: 36972123
Abstract:
Pattern separation, or the process by which highly similar stimuli or experiences in memory are represented by non-overlapping neural ensembles, has typically been ascribed to processes supported by the hippocampus. … >>>
Pattern separation, or the process by which highly similar stimuli or experiences in memory are represented by non-overlapping neural ensembles, has typically been ascribed to processes supported by the hippocampus. Converging evidence from a wide range of studies, however, suggests that pattern separation is a multistage process supported by a network of brain regions. Based on this evidence, considered together with related findings from the interference resolution literature, we propose the 'cortico-hippocampal pattern separation' (CHiPS) framework, which asserts that brain regions involved in cognitive control play a significant role in pattern separation. Particularly, these regions may contribute to pattern separation by (1) resolving interference in sensory regions that project to the hippocampus, thus regulating its cortical input, or (2) directly modulating hippocampal processes in accordance with task demands. Considering recent interest in how hippocampal operations are modulated by goal states likely represented and regulated by extra-hippocampal regions, we argue that pattern separation is similarly supported by neocortical-hippocampal interactions. <<<
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569.
Ricardo (2023-03-31 22:43):
#paper Growth charts of brain morphometry for preschool children https://doi.org/10.1016/j.neuroimage.2022.119178 从1到6岁的大脑发育确定了广泛的功能能力,并带有神经发育障碍的早期迹象。然而,目前缺乏描述大脑形态变化和进行个性化推断的定量模型,阻碍了这一时期早期大脑非典型性的识别。通过285个样本,我们描述了神经功能正常儿童皮层厚度和皮层下体积的年龄依赖性,并构建了学龄前儿童所有大脑区域的定量生长图表。大部分脑区的皮质厚度随年龄的增加而减小,而内嗅区和海马旁区则呈现出倒u型的年龄依赖关系。与皮层厚度相比,皮层下区域的归一化体积变化趋势更为发散,有的区域增大,有的区域减小,有的区域呈倒u型变化趋势。所有大脑区域的生长曲线模型在识别大脑非典型性方面显示出效用。生长曲线的百分位数测量有助于识别发育性言语和语言障碍儿童,其准确率为0.875。该结果填补了关键发育时期脑形态测量学的知识空白,并为个性化的脑发育状态评估提供了一条途径,具有良好的敏感性。
IF:4.700Q1 NeuroImage, 2022-07-15. DOI: 10.1016/j.neuroimage.2022.119178 PMID: 35430358
Abstract:
Brain development from 1 to 6 years of age anchors a wide range of functional capabilities and carries early signs of neurodevelopmental disorders. However, quantitative models for depicting brain morphology … >>>
Brain development from 1 to 6 years of age anchors a wide range of functional capabilities and carries early signs of neurodevelopmental disorders. However, quantitative models for depicting brain morphology changes and making individualized inferences are lacking, preventing the identification of early brain atypicality during this period. With a sample size of 285, we characterized the age dependence of the cortical thickness and subcortical volume in neurologically normal children and constructed quantitative growth charts of all brain regions for preschool children. While the cortical thickness of most brain regions decreased with age, the entorhinal and parahippocampal regions displayed an inverted-U shape of age dependence. Compared to the cortical thickness, the normalized volume of subcortical regions exhibited more divergent trends, with some regions increasing, some decreasing, and some displaying inverted-U-shaped trends. The growth curve models for all brain regions demonstrated utilities in identifying brain atypicality. The percentile measures derived from the growth curves facilitate the identification of children with developmental speech and language disorders with an accuracy of 0.875 (area under the receiver operating characteristic curve: 0.943). Our results fill the knowledge gap in brain morphometrics in a critical development period and provide an avenue for individualized brain developmental status evaluation with demonstrated sensitivity. The brain growth charts are shared with the public (http://phi-group.top/resources.html). <<<
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570.
张贝 (2023-03-31 22:30):
#paper RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science. 2019 Jun 7;364(6444):eaaw0726.doi: 10.1126/science.aaw0726. 体细胞突变是如何在正常细胞中积累的,目前尚不清楚。本文通过对来自29个正常组织的6700个样本的RNA测序数据的综合分析揭示了多个体细胞变异,表明在许多正常组织中可以发现宏观克隆。本文证实阳光照射的皮肤、食道和肺比其他测试组织有更高的突变负担,这表明环境因素可以促进体细胞嵌合。突变负担与年龄和组织特异性细胞增殖率相关,强调突变随着时间和细胞分裂数量的增加而积累。最后,作者发现正常组织中存在已知癌症基因和热点突变。本研究提供了人体组织中宏观克隆扩增的广阔视野,从而作为将克隆扩增与环境因素、衰老和疾病风险联系起来的基础
Abstract:
How somatic mutations accumulate in normal cells is poorly understood. A comprehensive analysis of RNA sequencing data from ~6700 samples across 29 normal tissues revealed multiple somatic variants, demonstrating that … >>>
How somatic mutations accumulate in normal cells is poorly understood. A comprehensive analysis of RNA sequencing data from ~6700 samples across 29 normal tissues revealed multiple somatic variants, demonstrating that macroscopic clones can be found in many normal tissues. We found that sun-exposed skin, esophagus, and lung have a higher mutation burden than other tested tissues, which suggests that environmental factors can promote somatic mosaicism. Mutation burden was associated with both age and tissue-specific cell proliferation rate, highlighting that mutations accumulate over both time and number of cell divisions. Finally, normal tissues were found to harbor mutations in known cancer genes and hotspots. This study provides a broad view of macroscopic clonal expansion in human tissues, thus serving as a foundation for associating clonal expansion with environmental factors, aging, and risk of disease. <<<
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571.
大勇 (2023-03-31 21:39):
#paper Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer. Immunity. 2022 Mar 8;55(3):527-541.e5. doi: 10.1016/j.immuni.2022.02.001. Epub 2022 Feb 28. PMID: 35231421这篇文献主要通过空间转录组的数据和计算机成像,给我们展示了肿瘤组织中三级淋巴结构的微环境细胞图谱,发现B细胞聚集区以及B细胞抗原刺激的过程。并且CXCL12的成纤维细胞可以促进B细胞的扩散和发挥抗体介导的肿瘤ADCC的作用。
IF:25.500Q1 Immunity, 2022-03-08. DOI: 10.1016/j.immuni.2022.02.001 PMID: 35231421
Abstract:
The presence of intratumoral tertiary lymphoid structures (TLS) is associated with positive clinical outcomes and responses to immunotherapy in cancer. Here, we used spatial transcriptomics to examine the nature of … >>>
The presence of intratumoral tertiary lymphoid structures (TLS) is associated with positive clinical outcomes and responses to immunotherapy in cancer. Here, we used spatial transcriptomics to examine the nature of B cell responses within TLS in renal cell carcinoma (RCC). B cells were enriched in TLS, and therein, we could identify all B cell maturation stages toward plasma cell (PC) formation. B cell repertoire analysis revealed clonal diversification, selection, expansion in TLS, and the presence of fully mature clonotypes at distance. In TLS+ tumors, IgG- and IgA-producing PCs disseminated into the tumor beds along fibroblastic tracks. TLS+ tumors exhibited high frequencies of IgG-producing PCs and IgG-stained and apoptotic malignant cells, suggestive of anti-tumor effector activity. Therapeutic responses and progression-free survival correlated with IgG-stained tumor cells in RCC patients treated with immune checkpoint inhibitors. Thus, intratumoral TLS sustains B cell maturation and antibody production that is associated with response to immunotherapy, potentially via direct anti-tumor effects. <<<
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572.
小小小小小小萌 (2023-03-31 21:16):
#paper https://www.nature.com/articles/s41421-022-00416-z Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver. 这篇文章运用了基因组学尤其是三维基因组学功能研究中最常用的实验技术,包括ChIP-seq,Hi-C,ATAC-seq和RNA-seq,研究了猪的肝脏在胚胎形成阶段的两个时期及猪出生后肝脏生长至2.5cm, 8cm, 10cm的基因组学变化情况。揭示了肝脏发育过程中染色质空间结构的建立以及参与转录调控的过程。同时,对成年后高脂饮食诱导肥胖组的分析表明猪的各项代谢指标和染色质层级构象在体重增加的过程中并未发生明显变化。
IF:13.000Q1 Cell discovery, 2022-Jun-14. DOI: 10.1038/s41421-022-00416-z PMID: 35701393
Abstract:
Liver development is a complex process that is regulated by a series of signaling pathways. Three-dimensional (3D) chromatin architecture plays an important role in transcriptional regulation; nonetheless, its dynamics and … >>>
Liver development is a complex process that is regulated by a series of signaling pathways. Three-dimensional (3D) chromatin architecture plays an important role in transcriptional regulation; nonetheless, its dynamics and role in the rapid transition of core liver functions during development and obesity-induced metabolic stress remain largely unexplored. To investigate the dynamic chromatin architecture during liver development and under metabolic stress, we generated high-resolution maps of chromatin architecture for porcine livers across six major developmental stages (from embryonic day 38 to the adult stage) and under a high-fat diet-induced obesity. The characteristically loose chromatin architecture supports a highly plastic genome organization during early liver development, which fundamentally contributes to the rapid functional transitions in the liver after birth. We reveal the multi-scale reorganization of chromatin architecture and its influence on transcriptional regulation of critical signaling processes during liver development, and show its close association with transition in hepatic functions (i.e., from hematopoiesis in the fetus to metabolism and immunity after birth). The limited changes in chromatin structure help explain the observed metabolic adaptation to excessive energy intake in pigs. These results provide a global overview of chromatin architecture dynamics associated with the transition of physiological liver functions between prenatal development and postnatal maturation, and a foundational resource that allows for future in-depth functional characterization. <<<
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573.
AI 5.0.3 (2023-03-31 20:44):
#paper 主要内容:快速伽马震荡精准协调上下神经系统,分别从海马外内侧收集神经元信息传入海马实现在物体识别和方位判断的作用。主要结论:空间导航中快伽马震荡协调齿状回和MEC,慢伽马震荡协调齿状回和LEC,MEC和LEC的信息以伽马周期对任务进行特异性选择。A. Fernández-Ruiz et al., Science 372, eabf3119 (2021). DOI: 10.1126/science.abf3119
Abstract:
Gamma oscillations are thought to coordinate the spike timing of functionally specialized neuronal ensembles across brain regions. To test this hypothesis, we optogenetically perturbed gamma spike timing in the rat … >>>
Gamma oscillations are thought to coordinate the spike timing of functionally specialized neuronal ensembles across brain regions. To test this hypothesis, we optogenetically perturbed gamma spike timing in the rat medial (MEC) and lateral (LEC) entorhinal cortices and found impairments in spatial and object learning tasks, respectively. MEC and LEC were synchronized with the hippocampal dentate gyrus through high- and low-gamma-frequency rhythms, respectively, and engaged either granule cells or mossy cells and CA3 pyramidal cells in a task-dependent manner. Gamma perturbation disrupted the learning-induced assembly organization of target neurons. Our findings imply that pathway-specific gamma oscillations route task-relevant information between distinct neuronal subpopulations in the entorhinal-hippocampal circuit. We hypothesize that interregional gamma-time-scale spike coordination is a mechanism of neuronal communication. <<<
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574.
cellsarts (2023-03-31 19:54):
#Paper https://doi.org/10.1038/s41396-022-01195-x 海底热液羽流中硫氧化细菌(SUP05)的生态位分化 Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes热液柱将还原态的化学物质和金属输送到开阔的海洋中。尽管它们对生物地球化学循环有广泛及巨大的影响,但对热液柱之中的丰富的微生物演化支的生态位分化知之甚少。在这里,我们分析了在南太平洋的克马德克海内弧上两个热泉的——(兄弟火山;brv锥和西北破火山口;NWC)和中海火山(Macauley火山;McV)絮凝物物微生物生态。通过结合16S rRNA基因、荧光原位杂交和宏基因组分析确定的微生物群落结构与在其他富硫羽流中观察到的群落相似。这包括排硫特征的SUP05分支的优势(在McV中高达22%,在BrV中高达51%)。在分析的三个羽中,群落由不同的尚未培养的化学自养SUP05物种主导,这里暂时命名为Candidatus Thioglobus vadi (McV), Candidatus thiglobus vulcanius (BrV-cone)和Candidatus thiglobus plumae (BrV-NWC)。统计分析、基因组潜能和mRNA表达谱表明,SUP05的生态位划分基于硫化物和铁浓度以及水深。第四种SUP05在整个研究的絮凝状样品中出现频率很低,可能具有异养或混合生长的能力。综上所述,我们认为环境参数和深度的微小变化推动了热液柱中SUP05生态位的划分。
Abstract:
Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly … >>>
Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (up to 22% in McV and 51% in BrV). In each of the three plumes analyzed, the community was dominated by a different yet uncultivated chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles suggested a SUP05 niche partitioning based on sulfide and iron concentration as well as water depth. A fourth SUP05 species was present at low frequency throughout investigated plume samples and may be capable of heterotrophic or mixotrophic growth. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes. <<<
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575.
LXJ (2023-03-31 19:51):
#paper Gut-innervating nociceptors regulate the intestinal microbiota to promote tissue protection. Cell. 2022 Oct 27;185(22):4170-4189.e20. doi: 10.1016/j.cell.2022.09.008. 伤害性疼痛是许多慢性炎症性疾病的标志,包括炎症性肠病(IBD);然而,痛觉神经元是否会影响肠道炎症仍不清楚。利用化学遗传学沉默、腺病毒介导的结肠特异性沉默和TRPV1+伤害感受器的药理学消融,我们在肠道损伤和炎症的小鼠模型中观察到更严重的炎症和有缺陷的组织保护性修复过程。破坏的伤害感受导致肠道微生物群的显著改变和可传播的微生态失调,而革兰氏+梭菌对无菌小鼠的单定殖。通过伤害感受器依赖性途径促进肠道组织保护。从机制上讲,伤害感受的破坏导致P物质水平下降,而P物质的治疗性递送以微生物群依赖的方式促进了TRPV1+伤害感受器发挥的组织保护作用。最后,在IBD患者的肠道活检中观察到伤害感受器基因表达失调。总之,这些发现表明,伤害感受、肠道微生物群和肠道稳态恢复之间存在进化上保守的功能联系。
IF:45.500Q1 Cell, 2022-10-27. DOI: 10.1016/j.cell.2022.09.008 PMID: 36240781
Abstract:
Nociceptive pain is a hallmark of many chronic inflammatory conditions including inflammatory bowel diseases (IBDs); however, whether pain-sensing neurons influence intestinal inflammation remains poorly defined. Employing chemogenetic silencing, adenoviral-mediated colon-specific … >>>
Nociceptive pain is a hallmark of many chronic inflammatory conditions including inflammatory bowel diseases (IBDs); however, whether pain-sensing neurons influence intestinal inflammation remains poorly defined. Employing chemogenetic silencing, adenoviral-mediated colon-specific silencing, and pharmacological ablation of TRPV1 nociceptors, we observed more severe inflammation and defective tissue-protective reparative processes in a murine model of intestinal damage and inflammation. Disrupted nociception led to significant alterations in the intestinal microbiota and a transmissible dysbiosis, while mono-colonization of germ-free mice with GramClostridium spp. promoted intestinal tissue protection through a nociceptor-dependent pathway. Mechanistically, disruption of nociception resulted in decreased levels of substance P, and therapeutic delivery of substance P promoted tissue-protective effects exerted by TRPV1 nociceptors in a microbiota-dependent manner. Finally, dysregulated nociceptor gene expression was observed in intestinal biopsies from IBD patients. Collectively, these findings indicate an evolutionarily conserved functional link between nociception, the intestinal microbiota, and the restoration of intestinal homeostasis. <<<
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576.
半面阳光 (2023-03-31 19:02):
#paper DOI: 10.1016/j.ajhg.2012.12.006, Am J Hum Genet. 2013, Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma. 基于NGS的NIPT检测染色体非整倍体技术建立之后,进一步的研究重点和热点之一是将NIPT从检测染色体非整倍体拓展到检测染色体上的微缺失微重复片段。这篇文献可能是首次系统性建立用于检测微缺失和微重复的NIPT方法学文章。
Abstract:
The purpose of this study was to determine the deep sequencing and analytic conditions needed to detect fetal subchromosome abnormalities across the genome from a maternal blood sample. Cell-free (cf) … >>>
The purpose of this study was to determine the deep sequencing and analytic conditions needed to detect fetal subchromosome abnormalities across the genome from a maternal blood sample. Cell-free (cf) DNA was isolated from the plasma of 11 pregnant women carrying fetuses with subchromosomal duplications and deletions, translocations, mosaicism, and trisomy 20 diagnosed by metaphase karyotype. Massively parallel sequencing (MPS) was performed with 25-mer tags at approximately 10(9) tags per sample and mapped to reference human genome assembly hg19. Tags were counted and normalized to fixed genome bin sizes of 1 Mb or 100 kb to detect statistically distinct copy-number changes compared to the reference. All seven cases of microdeletions, duplications, translocations, and the trisomy 20 were detected blindly by MPS, including a microdeletion as small as 300 kb. In two of these cases in which the metaphase karyotype showed additional material of unknown origin, MPS identified both the translocation breakpoint and the chromosomal origin of the additional material. In the four mosaic cases, the subchromosomal abnormality was not demonstrated by MPS. This work shows that in nonmosaic cases, it is possible to obtain a fetal molecular karyotype by MPS of maternal plasma cfDNA that is equivalent to a chromosome microarray and in some cases is better than a metaphase karyotype. This approach combines the advantage of enhanced fetal genomic resolution with the improved safety of a noninvasive maternal blood test. <<<
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577.
小W (2023-03-31 16:57):
#paper doi:https://doi.org/10.1038/s41576-022-00511-7 Measuring biological age using omics data. 生物老化是随着实际年龄的增长而发生的系统完整性进行性下降 ,最终导致疾病、残疾和死亡。本文是利用组学数据量化生物衰老方法(衰老时钟)研究的综述文章,介绍了表观遗传、转录组学、蛋白质组学、代谢组学等方面衰老时钟的研究原理、局限性和优化。比较有意思的一点,第一代表观时钟彼此之间只有轻微的相关性,增大样本量的情况下训练第一代甲基化时钟过拟合,又消除了年龄和生物学年龄之间的联系。这里提出对之后开发衰老时钟的展望,定义衰老时钟的应用场景,通过有目的的特征选择或通过开发复合训练指标,将衰老生物学的特定方面纳入其中的建模方法应有助于提高模型的可解释性,并指导它们识别衰老的因果特征。一个大胆的方法是在时钟的训练中排除年龄,从而更接近于测量老化生物学特征。
Abstract:
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' … >>>
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing. <<<
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578.
小年 (2023-03-31 15:44):
#paper doi: 10.3389/fonc.2021.641487. Establishment of a Prognostic Model for Hepatocellular Carcinoma Based on Endoplasmic Reticulum Stress-Related Gene Analysis. Front Oncol. 2021; 11: 641487. 这篇文章基于88个内质网应激(ERS)相关基因,用Cox回归分析鉴定了肝癌中由5个ERS基因组成的预后生物标志物,并构建预后模型,同时评估模型的性能。其次分析了临床信息与生存预后的关系,识别了独立预后因素并建立预测列线图。还对5个预后基因做了多组学分析(包括mutation、methylation、copy number、post-transcriptional regulation)。 该文值得我们借鉴的是不局限于RNA-seq层面开发预后模型,不仅从多组学维度分析了这些ERS基因在促进肝癌的作用,最后还讨论了关于数据库中一些重要参数和临床资料的局限性,对我们以后的研究有一些启发。
Abstract:
Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide and its incidence continues to increase year by year. Endoplasmic reticulum stress (ERS) caused by protein misfolding … >>>
Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide and its incidence continues to increase year by year. Endoplasmic reticulum stress (ERS) caused by protein misfolding within the secretory pathway in cells and has an extensive and deep impact on cancer cell progression and survival. Growing evidence suggests that the genes related to ERS are closely associated with the occurrence and progression of HCC. This study aimed to identify an ERS-related signature for the prospective evaluation of prognosis in HCC patients. RNA sequencing data and clinical data of patients from HCC patients were obtained from The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC). Using data from TCGA as a training cohort (n=424) and data from ICGC as an independent external testing cohort (n=243), ERS-related genes were extracted to identify three common pathways IRE1, PEKR, and ATF6 using the GSEA database. Through univariate and multivariate Cox regression analysis, 5 gene signals in the training cohort were found to be related to ERS and closely correlated with the prognosis in patients of HCC. A novel 5-gene signature (including HDGF, EIF2S1, SRPRB, PPP2R5B and DDX11) was created and had power as a prognostic biomarker. The prognosis of patients with high-risk HCC was worse than that of patients with low-risk HCC. Multivariate Cox regression analysis confirmed that the signature was an independent prognostic biomarker for HCC. The results were further validated in an independent external testing cohort (ICGC). Also, GSEA indicated a series of significantly enriched oncological signatures and different metabolic processes that may enable a better understanding of the potential molecular mechanism mediating the progression of HCC. The 5-gene biomarker has a high potential for clinical applications in the risk stratification and overall survival prediction of HCC patients. In addition, the abnormal expression of these genes may be affected by copy number variation, methylation variation, and post-transcriptional regulation. Together, this study indicated that the genes may have potential as prognostic biomarkers in HCC and may provide new evidence supporting targeted therapies in HCC. <<<
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579.
Vincent (2023-03-31 15:34):
#paper https://doi.org/10.48550/arXiv.1904.10098 ICML 2019 DAG-GNN: DAG Structure Learning with Graph Neural Networks. 有向无环图(DAG)的结构学习是一项十分具有挑战性的工作,其搜索空间随着节点数的增多而呈现指数式的增长。常用的研究手段是将结构学习转化为一种score的优化问题。为了让问题可解,传统的方法通常考虑线性结构方程模型(Linear SEM),这篇文章基于线性SEM的框架,发展了一套基于变分自编码器VAE和图神经网络GNN的DAG学习方法,得益于神经网络的非线性拟合,这套方法在保证至少比线性SEM好的情况下还能解决一些非线性的问题。通过数据仿真和真实数据的学习,文章验证了该方法的准确度比线性SEM好,假发现率比线性SEM低。
Abstract:
Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph … >>>
Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough formulates the problem as a continuous optimization with a structural constraint that ensures acyclicity (Zheng et al., 2018). The authors apply the approach to the linear structural equation model (SEM) and the least-squares loss function that are statistically well justified but nevertheless limited. Motivated by the widespread success of deep learning that is capable of capturing complex nonlinear mappings, in this work we propose a deep generative model and apply a variant of the structural constraint to learn the DAG. At the heart of the generative model is a variational autoencoder parameterized by a novel graph neural network architecture, which we coin DAG-GNN. In addition to the richer capacity, an advantage of the proposed model is that it naturally handles discrete variables as well as vector-valued ones. We demonstrate that on synthetic data sets, the proposed method learns more accurate graphs for nonlinearly generated samples; and on benchmark data sets with discrete variables, the learned graphs are reasonably close to the global optima. The code is available at \url{this https URL}. <<<
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580.
庞庞 (2023-03-31 15:06):
#paper https://doi.org/10.1038/s41380-023-01958-8 Individualized fMRI connectivity defines signatures of antidepressant and placebo responses in major depression 由于个体的异质性,不同个体对抗抑郁药物的缓释程度各有不同。因此,理解抗抑郁药物的作用机制对个性化医疗至关重要。本文采用去除组成分的COBE算法,获得个体化的功能连接矩阵,作为特征对抗抑郁药物舍曲林和安慰剂的疗效进行预测。研究发现,个体化的功能连接比起组水平的功能连接显著提高了预测准确率;对预测舍曲林贡献高的脑区主要位于左侧颞中皮层和右侧脑岛;对安慰剂贡献高的主要位于双侧扣带皮层和左侧颞上皮层。这位抗抑郁的疗效预测标志物提供了新视角。
IF:9.600Q1 Molecular psychiatry, 2023-06. DOI: 10.1038/s41380-023-01958-8 PMID: 36732585
Abstract:
Though sertraline is commonly prescribed in patients with major depressive disorder (MDD), its superiority over placebo is only marginal. This is in part due to the neurobiological heterogeneity of the … >>>
Though sertraline is commonly prescribed in patients with major depressive disorder (MDD), its superiority over placebo is only marginal. This is in part due to the neurobiological heterogeneity of the individuals. Characterizing individual-unique functional architecture of the brain may help better dissect the heterogeneity, thereby defining treatment-predictive signatures to guide personalized medication. In this study, we investigate whether individualized brain functional connectivity (FC) can define more predictable signatures of antidepressant and placebo treatment in MDD. The data used in the present work were collected by the Establishing Moderators and Biosignatures of Antidepressant Response in Clinical Care (EMBARC) study. Patients (N = 296) were randomly assigned to antidepressant sertraline or placebo double-blind treatment for 8 weeks. The whole-brain FC networks were constructed from pre-treatment resting-state functional magnetic resonance imaging (rs-fMRI). Then, FC was individualized by removing the common components extracted from the raw baseline FC to train regression-based connectivity predictive models. With individualized FC features, the established prediction models successfully identified signatures that explained 22% variance for the sertraline group and 31% variance for the placebo group in predicting HAMD change. Compared with the raw FC-based models, the individualized FC-defined signatures significantly improved the prediction performance, as confirmed by cross-validation. For sertraline treatment, predictive FC metrics were predominantly located in the left middle temporal cortex and right insula. For placebo, predictive FC metrics were primarily located in the bilateral cingulate cortex and left superior temporal cortex. Our findings demonstrated that through the removal of common FC components, individualization of FC metrics enhanced the prediction performance compared to raw FC. Associated with previous MDD clinical studies, our identified predictive biomarkers provided new insights into the neuropathology of antidepressant and placebo treatment. <<<
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