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Charting paths to recovery: Navigating traumatic brain injury comorbidities through graph theory–exploring benefits and challenges 绘制康复之路:通过图表理论探索创伤性脑损伤并发症--探索益处与挑战
Pub Date : 2024-03-30 DOI: 10.1016/j.bosn.2024.03.002
Shyam Kumar Sudhakar, Kaustav Mehta

Traumatic brain injuries (TBIs) are characterized by widespread complications that exert a debilitating effect on the well-being of the affected individual. TBIs are associated with a multitude of psychiatric and medical comorbidities over the long term. Furthermore, no medications prevent secondary injuries associated with a primary insult. In this perspective article, we propose applying graph theory via the construction of disease comorbidity networks to identify high-risk patient groups, offer preventive care to affected populations, and reduce the disease burden. We describe the challenges associated with monitoring the development of comorbidities in TBI subjects and explain how disease comorbidity networks can reduce disease burden by preventing disease-related complications. We further discuss the various methods used to construct disease comorbidity networks and explain how features derived from a network can help identify subjects who might be at risk of developing post-traumatic comorbidities. Lastly, we address the potential challenges of using graph theory to successfully manage comorbidities following a TBI.

创伤性脑损伤(TBIs)的特点是具有广泛的并发症,会对受影响者的福祉造成削弱性影响。从长远来看,创伤性脑损伤与多种精神和医疗并发症有关。此外,没有任何药物可以预防与原发性损伤相关的继发性损伤。在这篇透视文章中,我们建议通过构建疾病合并症网络来应用图论,以识别高风险患者群体,为受影响人群提供预防性护理,并减轻疾病负担。我们描述了与监测创伤性脑损伤受试者合并症发展相关的挑战,并解释了疾病合并症网络如何通过预防疾病相关并发症来减轻疾病负担。我们进一步讨论了用于构建疾病并发症网络的各种方法,并解释了从网络中得出的特征如何帮助识别可能有患创伤后并发症风险的受试者。最后,我们探讨了利用图论成功管理创伤后并发症可能面临的挑战。
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引用次数: 0
Effect of blood oxygen-level-dependent signal data trimming on functional connectivity metrics 血氧水平依赖性信号数据修剪对功能连接性指标的影响
Pub Date : 2024-03-14 DOI: 10.1016/j.bosn.2024.03.001
Duarte Oliveira-Saraiva, Hugo Alexandre Ferreira

In the big data era, with a lack of comparable functional neuroimaging data, researchers try to combine heterogeneous data of different lengths, trimming those to the same number of timepoints (NTPs). However, the effects of trimming blood-oxygen-level dependent (BOLD) signal data on functional connectivity (FC) are still poorly understood.

Resting-state functional magnetic resonance imaging data from thirty healthy subjects were pre-processed for five different NTPs, from which FC matrices were computed. These BOLD signal correlation matrices were binarized for several thresholds, excluding weak correlations. Graph metrics were computed to study FC differences between different NTPs. The study included node degree analysis for each brain region and assessment of small-worldness coefficients (σ and ω), whereas in small-world networks, characteristic values are σ > 1 and ω 0, indicating a balance between high clustering coefficients and short characteristic path lengths.

A tendency of decreasing global network degrees for higher NTPs was observed, translating the loss of stronger correlations with longer BOLD signals. Trimming such data affects brain regions differently, probably due to brain network dynamics. Regarding small-worldness, we observed that σ was greater than 1 for all the different NTPs, showing an increasing trend for higher NTPs (median value: σBRAIN= 3.05). In addition, ω consistently remained greater than 0 for all NTPs, gradually approaching 0 as the NTPs increased (median value ωBRAIN= 0.20). As such, the results suggest a tendency for an increase of small-world properties for increasing NTPs. Nonetheless, the overall properties of brain networks almost remain constant. In conclusion, trimming BOLD signal data leads to small differences in FC.

在大数据时代,由于缺乏可比的功能神经成像数据,研究人员试图将不同长度的异构数据结合起来,修剪成相同数量的时间点(NTPs)。研究人员对 30 名健康受试者的静息态功能磁共振成像数据进行了预处理,从中计算出 FC 矩阵。这些 BOLD 信号相关矩阵经过多个阈值的二值化处理,排除了弱相关性。计算图表度量以研究不同 NTP 之间的 FC 差异。该研究包括每个脑区的节点度分析和小世界系数(σ和ω)评估,而在小世界网络中,特征值为σ >1和ω ≈0,表明高聚类系数和短特征路径长度之间的平衡。对这些数据进行修剪会对大脑区域产生不同的影响,这可能是大脑网络动态变化的结果。关于小世界性,我们观察到所有不同的 NTP 的 σ 都大于 1,并呈现出 NTP 越高越大的趋势(中位值:σBRAIN= 3.05)。此外,ω 在所有 NTP 中始终大于 0,随着 NTP 的增加逐渐接近 0(中位值 ωBRAIN=0.20)。因此,研究结果表明,随着 NTPs 的增加,小世界的属性也有增加的趋势。尽管如此,大脑网络的整体特性几乎保持不变。总之,修剪 BOLD 信号数据会导致 FC 的微小差异。
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引用次数: 0
Functional connectivity of interictal iEEG and the connectivity of high-frequency components in epilepsy 癫痫发作间期 iEEG 的功能连接性和高频成分的连接性
Pub Date : 2023-12-01 DOI: 10.1016/j.bosn.2023.11.001
Christos Stergiadis , David M. Halliday , Dimitrios Kazis , Manousos A. Klados

Epilepsy is a disease of altered brain networks. The monitoring and analysis of functional connectivity and network properties can yield a better understanding of the underlying pathology, and improve treatment and prognostics. Identifying hub network regions has been in the spotlight of network neuroscience studies in epilepsy, as monitoring these areas can provide a perspective of the network’s local and global organization. Functional network analysis can be especially useful in Medically Refractory Epilepsy (MRE) cases, where surgical intervention is necessary for seizure relief. In such cases, the delineation of the epileptogenic zone, which represents the surgical target, is a very crucial procedure, which can be enhanced by understanding the underlying network topology. In this review, we will explore the expanding body of literature on functional connectivity of interictal intracranial electrophysiologic data, focusing on the interpretation of network properties, global or local, for identifying epileptogenic tissue. We will emphasize functional connectivity at high frequencies (above 80 Hz), as during the past decade High-Frequency Oscillations (HFOs) have been increasingly recognized as a promising biomarker of the seizure onset zone. We will conclude the review with an assessment of current limitations and a discussion of future research paths.

癫痫是一种大脑网络改变的疾病。通过监测和分析功能连接性和网络特性,可以更好地了解潜在病理,改善治疗和预后。识别枢纽网络区域一直是癫痫网络神经科学研究的焦点,因为监测这些区域可以透视网络的局部和全局组织。功能网络分析在药物难治性癫痫(MRE)病例中尤其有用,因为在这些病例中,必须通过手术干预才能缓解癫痫发作。在这类病例中,代表手术目标的致痫区的划定是一个非常关键的过程,而了解潜在的网络拓扑结构可以增强这一过程。在这篇综述中,我们将探讨有关发作间期颅内电生理数据功能连通性的不断扩展的文献,重点是解释用于识别致痫组织的全局或局部网络特性。我们将强调高频(80 Hz 以上)的功能连通性,因为在过去十年中,高频振荡 (HFO) 已逐渐被认为是癫痫发作起始区的一种有前途的生物标志物。最后,我们将评估目前的局限性并讨论未来的研究方向。
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引用次数: 0
Navigating the frontiers of neuroscience 引领神经科学的前沿
Pub Date : 2023-10-30 DOI: 10.1016/j.bosn.2023.10.001
Manousos Klados, Luisa Pinto
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引用次数: 0
Inkjet-based bioprinting for tissue engineering 用于组织工程的喷墨生物打印
Pub Date : 2023-08-25 DOI: 10.51335/organoid.2023.3.e12
J. A. Park, Yunji Lee, Sungjune Jung
Inkjet bioprinting, a derivative of traditional inkjet technology, is gaining recognition in the fields of life sciences and tissue engineering due to its ability to produce picoliter volume droplets at high speeds in a non-contact fashion. This method has impressively evolved from enabling the production of 2-dimensional (2D) prints to complex 3-dimensional (3D) structures, and is increasingly being used in the manufacturing of electronic components. More recently, this technology has been effectively adapted for a variety of medical applications, such as cell patterning, scaffold construction, and 3D tissue fabrication. In this review, we delve into the principles and biological uses of inkjet technology. We provide an in-depth discussion on the latest developments in inkjet bioprinting, with a focus on cell patterning and 3D fabrication of tissue models, including multilayered lung, bladder, and skin. We also explore the potential of high-throughput 3D-bioprinted tissue models in toxicology and drug efficacy testing.
喷墨生物打印是传统喷墨技术的衍生产品,由于能够以非接触的方式高速产生皮升体积的液滴,因此在生命科学和组织工程领域得到了广泛的认可。这种方法已经令人印象深刻地从能够生产二维(2D)打印到复杂的三维(3D)结构,并且越来越多地用于制造电子元件。最近,这项技术已经有效地适用于各种医学应用,如细胞图案,支架结构和3D组织制造。本文综述了喷墨技术的原理及其在生物领域的应用。我们对喷墨生物打印的最新发展进行了深入的讨论,重点是细胞图案和组织模型的3D制造,包括多层肺,膀胱和皮肤。我们还探索了高通量3d生物打印组织模型在毒理学和药物功效测试中的潜力。
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引用次数: 0
A novel method for generating induced pluripotent stem cell (iPSC)-derived alveolar organoids: a comparison of their ability depending on iPSC origin 一种生成诱导多能干细胞(iPSC)衍生肺泡类器官的新方法:它们的能力取决于iPSC来源的比较
Pub Date : 2023-07-18 DOI: 10.51335/organoid.2023.3.e11
Min Jae Lim, A. Jo, Sung-Won Kim
Background: Alveolar organoids may be useful tools in drug discovery for lung diseases, such as chronic obstructive pulmonary disease, and for studying the effects of respiratory viruses, such as severe acute respiratory syndrome coronavirus 2. Induced pluripotent stem cell (iPSC)-derived alveolar organoids offer ethical and cost-effective alternatives to animal testing and primary cell-based methods. In this study, we present generating alveolar organoids from iPSCs and compare the efficiency of generating iPSCs from alveolar type 2 (AT2) and umbilical cord blood (UCB) cells.Methods: The protocol started with a two-dimensional culture and transitioned to a three-dimensional culture using Matrigel after the endoderm stage. Organoid cultivation lasted for at least 40 days, and the characteristics of alveolar organoids were assessed using flow cytometry, real-time polymerase chain reaction, and immunostaining.Results: iPSCs derived from AT2 cells showed a better ability to generate alveolar organoids than those derived from UCB cells. This difference in the ability of AT2 iPSCs and UCB iPSCs to generate alveolar organoids appeared during the definitive endoderm differentiation stage. AT2 iPSCs showed higher expression of the anterior foregut endoderm marker SOX2 and lung progenitor gene expression markers, such as NKX2.1 and CPM, which are associated with the lung progenitor differentiation stage.Conclusion: This protocol successfully generated alveolar organoids from AT2 iPSCs; however, the efficiency of differentiation varied depending on the origin of the iPSCs. This study also found differences in gene expression and developmental potential between iPSCs, which may have contributed to the observed differences in differentiation efficiency.
背景:肺泡类器官可能是肺部疾病(如慢性阻塞性肺疾病)的药物发现和研究呼吸道病毒(如严重急性呼吸综合征冠状病毒)影响的有用工具2。诱导多能干细胞(iPSC)衍生的肺泡类器官为动物实验和基于原代细胞的方法提供了道德和经济的替代方法。在这项研究中,我们介绍了从iPSCs生成肺泡类器官,并比较了从肺泡2型(AT2)细胞和脐带血(UCB)细胞生成iPSCs的效率。方法:从二维培养开始,在内胚层阶段后使用Matrigel进行三维培养。类器官培养持续至少40天,通过流式细胞术、实时聚合酶链反应和免疫染色评估肺泡类器官的特征。结果:来自AT2细胞的iPSCs比来自UCB细胞的iPSCs具有更好的肺泡类器官生成能力。这种AT2型iPSCs和UCB型iPSCs产生肺泡类器官的能力差异出现在最终的内胚层分化阶段。AT2 iPSCs表达较高的前肠内胚层标记物SOX2和肺祖细胞基因表达标记物NKX2.1、CPM等与肺祖细胞分化阶段相关。结论:该方案成功地从AT2 iPSCs中生成肺泡类器官;然而,分化的效率取决于多能干细胞的来源。本研究还发现了iPSCs之间基因表达和发育潜能的差异,这可能是分化效率差异的原因。
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引用次数: 0
Kidney organoids: development and applications 肾类器官:发展与应用
Pub Date : 2023-06-25 DOI: 10.51335/organoid.2023.3.e10
Hye-Youn Kim, Seyoung Yu, Yo Jun Choi, H. Gee
Since the first publication on generating kidney-like cell aggregates from pluripotent stem cells, various modifications have been made to develop more complex and detailed kidney structures. In contrast to earlier models that featured nephron-like structures, these advances have improved the differentiation efficiency and similarity to the human kidney. Presently, kidney organoids contain not only nephrons and ureteric buds but also stromal cells. These organoids mimic the structural similarities and developmental processes of the kidneys, while reflecting their physiological properties. Kidney tubuloids derived from adult stem cells offer the advantage of long-term culture and expansion, but they include only tubular structures and lack glomerular components. In this review, we discuss the induction protocols for kidney organoids and tubuloids, as well as their potential applications in understanding kidney development, renal pathogenesis, and drug screening.
自从第一次发表关于从多能干细胞中产生肾样细胞聚集体的文章以来,已经进行了各种修改以开发更复杂和详细的肾脏结构。与早期具有肾元样结构的模型相比,这些进展提高了分化效率和与人类肾脏的相似性。目前,肾类器官不仅包括肾单位和输尿管芽,还包括间质细胞。这些类器官模仿肾脏的结构相似性和发育过程,同时反映其生理特性。来源于成体干细胞的肾小管具有长期培养和扩张的优势,但它们只包括管状结构,缺乏肾小球成分。在这篇综述中,我们讨论了肾脏类器官和小管的诱导方案,以及它们在了解肾脏发育、肾脏发病机制和药物筛选方面的潜在应用。
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引用次数: 0
Suspension-cultured taste bud organoids recapitulate in vivo taste buds 悬浮液培养的味蕾类器官再现活体味蕾
Pub Date : 2023-05-25 DOI: 10.51335/organoid.2023.3.e9
Anish Ashok Adpaikar, Jong‐Min Lee, Han-Sung Jung
Background: Taste buds are a complex organ and require a plethora of growth factors for their development, homeostasis, and regeneration. Taste bud organoids provide a platform for understanding their development, disease and regeneration.Methods: In this study, we focused on identifying the localization of receptors involved during taste bud development in taste bud organoids, either in an extracellular matrix scaffold (Matrigel) or in the absence of a scaffold with suspension culture.Results: Compared to Matrigel-cultured organoids, suspension organoids showed stable expression of nerve growth factor receptor (NGFR) cells, which are important for innervation. Transporters for glucose metabolism, such as GLUT1, GLUT2, and the insulin receptor (IGF1R), were observed in suspension-cultured organoids. Furthermore, immunostaining for downstream phosphorylated signaling molecules indicated that the NGFR and IGFR pathways were functional and active in the organoids.Conclusion: Based on these results, suspension-cultured organoids may provide an efficient model for mimicking in vivo taste buds compared to conventional Matrigel organoids.
背景:味蕾是一个复杂的器官,它的发育、体内平衡和再生需要大量的生长因子。味蕾类器官为了解它们的发育、疾病和再生提供了一个平台。方法:在这项研究中,我们重点研究了味蕾类器官中参与味蕾发育的受体的定位,无论是在细胞外基质支架(Matrigel)中,还是在没有悬浮培养支架的情况下。结果:与基质培养的类器官相比,悬浮液培养的类器官具有稳定的神经生长因子受体(NGFR)细胞表达。在悬浮培养的类器官中观察到葡萄糖代谢的转运蛋白,如GLUT1、GLUT2和胰岛素受体(IGF1R)。此外,对下游磷酸化信号分子的免疫染色表明,NGFR和IGFR通路在类器官中具有功能和活性。结论:与传统的基质类器官相比,悬浮培养的类器官可以提供一种有效的模拟活体味蕾的模型。
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引用次数: 0
Microengineered organoids: reconstituting organ-level functions in vitro 微工程类器官:体外重建器官水平功能
Pub Date : 2023-04-25 DOI: 10.51335/organoid.2023.3.e5
S. Park, Harshita Sharma, W. Kim, Yonghyun Gwon, H. Kim, Y. Choung, Jangho Kim
In vitro miniaturized organoids are innovative tools with varying applications in biomedical engineering, such as drug testing, disease modeling, organ development studies, and regenerative medicine. However, conventional organoid development has several hurdles in reproducing and reconstituting organ-level functions in vitro, hampering advanced and impactful studies. In this review, we summarize the emerging microengineering-based organoid development techniques aiming to overcome these hurdles. First, we provide basic information on microengineering techniques, including those for reconstituting organoids with organ-level functions. We then focus on recent advances in microengineered organoids with better morphological, physiological, and functional characteristics than conventionally developed organoids. We believe that microengineered organoids possessing organ-level functions in vitro will enable widespread studies in the field of biological sciences and have clinical applications.
体外微型类器官是生物医学工程中具有多种应用的创新工具,如药物测试、疾病建模、器官发育研究和再生医学。然而,传统的类器官开发在体外复制和重建器官水平功能方面存在一些障碍,阻碍了先进和有影响力的研究。在这篇综述中,我们总结了新兴的基于微工程的类器官开发技术,旨在克服这些障碍。首先,我们提供了微工程技术的基本信息,包括重建具有器官水平功能的类器官的技术。然后,我们重点介绍了微工程类器官的最新进展,这些类器官具有比常规开发的类器官更好的形态、生理和功能特征。我们相信,体外具有器官水平功能的微工程类器官将使生物科学领域的广泛研究和临床应用成为可能。
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引用次数: 0
Development of otic organoids and their current status 耳类器官的发展与现状
Pub Date : 2023-04-25 DOI: 10.51335/organoid.2023.3.e7
Hantai Kim, Young Sun Kim, Y. Kim, Jungho Ha, Siung Sung, J. Jang, S. Park, Jangho Kim, Kyungeun Kim, Y. Choung
The inner ear is responsible for both hearing and balance in the body, and since the initial development of otic (inner ear) organoids from mouse pluripotent stem cells (PSCs) in 2013, significant advances have been made in this field. Bone morphogenetic proteins, fibroblast growth factors, and Wnt agonists, which are signaling molecules in the early development of the inner ear, can induce PSCs into the otic fate. In the inner ear, hair cells and the surrounding supporting cells are essential for proper function and structure. Recent advancements in otic organoid research have enabled the generation of cells that closely resemble these key components. The developed otic organoids contain both hair cell-like cells and supporting cells, which have been confirmed to have the intrinsic function of those cell types. Otic organoids have been used for disease modeling and are expected to be more widely applied in various areas of research on the inner ear. However, the otic organoids developed to date remain immature. Although they mimic hair cells, their properties resemble vestibular (balance) hair cells more closely than cochlear (auditory) hair cells. The ultimate goal of research on the inner ear is hearing restoration and prevention; thus, it is essential to produce otic organoids that contain cochlear hair cells. In addition, the organ of Corti—a cell arrangement unique to the cochlea—has not yet been simulated. Along with a description of the current status of otic organoids, this review article will discuss future directions for otic organoids in inner ear research.
内耳在人体中负责听力和平衡,自2013年从小鼠多能干细胞(PSCs)中初步开发出耳(内耳)类器官以来,该领域取得了重大进展。骨形态发生蛋白、成纤维细胞生长因子和Wnt激动剂是内耳早期发育的信号分子,可诱导PSCs进入耳部命运。在内耳中,毛细胞和周围的支持细胞对正常的功能和结构至关重要。最近在类器官研究方面取得的进展已经能够产生与这些关键成分非常相似的细胞。发育的耳类器官既有毛细胞样细胞,也有支持细胞,已被证实具有这些细胞类型的内在功能。耳类器官已被用于疾病建模,并有望在内耳研究的各个领域得到更广泛的应用。然而,迄今为止,发育的类器官仍然不成熟。虽然它们模仿毛细胞,但它们的特性更像前庭(平衡)毛细胞,而不是耳蜗(听觉)毛细胞。内耳研究的最终目的是恢复和预防听力;因此,产生含有耳蜗毛细胞的耳类器官是必要的。此外,皮质器官——耳蜗特有的细胞排列——还没有被模拟出来。本文综述了耳类器官的研究现状,并对耳类器官在内耳研究中的应用前景进行了展望。
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引用次数: 0
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Brain Organoid and Systems Neuroscience Journal
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