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英文中文

Future of Exosome Bioinformatics. 外泌体生物信息学的未来。

EMBnet.journal

Pub Date : 2023-01-01 DOI: 10.14806/ej.28.0.1015

Dimitrios P Vlachakis, Kalliopi Io Diakou, George P Chrousos

Exosomes are under intense study as a promising means for drug or biomarker discovery, primarily due to their implication in intercellular communication and the emergence of disease states and their potential as a cutting-edge, natural delivery system at a nanoscale level. The proteins and nucleic acid cargo of exosomes has been at the center of exosome bioinformatic analysis in the context of health and disease, towards the hunt for novel biomarkers and diagnostics. However, the exosomal lipid composition has been emerging as an interesting target of study as well. Exosomes derived from different sources exhibit enrichment of specific lipid classes and various lipid compositions under different physiological conditions. Therefore, there is a mounting need for exosome lipidomic studies to build the foundation for novel therapeutic studies that use exosomal components. Bioinformatic pipelines are under development to efficiently identify, quantify and elucidate the exosomal lipids and their roles in disease. Cutting-edge bioinformatic tools, such as LipidXplorer, LUX Score, and LipidHome allow the execution of essential analyses such as shotgun lipidomics, and the detection of systematic differences in lipid composition and metadata processing. In the case of pancreatic cancer, an admittedly prevalent and life-threatening disease, these tools have yielded novel exosome lipid biomarkers. Furthermore, bioinformatic platforms such as “Lipidomics Informatics for Life-Science” enable fast and integrated access to these pipelines in a user-friendly manner. Modern bioinformatic methods facilitate the processing of exosome lipidomics

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引用次数: 0

Validation of the Greek Version of Social Appearance Anxiety Scale in Adolescents and Young Adults. 希腊版青少年和青年社会外表焦虑量表的验证。

EMBnet.journal

Pub Date : 2023-01-01 DOI: 10.14806/ej.28.0.1027

Triada Konstantina Papapanou, Flora Bacopoulou, Maria Michou, Christina Kanaka-Gantenbein, Dimitrios Vlachakis, George P Chrousos, Christina Darviri

Many people are worried about their social appearance. The fear of negative evaluation and judgment regarding one's look in social circumstances is referred to as social appearance anxiety. Social appearance anxiety belongs to social anxiety. The aim of the present study was to validate the Social Appearance Anxiety Scale (SAAS) in the Greek language and to examine its psychometric properties. An online survey was conducted in a Greek population sample of adolescents and young adults aged 18 to 35 years. The survey instruments included the Social Appearance Anxiety Scale, the Social Physique Anxiety Scale (SPAS), 2 subscales of Multidimensional Body-Self Relations Questionnaire Appearance Scale (MBSRQ), the Appearance Schemas Inventory-Revised Scale (ASI-R) and the Depression Anxiety Stress Scale (DASS). A total of 429 respondents participated in this research. The statistical analysis showed that the Greek version of the SAAS has good psychometric properties. The internal consistency of questions within the SAAS was 0.942. Positive correlations were found between SAAS and SPAS, the overweight preoccupation subscale of MBSRQ, the ASI-R and the DASS, while negative correlations were observed between SAAS and the appearance evaluation subscale of MBSRQ and age. The results of this study suggest that the Greek version of SAAS can be used as a reliable and valid instrument in the Greek population.

许多人担心自己的社交形象。害怕在社交场合对自己外表的负面评价和判断被称为社交外表焦虑。社交表象焦虑属于社交焦虑。本研究的目的是验证希腊语言的社会外观焦虑量表(SAAS)，并检验其心理测量特性。一项在线调查在希腊18至35岁的青少年和年轻人中进行。调查工具包括社会外貌焦虑量表、社会体质焦虑量表(SPAS)、多维身自关系问卷外貌量表(MBSRQ)、外貌图式修正量表(ASI-R)和抑郁焦虑压力量表(DASS)。共有429名受访者参与了这项研究。统计分析表明，希腊文版本的SAAS具有良好的心理测量特性。SAAS内部问题的一致性为0.942。SAAS与SPAS、MBSRQ超重关注分量表、ASI-R和DASS呈显著正相关，与MBSRQ外貌评价分量表和年龄呈显著负相关。本研究的结果表明，希腊版本的SAAS可以作为一个可靠和有效的工具，在希腊人口。

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引用次数: 1

Validation of the Eating Habits Questionnaire in Greek adults. 希腊成年人饮食习惯问卷的验证。

EMBnet.journal

Pub Date : 2023-01-01 DOI: 10.14806/ej.28.0.1029

Georgia Bali, Ioulia Kokka, Fragiskos Gonidakis, Eleni Papakonstantinou, Dimitrios Vlachakis, George P Chrousos, Christina Kanaka-Gantenbein, Flora Bacopoulou

Healthy eating has gained ground in people's daily lives in modern society. However, an overwhelming preoccupation with healthy eating can lead to a pathological form setting the ground for orthorexia nervosa. This study aimed to validate the Greek version of the Eating Habits Questionnaire (EHQ) in adults 18 to 65 years old. The EHQ evaluates orthorexia nervosa traits. An online survey was conducted among adults of the general Greek population by administrating a battery of self-report instruments. The IPIP Big-Five personality questionnaire, Beck's Depression Inventory, the Obsessive-Compulsive Inventory-Revised, the Bulimic Investigatory Test, the Edinburg BITE, and the Eating Attitudes Test-13 were used. Internal consistency, test-retest reliability, and convergent and criterion validity were examined. A total of 551 adults (92.2% females) voluntarily participated in the study. Results suggest that the Greek version of the instrument has good psychometric properties. Analysis revealed a 3-factor model explaining 48.20% of the total variance. Cronbach's alphas ranged between 0.80 to 0.82, indicating good internal consistency. The test-retest reliability analysis showed no statistically significant difference between the measurements of the first and the post-2 weeks. Correlations with other eating disorder-related constructs were found to be weak to moderate. Body mass index was not significantly correlated with neither of the three EHQ subscales. The Greek version of EHQ is a robust instrument that could be used in clinical practice and research in the field of eating disorders in Greece.

在现代社会，健康饮食已经在人们的日常生活中占据了一席之地。然而，对健康饮食的过度关注可能导致一种病理形式，为神经性厌食症奠定了基础。本研究旨在验证希腊版饮食习惯问卷(EHQ)在18至65岁成年人中的有效性。EHQ评估神经性厌食症的特征。一项在线调查是通过管理一系列自我报告工具在希腊普通成年人中进行的。采用IPIP大五人格问卷、贝克抑郁量表、强迫症量表修订版、暴食调查测试、爱丁堡BITE测试和饮食态度测试13。检验了内部一致性、重测信度、收敛效度和标准效度。共有551名成年人(92.2%为女性)自愿参与研究。结果表明，希腊版本的仪器具有良好的心理测量性能。分析显示一个3因素模型解释48.20%的总方差。Cronbach's alpha在0.80 - 0.82之间，表明内部一致性良好。重测信度分析显示，第1周与第2周后的测量结果无统计学差异。与其他饮食失调相关结构的相关性被发现是弱到中等的。身体质量指数与三个EHQ分量表均无显著相关。希腊版本的EHQ是一种强大的工具，可用于希腊饮食失调领域的临床实践和研究。

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引用次数: 1

A Bioinformatics pipeline for variant discovery from Targeted Next Generation Sequencing of the human mitochondrial genome 从下一代人类线粒体基因组测序中发现变异的生物信息学管道

EMBnet.journal

Pub Date : 2022-09-30 DOI: 10.14806/ej.28.0.1007

L. Jayasekera, K. Senanayake, R. Ranasinghe, K. Tennekoon

Sequence variants of human mitochondrial DNA (mt DNA) have been implicated in a variety of disorders and conditions. Massive parallel sequencing is becoming increasingly popular due to its efficiency and cost-effectiveness. In relation to acquiring significant sequence information like levels of heteroplasmy in mt DNA, it offers a marked improvement compared to previous methods used. Here we describe a variant calling pipeline for human mitochondrial DNA using Next Generation Sequencing (NGS) data obtained by enriching the sample only for mitochondria prior to sequencing.

人类线粒体DNA (mt DNA)的序列变异与多种疾病和病症有关。大规模并行测序由于其效率和成本效益而越来越受欢迎。关于获取重要的序列信息，如mt DNA的异质性水平，与以前使用的方法相比，它提供了显着的改进。在这里，我们描述了一个人类线粒体DNA的变体调用管道，使用下一代测序(NGS)数据，该数据通过在测序前仅为线粒体富集样品获得。

引用次数: 0

In memory of Dr. Allan Orozco 为了纪念艾伦·奥罗斯科博士

EMBnet.journal

Pub Date : 2022-07-25 DOI: 10.14806/ej.27.0.1017

Emiliano Barreto-Hernández

Obituary

讣告

引用次数: 0

Structural analysis on mutations related to Alzheimer’s disease 阿尔茨海默病相关突变的结构分析

EMBnet.journal

Pub Date : 2022-07-07 DOI: 10.14806/ej.27.0.1011

A. Avramouli, Eleftheria Polychronidou, P. Vlamos

Proteins have a significant role in all biological processes. The functional properties of proteins rely upon their three-dimensional structures. Over the last twenty years substantial advances in genomic technologies have enhanced our knowledge of the genetics of Alzheimer’s disease. To that end the identification of mutations pathogenicity is still of vital importance. The methodology of the present research work focuses on the structural analysis of proteins related to Alzheimer’s disease and the comparative study to create groups with clear structural similarity and pathogenicity. To achieve that, three-dimensional descriptors (fpfh, rsd and 3dsc) were applied along with supervised machine learning classification methods. In total, 62 APP, 286 PSEN1, 68 PSEN2 and 25 MAPT variants were evaluated in our study.The output of the methodology characterized thirty mutations that were unclear at the point of the data collection.

蛋白质在所有生物过程中都起着重要的作用。蛋白质的功能特性依赖于它们的三维结构。在过去的二十年中，基因组技术的巨大进步增强了我们对阿尔茨海默病遗传学的认识。为此目的，鉴定突变的致病性仍然至关重要。本研究工作的方法学侧重于对阿尔茨海默病相关蛋白的结构分析和比较研究，以创建具有明确结构相似性和致病性的群体。为了实现这一目标，三维描述符(fpfh, rsd和3dsc)与监督机器学习分类方法一起应用。在我们的研究中，总共评估了62个APP, 286个PSEN1, 68个PSEN2和25个MAPT变体。该方法的输出表征了在数据收集时尚不清楚的30个突变。

引用次数: 0

A rational structure-based drug design strategy for the discovery of novel antiviral agents against the Yellow Fever Virus helicase 一种基于合理结构的药物设计策略，用于发现针对黄热病病毒解旋酶的新型抗病毒药物

EMBnet.journal

Pub Date : 2022-07-07 DOI: 10.14806/ej.27.0.1009

Eleni D Papakonstantinou, Katerina Pierouli, G. Goulielmos, E. Eliopoulos

Yellow Fever is a viral hemorrhagic disease that is transmitted mainly through arthropods with high mortality rates. Yellow Fever Virus (YFV) is an enveloped positive sense single-stranded RNA virus, member of the Flaviviridae family and the Flavivirus genus, and is endemic in countries of Africa and South America. However, recent cases of infection in North America, Asia and Europe are highlighting the potential risk of an outbreak with no effective treatment available and the urgent need to develop potent antiviral agents against the YFV. In this direction a range of specific modulators were designed and in silico evaluated in an effort to hinder the enzymatic activity of the YFV helicase as a prominent pharmacological target. Following a structure-based rational drug design pipeline, a phylogenetic analysis of Flaviviridae viruses and an in-depth evolutionary study on the Yellow Fever Virus helicase has provided invaluable insights into structural conservation and structural elements and features that are vital for the viral helicase function. Using comparative modelling and molecular dynamics simulations the YFV helicase-ssRNA complex was established, and the specific molecular interactions and physicochemical properties of the complex could be analyzed and used towards the designing and elucidation of a specific YFV 3D pharmacophore model. A high throughput virtual screening simulation was conducted to assess a set of in-house maintained low molecular weight compounds as bioactive inhibitors of the YFV helicase enzyme. The in-silico study described herein, could pave the way towards the designing and more efficient screening of potential novel modulator compounds against the YFV as well as attest and designate the NS3 helicase as an antiviral pharmacological target of uttermost value and potential.

黄热病是一种病毒性出血性疾病，主要通过节肢动物传播，死亡率高。黄热病病毒(YFV)是一种包膜阳性单链RNA病毒，属黄病毒科和黄病毒属，在非洲和南美洲国家流行。然而，最近在北美、亚洲和欧洲发生的感染病例突出表明，在没有有效治疗方法的情况下，有爆发疫情的潜在风险，迫切需要开发针对YFV的强效抗病毒药物。在这个方向上，设计了一系列特定的调节剂，并在计算机上进行了评估，以阻止YFV解旋酶作为一个突出的药理靶点的酶活性。在基于结构的合理药物设计管道之后，黄病毒科病毒的系统发育分析和对黄热病病毒解旋酶的深入进化研究为病毒解旋酶功能至关重要的结构保守和结构元件和特征提供了宝贵的见解。通过比较建模和分子动力学模拟，建立了YFV解旋酶- ssrna复合物，分析了复合物的特定分子相互作用和物理化学性质，并用于设计和阐明特定的YFV三维药效团模型。通过高通量虚拟筛选模拟来评估一组内部维持的低分子量化合物作为YFV解旋酶的生物活性抑制剂。本文所述的计算机研究可以为设计和更有效地筛选针对YFV的潜在新型调节剂化合物铺平道路，并证明和指定NS3解旋酶作为最有价值和潜力的抗病毒药理学靶点。

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引用次数: 0

Deep Learning concepts for genomics : an overview 基因组学的深度学习概念:概述

EMBnet.journal

Pub Date : 2022-06-03 DOI: 10.14806/ej.27.0.990

Merouane Elazami Elhassani, Loïc Maisonnasse, Antoine Olgiati, Rey Jerome, Majda Rehali, P. Duroux, V. Giudicelli, S. Kossida

Nowadays, Deep Learning is taking the world by a storm, known as a technology that makes use of Artificial Neural Networks to automatically extrapolate knowledge from a training data set, then uses this knowledge to give predictions for unseen samples. This data driven paradigm gained a widespread adoption in many disciplines, from handwriting recognition, driving an autonomous car to cracking the 50-year-old protein folding problem. With this review, we shed some light on the concepts of Deep Learning and provide some visualizations, skim over the different architectures such as Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) and touch upon the modern architectures such as Transformers and BERT. We also provide various examples targeting the genomics field, reference utilities, libraries useful for newcomers and disseminate our feedback.

如今，深度学习正在风靡全球，它是一种利用人工神经网络从训练数据集中自动推断知识，然后利用这些知识对未见过的样本进行预测的技术。这种数据驱动的范式在许多学科中得到了广泛的采用，从手写识别、自动驾驶汽车到破解已有50年历史的蛋白质折叠问题。通过这篇综述，我们揭示了一些深度学习的概念，并提供了一些可视化，浏览了不同的架构，如深度神经网络(DNN)，卷积神经网络(CNN)，循环神经网络(RNN)，并触及了现代架构，如变形金刚和BERT。我们还提供了针对基因组学领域的各种示例，参考实用程序，对新手有用的库，并传播我们的反馈。

引用次数: 0

Molecular fusion events in carcinogenic organisms: a bioinformatics study for the detection of fused proteins between viruses, bacteria and eukaryotes. 致癌生物中的分子融合事件:检测病毒、细菌和真核生物之间融合蛋白的生物信息学研究。

EMBnet.journal

Pub Date : 2022-04-01 DOI: 10.14806/ej.27.0.1004

Eleni D Papakonstantinou, K. Diakou, Thanasis Mitsis, Konstantina Dragoumani, F. Bacopoulou, V. Megalooikonomou, S. Kossida, G. Chrousos, D. Vlachakis

Molecular fusion events have a prominent role in the initial steps of carcinogenesis. In this study, a bioinformatics analysis was performed between four organisms that are known to induce cancer development in humans: two viruses, Human Herpesvirus 4, and Human T-cell leukaemia virus, one bacterium, Helicobacter Pylori, and one trematode, Schistosoma mansoni. The annotated proteomes from these organisms were analysed using the SAFE software to identify protein fusion events, which may provide insight into protein function similarities and possible merging events during the course of evolution. Based on the results, five fused proteins with very similar functions were detected, whereas proteins with different functions that might act in the same molecular complex or biochemical pathway were not found. Thus, this study analysed the above four well-known cancer-related organisms with de novo bioinformatics programs and provided useful information on protein fusion events, hopefully leading to deeper understanding of carcinogenenesis.

分子融合事件在癌变的初始阶段起着重要作用。在这项研究中，对四种已知可诱导人类癌症发展的生物进行了生物信息学分析:两种病毒，人类疱疹病毒4和人类t细胞白血病病毒，一种细菌，幽门螺杆菌和一种吸虫，曼氏血吸虫。使用SAFE软件对这些生物体的注释蛋白质组进行分析，以确定蛋白质融合事件，这可能有助于深入了解进化过程中蛋白质功能的相似性和可能的合并事件。在此基础上，检测到5种功能非常相似的融合蛋白，而未发现可能在同一分子复合物或生化途径中起作用的功能不同的蛋白。因此，本研究利用de - novo生物信息学程序对上述四种已知的癌症相关生物进行了分析，并提供了有关蛋白质融合事件的有用信息，以期对癌变机制有更深入的了解。

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引用次数: 0

The medical cyborg concept 医疗生化人的概念

EMBnet.journal

Pub Date : 2022-04-01 DOI: 10.14806/ej.27.0.1005

Eleni D Papakonstantinou, Thanasis Mitsis, Konstantina Dragoumani, F. Bacopoulou, V. Megalooikonomou, G. Chrousos, D. Vlachakis

Medical technology has made significant advances in the 21st century and, at present, medicine makes use of information technology, telecommunications, and state-of-the-art engineering to provide the best possible healthcare services. Electronic sensors provide health practitioners with the ability to constantly monitor their patients’ health, to streamlines a number of medical processes, and to increase patients’ access to health services. Mobile phones also empower patients and play a major role in their health’s monitoring. The use of cybernetics technology can now help patients overcome even serious disabilities, enabling many disabled patients to live their lives similarly to their non-disabled fellow men through the use of artificial organs and implants. All these advances have paved the way for a more personalized type of healthcare that provides individualized solutions to each patient. Once a number of hurdles are overcome, medical technology will bring forth a new era of more precise and enabling medicine.

医疗技术在21世纪取得了重大进展，目前，医学利用信息技术、电信和最先进的工程来提供尽可能最好的医疗保健服务。电子传感器为卫生从业人员提供了持续监测患者健康状况的能力，简化了一些医疗流程，并增加了患者获得卫生服务的机会。移动电话还赋予患者权力，并在他们的健康监测中发挥重要作用。控制论技术的使用现在可以帮助患者克服甚至严重的残疾，使许多残疾患者通过使用人造器官和植入物过上与正常人相似的生活。所有这些进步都为更加个性化的医疗保健铺平了道路，为每位患者提供个性化的解决方案。一旦克服了一些障碍，医疗技术将带来一个更精确和更有利的医疗的新时代。

引用次数: 1

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