scientific literature

科学文献
  • 文章类型: Journal Article
    科学知识正以前所未有的速度在生物医学文献中积累。最广泛使用的数据库与生物医学相关的文章摘要,PubMed,目前包含超过3600万个条目。在该数据库中搜索感兴趣的主题的用户面临难以手动处理的数千个条目(文章)。在这项工作中,我们提出了一种交互式工具,用于自动消化大量PubMed文章:PMIDigest(PubMedID消化器)。该系统允许根据不同的标准对物品进行分类/排序,包括文章类型和不同的引文相关数字。它还计算感兴趣类别的MeSH(医学主题词)术语的分布,提供一组主题的图片。这些MeSH术语在文章摘要中以不同的颜色突出显示,具体取决于类别。还提供了文章间引用网络的交互式表示,以便轻松定位与特定主题相关的文章“集群”,以及他们相应的“集线器”文章。除了PubMed文章,系统还可以处理一组Scopus或WebofScience条目。总之,有了这个系统,用户可以拥有大量文章及其主要主题趋势的“鸟瞰”,并获得在简单的摘要列表中不明显的其他信息。
    Scientific knowledge is being accumulated in the biomedical literature at an unprecedented pace. The most widely used database with biomedicine-related article abstracts, PubMed, currently contains more than 36 million entries. Users performing searches in this database for a subject of interest face thousands of entries (articles) that are difficult to process manually. In this work, we present an interactive tool for automatically digesting large sets of PubMed articles: PMIDigest (PubMed IDs digester). The system allows for classification/sorting of articles according to different criteria, including the type of article and different citation-related figures. It also calculates the distribution of MeSH (medical subject headings) terms for categories of interest, providing in a picture of the themes addressed in the set. These MeSH terms are highlighted in the article abstracts in different colors depending on the category. An interactive representation of the interarticle citation network is also presented in order to easily locate article \"clusters\" related to particular subjects, as well as their corresponding \"hub\" articles. In addition to PubMed articles, the system can also process a set of Scopus or Web of Science entries. In summary, with this system, the user can have a \"bird\'s eye view\" of a large set of articles and their main thematic tendencies and obtain additional information not evident in a plain list of abstracts.
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  • 文章类型: Journal Article
    神经母细胞瘤是一种儿童神经系统肿瘤,影响全世界成千上万的儿童,关于其预后的信息对患者来说是至关重要的,他们的家人,和临床医生。相关生物信息学分析的主要目标之一是提供能够包括其表达水平可以有效预测患者预后的基因的稳定遗传特征。在这项研究中,我们收集了生物医学文献中发表的神经母细胞瘤的预后特征,并注意到其中最常见的基因是三个:AHCY,DPYLS3和NME1。因此,我们通过对诊断为神经母细胞瘤的不同组患者的多个基因表达数据集进行生存分析和二元分类来研究这三个基因的预后能力。最后,我们讨论了这三个基因与神经母细胞瘤相关的文献中的主要研究。我们的结果,在这三个验证步骤中,确认AHCY的预后能力,DPYLS3和NME1,并强调它们在神经母细胞瘤预后中的关键作用。我们的结果可以对神经母细胞瘤遗传学研究产生影响:生物学家和医学研究人员可以更加关注这三个基因在神经母细胞瘤患者中的调控和表达,因此,可以开发出更好的治疗和治疗方法,可以挽救病人的生命。
    Neuroblastoma is a childhood neurological tumor which affects hundreds of thousands of children worldwide, and information about its prognosis can be pivotal for patients, their families, and clinicians. One of the main goals in the related bioinformatics analyses is to provide stable genetic signatures able to include genes whose expression levels can be effective to predict the prognosis of the patients. In this study, we collected the prognostic signatures for neuroblastoma published in the biomedical literature, and noticed that the most frequent genes present among them were three: AHCY, DPYLS3, and NME1. We therefore investigated the prognostic power of these three genes by performing a survival analysis and a binary classification on multiple gene expression datasets of different groups of patients diagnosed with neuroblastoma. Finally, we discussed the main studies in the literature associating these three genes with neuroblastoma. Our results, in each of these three steps of validation, confirm the prognostic capability of AHCY, DPYLS3, and NME1, and highlight their key role in neuroblastoma prognosis. Our results can have an impact on neuroblastoma genetics research: biologists and medical researchers can pay more attention to the regulation and expression of these three genes in patients having neuroblastoma, and therefore can develop better cures and treatments which can save patients\' lives.
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  • 文章类型: Journal Article
    在生物医学领域,生命或环境科学研究,根据研究人员的出发点,存在两种不同的策略:“是什么让我们生病?”或“是什么让我们健康?”。的确,基于风险的策略(RBS)试图将增加疾病发展可能性的风险因素降至最低。而基于资产的战略(ABS)试图促进和加强支持良好健康和福祉的因素。我们在同行评审的科学文献中提供了两种研究策略的最新概述,在人类健康领域,动植物健康和生态系统健康,以适应一个健康框架。更具体地说,我们通过研究大流行开始时与COVID-19相关的出版物来关注人类健康。
    对研究科学文献进行了快速审查,以在PubMed/MEDLINE数据库中确定采用RBS或ABS的同行评审文章的比例,在1900年1月1日至2019年12月31日的主要全球环境领域,与COVID-19相关,从2019年12月1日至2020年5月31日。
    我们搜索的已发表文章数量为1,957,905,其中RBS占91.3%,ABS占8.7%。检查每个字段时,我们发现只有10.5%的健康文章涉及ABS,动物健康5.5%,生态系统健康2.2%,1.0%用于植物健康,2.7%用于环境介质。我们注意到,所有卫生领域都发表了采用这两种策略的文章。在有关COVID-19的文章中,5854篇(55.9%),542篇(5.2%)采用了RBS和ABS,分别,而4069(38.9%)同时提出两种策略。
    我们的研究结果使我们能够评估20世纪优先考虑的生物医学研究策略。我们分析过的这两种策略现在似乎很有可能被选择,以促进公共卫生措施的平衡,在各个层面指导一个健康干预措施,旨在帮助人们,动物,和植物过上更健康的生活。
    In biomedical, life or environmental science research, two different strategies exist depending on the starting point of the researchers: \"what makes us ill? \" or \"what makes us healthy?\". Indeed, a risk-based strategy (RBS) attempts to minimize risk factors increasing the likelihood of developing a disease, while an asset-based strategy (ABS) attempts to promote and strengthen the factors that support good health and wellbeing. We provided an up-to-date overview of both research strategies in peer-reviewed scientific literature, in the fields of human health, animal and plant health and ecosystem health, to fit with the One Health framework. More particularly, we focused on human health by studying publications related to the COVID-19 at the beginning of the pandemic.
    A rapid review of research science literature was carried out to identify in the PubMed/MEDLINE database the proportion of peer-reviewed articles adopting either a RBS or an ABS, in the main global environment fields from January 01, 1900 to December 31, 2019 and, related to COVID-19, from December 1, 2019 to May 31, 2020.
    The number of published articles resulting from our search was 1,957,905, including 91.3% with an RBS and 8.7% with an ABS. When examining each field, we found that only 10.5% of human health articles deal with ABS, 5.5% for animal health, 2.2% for ecosystem health, 1.0% for plant health and 2.7% for environmental media. We noted that articles adopting both strategies were published in all health fields. Among the articles concerning COVID-19, 5,854 (55.9%), 542 articles (5.2%) adopted RBS and ABS, respectively, while 4069 (38.9%) simultaneously presenting both strategies.
    Our results have allowed us to take stock of the biomedical research strategies prioritized during the twentieth century. It seems highly likely that the two strategies we have analyzed can now be chosen in such a way as to promote a balance in public health measures, at every level to guide One Health interventions aimed at helping people, animals, and plants to lead healthier lives.
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  • 文章类型: Journal Article
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  • 文章类型: Journal Article
    近年来,气候变化对持久性有机污染物(POPs)浓度的影响已成为值得关注的话题。平均气温升高等环境条件的变化,或者UV-B辐射,可能会影响持久性有机污染物的命运和行为,最终影响人类暴露。气候变化对持久性有机污染物环境浓度的影响的最新水平,以及人类健康风险,在这里审查。还发现了研究差距,同时建议未来的研究。气候变化和持久性有机污染物是一个热点问题,这不仅应该引起科学家的广泛关注,但也主要是政策制定者。科学文献中报道的大多数研究都集中在遗留持久性有机污染物上,主要是多氯二苯并对二恶英和二苯并呋喃(PCDD/Fs),多氯联苯(PCBs)和农药。然而,旨在评估气候变化对多环芳烃(PAHs)环境水平影响的调查数量很少,尽管暴露于PAHs和光降解副产物可能会导致不利的健康影响。此外,科学文献中目前没有关于新出现的持久性有机污染物的数据.因此,需要加强研究,以确定和减轻气候变化对持久性有机污染物命运的间接影响,以最大程度地减少对人类健康的影响。此外,这是一个全球性的问题,必须从国际角度解决气候变化与持久性有机污染物之间的相互作用。
    In recent years, the climate change impact on the concentrations of persistent organic pollutants (POPs) has become a topic of notable concern. Changes in environmental conditions such as the increase of the average temperature, or the UV-B radiation, are likely to influence the fate and behavior of POPs, ultimately affecting human exposure. The state of the art of the impact of climate change on environmental concentrations of POPs, as well as on human health risks, is here reviewed. Research gaps are also identified, while future studies are suggested. Climate change and POPs are a hot issue, for which wide attention should be paid not only by scientists, but also and mainly by policy makers. Most studies reported in the scientific literature are focused on legacy POPs, mainly polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and pesticides. However, the number of investigations aimed at estimating the impact of climate change on the environmental levels of polycyclic aromatic hydrocarbons (PAHs) is scarce, despite of the fact that exposure to PAHs and photodegradation byproducts may result in adverse health effects. Furthermore, no data on emerging POPs are currently available in the scientific literature. In consequence, an intensification of studies to identify and mitigate the indirect effects of the climate change on POP fate is needed to minimize the human health impact. Furthermore, being this a global problem, interactions between climate change and POPs must be addressed from an international perspective.
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