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Best practices for data management and sharing in experimental biomedical research. 生物医学实验研究数据管理与共享的最佳实践。
IF 29.9 1区 医学 Q1 PHYSIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-03-07 DOI: 10.1152/physrev.00043.2023
Teresa Cunha-Oliveira, John P A Ioannidis, Paulo J Oliveira

Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.

有效的数据管理对于科学完整性和可重复性至关重要,是科学进步的基石。有条理、有据可查的数据有助于验证和巩固成果。数据管理包括组织、记录、存储、共享和保存等活动。健全的数据管理可建立可信度,促进科学界的信任,并有利于研究人员的职业发展。在生物医学实验中,由于通常需要复杂的实验方案、广泛的元数据和庞大的数据集,因此全面的数据管理至关重要。低通量实验尤其需要精心管理,以解决方案和原始数据质量方面的变化和错误。透明、负责的研究实践有赖于对程序、数据收集和分析方法的准确记录。适当的数据管理可确保宝贵数据集的长期保存和可访问性。管理得当的数据可以被重新研究,有助于知识的积累和潜在的新发现。公共资助的研究在透明度、资源分配和避免重复方面负有更多责任。要满足资助机构的期望,越来越需要严格的方法、遵守标准、全面的文档以及广泛的数据、代码和其他辅助资源共享。本综述对原始数据和处理过的数据、元数据、高通量数据集与低通量数据集、文档的通用语言、实验和报告指南、高效的数据管理系统、共享实践以及相关资源库提供了重要的见解。我们系统地介绍了可供生物医学实验研究人员广泛使用的可用资源和最佳实践。
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引用次数: 0
The anterior chamber of the eye technology and its anatomical, optical, and immunological bases. 眼球前房技术及其解剖学、光学和免疫学基础。
IF 29.9 1区 医学 Q1 PHYSIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-01-11 DOI: 10.1152/physrev.00024.2023
Shao-Nian Yang, Yue Shi, Per-Olof Berggren

The anterior chamber of the eye (ACE) is distinct in its anatomy, optics, and immunology. This guarantees that the eye perceives visual information in the context of physiology even when encountering adverse incidents like inflammation. In addition, this endows the ACE with the special nursery bed iris enriched in vasculatures and nerves. The ACE constitutes a confined space enclosing an oxygen/nutrient-rich, immune-privileged, and less stressful milieu as well as an optically transparent medium. Therefore, aside from visual perception, the ACE unexpectedly serves as an excellent transplantation site for different body parts and a unique platform for noninvasive, longitudinal, and intravital microimaging of different grafts. On the basis of these merits, the ACE technology has evolved from the prototypical through the conventional to the advanced version. Studies using this technology as a versatile biomedical research platform have led to a diverse range of basic knowledge and in-depth understanding of a variety of cells, tissues, and organs as well as artificial biomaterials, pharmaceuticals, and abiotic substances. Remarkably, the technology turns in vivo dynamic imaging of the morphological characteristics, organotypic features, developmental fates, and specific functions of intracameral grafts into reality under physiological and pathological conditions. Here we review the anatomical, optical, and immunological bases as well as technical details of the ACE technology. Moreover, we discuss major achievements obtained and potential prospective avenues for this technology.

眼球前房(ACE)在解剖学、光学和免疫学方面都与众不同。这保证了眼睛即使在遇到炎症等不利因素时,也能在生理环境中感知视觉信息。此外,这还赋予了 ACE 特殊的育儿床虹膜,其中富含血管和神经。ACE 是一个封闭的空间,内含氧气/营养丰富、免疫力高、压力小的环境以及光学透明的介质。因此,除了视觉感知外,ACE 还意外地成为不同身体部位的绝佳移植场所,以及对不同移植物进行无创、纵向和体内显微成像的独特平台。在这些优点的基础上,ACE 技术从原型到传统再到先进版本不断发展。将该技术作为一个多功能生物医学研究平台进行的研究,使人们获得了各种基础知识,并深入了解了各种细胞、组织和器官以及人造生物材料、药物和非生物物质。值得注意的是,该技术将巩膜内移植物在生理和病理条件下的形态特征、器官型特征、发育命运和特定功能的体内动态成像变成了现实。在此,我们回顾了 ACE 技术的解剖学、光学和免疫学基础以及技术细节。此外,我们还讨论了这项技术取得的主要成就和潜在的发展前景。
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引用次数: 0
Ceramides are fuel gauges on the drive to cardiometabolic disease. 神经酰胺是通往心脏代谢疾病的 "燃料计"。
IF 29.9 1区 医学 Q1 PHYSIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-02-01 DOI: 10.1152/physrev.00008.2023
Joseph L Wilkerson, Sean M Tatum, William L Holland, Scott A Summers

Ceramides are signals of fatty acid excess that accumulate when a cell's energetic needs have been met and its nutrient storage has reached capacity. As these sphingolipids accrue, they alter the metabolism and survival of cells throughout the body including in the heart, liver, blood vessels, skeletal muscle, brain, and kidney. These ceramide actions elicit the tissue dysfunction that underlies cardiometabolic diseases such as diabetes, coronary artery disease, metabolic-associated steatohepatitis, and heart failure. Here, we review the biosynthesis and degradation pathways that maintain ceramide levels in normal physiology and discuss how the loss of ceramide homeostasis drives cardiometabolic pathologies. We highlight signaling nodes that sense small changes in ceramides and in turn reprogram cellular metabolism and stimulate apoptosis. Finally, we evaluate the emerging therapeutic utility of these unique lipids as biomarkers that forecast disease risk and as targets of ceramide-lowering interventions that ameliorate disease.

神经酰胺是脂肪酸过剩的信号,当细胞的能量需求得到满足、营养储存达到饱和时,神经酰胺就会累积。随着这些鞘脂的累积,它们会改变包括心脏、肝脏、血管、骨骼肌、大脑和肾脏在内的全身细胞的新陈代谢和存活。这些神经酰胺的作用会引起组织功能障碍,而组织功能障碍是糖尿病、冠状动脉疾病、代谢相关性脂肪性肝炎和心力衰竭等心脏代谢性疾病的基础。在此,我们回顾了维持正常生理状态下神经酰胺水平的生物合成和降解途径,并讨论了神经酰胺平衡的丧失是如何导致心脏代谢疾病的。我们重点介绍了感知神经酰胺微小变化的信号节点,这些节点反过来会重新规划细胞代谢并刺激细胞凋亡。最后,我们评估了这些独特脂质作为预测疾病风险的生物标志物以及作为改善疾病的降神经酰胺干预目标的新兴治疗用途。
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引用次数: 0
The hormonal control of parturition. 分娩的荷尔蒙控制
IF 29.9 1区 医学 Q1 PHYSIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-02-08 DOI: 10.1152/physrev.00019.2023
Emily Hamburg-Shields, Sam Mesiano

Parturition is a complex physiological process that must occur in a reliable manner and at an appropriate gestation stage to ensure a healthy newborn and mother. To this end, hormones that affect the function of the gravid uterus, especially progesterone (P4), 17β-estradiol (E2), oxytocin (OT), and prostaglandins (PGs), play pivotal roles. P4 via the nuclear P4 receptor (PR) promotes uterine quiescence and for most of pregnancy exerts a dominant block to labor. Loss of the P4 block to parturition in association with a gain in prolabor actions of E2 are key transitions in the hormonal cascade leading to parturition. P4 withdrawal can occur through various mechanisms depending on species and physiological context. Parturition in most species involves inflammation within the uterine tissues and especially at the maternal-fetal interface. Local PGs and other inflammatory mediators may initiate parturition by inducing P4 withdrawal. Withdrawal of the P4 block is coordinated with increased E2 actions to enhance uterotonic signals mediated by OT and PGs to promote uterine contractions, cervix softening, and membrane rupture, i.e., labor. This review examines recent advances in research to understand the hormonal control of parturition, with focus on the roles of P4, E2, PGs, OT, inflammatory cytokines, and placental peptide hormones together with evolutionary biology of and implications for clinical management of human parturition.

分娩是一个复杂的生理过程,必须以可靠的方式在适当的妊娠阶段进行,以确保新生儿和母亲的健康。为此,影响妊娠子宫功能的激素,尤其是孕酮(P4)、17ß-雌二醇(E2)、催产素(OT)和前列腺素(PGs)发挥着关键作用。P4 通过核 P4 受体(PR)促进子宫静止,并在妊娠的大部分时间里对分娩起着主要的阻碍作用。P4 阻滞分娩作用的消失与促分娩作用 E2 的增加是导致分娩的激素级联中的关键转变。根据物种和生理环境的不同,P4 可通过各种机制退出。大多数物种的临产都涉及子宫组织内的炎症,尤其是母胎界面的炎症。局部 PGs 和其他炎症介质可能会通过诱导 P4 退出来启动分娩。P4 阻滞的撤出与 E2 作用的增强相协调,从而增强由 OT 和 PGs 介导的子宫收缩信号,促进子宫收缩、宫颈软化和胎膜破裂,即分娩。本综述探讨了了解分娩激素控制的最新研究进展,重点是 P4、E2、PGs、OT、炎性细胞因子和胎盘肽类激素的作用,以及人类分娩的进化生物学和对临床管理的影响。
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引用次数: 0
Degenerate Neuronal and Circuit Mechanisms Important for Generating Rhythmic Motor Patterns 生成节律性运动模式的重要退化神经元和电路机制
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-06-13 DOI: 10.1152/physrev.00003.2024
Ronald L Calabrese, Eve Marder
Physiological Reviews, Ahead of Print.
生理学评论》,提前出版。
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引用次数: 0
A versatile delivery vehicle for cellular oxygen and fuels, or metabolic sensor? - A review and perspective on the functions of myoglobin 细胞氧气和燃料的多功能输送工具,还是代谢传感器?- 肌红蛋白功能的回顾与展望
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-05-02 DOI: 10.1152/physrev.00031.2023
Kiran Kumar Adepu, Andriy Anishkin, Sean H. Adams, Sree V Chintapalli
Physiological Reviews, Ahead of Print.
生理学评论》,提前出版。
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引用次数: 0
Neuronal glucose sensing mechanisms and circuits in the control of insulin and glucagon secretion 控制胰岛素和胰高血糖素分泌的神经元葡萄糖传感机制和回路
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-25 DOI: 10.1152/physrev.00038.2023
Bernard Thorens
Glucose homeostasis is mainly under the control of the pancreatic islet hormones insulin and glucagon, which, respectively, stimulate glucose uptake and utilization by liver, fat, and muscle or glucose production by the liver. The balance between the secretion of these hormones is under the control of blood glucose concentrations. Indeed, pancreatic islet b-cells and a-cells can sense variations in glycemia and respond by an appropriate secretory response to restore euglycemia. However, the secretory activity of these cells is also under multiple additional metabolic, hormonal, and neuronal signals that combine to ensure the perfect control of glycemia over a lifetime. The central nervous system (CNS), which has an almost absolute requirement for glucose as a source of metabolic energy and, thus, a vital interest in ensuring that glycemic levels never fall below ~5mM, is equipped with populations of neurons responsive to changes in glucose concentrations. These neurons control pancreatic islet cells secretion activity in multiple ways: through both branches of the autonomic nervous system, through the hypothalamic-pituitary-adrenal axis, and by secreting vasopressin (AVP) in the blood at the level of the posterior pituitary. Here, we will present the autonomic innervation of the pancreatic islets; the mechanisms of neurons activation by a rise or a fall in glucose concentration; how current viral tracing, chemogenetic, and optogenetic techniques allow to integrate specific glucose sensing neurons in defined neuronal circuits that control endocrine pancreas function. Finally, how genetic screens in mice can untangle the diversity of the hypothalamic mechanisms controlling the response to hypoglycemia.
葡萄糖稳态主要受胰岛激素胰岛素和胰高血糖素的控制,这两种激素分别刺激肝脏、脂肪和肌肉摄取和利用葡萄糖,或刺激肝脏产生葡萄糖。这些激素分泌之间的平衡受血糖浓度的控制。事实上,胰岛 b 细胞和 a 细胞能够感知血糖的变化,并通过适当的分泌反应来恢复优血症。然而,这些细胞的分泌活动还受到新陈代谢、荷尔蒙和神经元等多种额外信号的影响,这些信号共同作用,确保在人的一生中完美地控制血糖。中枢神经系统(CNS)几乎绝对需要葡萄糖作为新陈代谢的能量来源,因此,确保血糖水平永远不低于约 5 毫摩尔对中枢神经系统来说至关重要。这些神经元通过多种方式控制胰岛细胞的分泌活动:通过自律神经系统的两个分支、通过下丘脑-垂体-肾上腺轴以及通过在垂体后叶水平分泌血液中的血管加压素(AVP)。在这里,我们将介绍胰岛的自主神经支配;葡萄糖浓度升高或降低激活神经元的机制;目前的病毒追踪、化学遗传和光遗传技术如何将特定的葡萄糖传感神经元整合到控制胰腺内分泌功能的神经元回路中。最后,小鼠基因筛选如何解开控制低血糖反应的下丘脑机制的多样性。
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引用次数: 0
NETosis creates a link between diabetes and Long COVID. Netosis在糖尿病和长期新冠肺炎之间建立了联系。
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-01 Epub Date: 2023-10-19 DOI: 10.1152/physrev.00032.2023
Alain R Thierry
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引用次数: 0
Mesenchymal stromal cells for improvement of cardiac function following acute myocardial infarction: a matter of timing. 间充质基质细胞用于改善急性心肌梗死后的心脏功能:时机问题。
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-01 Epub Date: 2023-08-17 DOI: 10.1152/physrev.00009.2023
Stéphanie Barrère-Lemaire, Anne Vincent, Christian Jorgensen, Christophe Piot, Joël Nargeot, Farida Djouad

Acute myocardial infarction (AMI) is the leading cause of cardiovascular death and remains the most common cause of heart failure. Reopening of the occluded artery, i.e., reperfusion, is the only way to save the myocardium. However, the expected benefits of reducing infarct size are disappointing due to the reperfusion paradox, which also induces specific cell death. These ischemia-reperfusion (I/R) lesions can account for up to 50% of final infarct size, a major determinant for both mortality and the risk of heart failure (morbidity). In this review, we provide a detailed description of the cell death and inflammation mechanisms as features of I/R injury and cardioprotective strategies such as ischemic postconditioning as well as their underlying mechanisms. Due to their biological properties, the use of mesenchymal stromal/stem cells (MSCs) has been considered a potential therapeutic approach in AMI. Despite promising results and evidence of safety in preclinical studies using MSCs, the effects reported in clinical trials are not conclusive and even inconsistent. These discrepancies were attributed to many parameters such as donor age, in vitro culture, and storage time as well as injection time window after AMI, which alter MSC therapeutic properties. In the context of AMI, future directions will be to generate MSCs with enhanced properties to limit cell death in myocardial tissue and thereby reduce infarct size and improve the healing phase to increase postinfarct myocardial performance.

急性心肌梗死(AMI)是心血管疾病死亡的主要原因,也是心力衰竭最常见的原因。重新开放闭塞的动脉,即再灌注,是挽救心肌的唯一方法。然而,由于再灌注悖论也会诱发特异性细胞死亡,缩小梗死面积的预期效果令人失望。这些缺血再灌注(I/R)病变可占最终梗死面积的 50%,是死亡率和心力衰竭风险(发病率)的主要决定因素。在这篇综述中,我们将详细介绍作为 I/R 损伤特征的细胞死亡和炎症机制,以及缺血后处理等心脏保护策略及其内在机制。由于间充质基质/干细胞(MSCs)的生物特性,其使用被认为是急性心肌梗死的一种潜在治疗方法。尽管在使用间充质干细胞的临床前研究中取得了令人鼓舞的结果和安全性证据,但临床试验中报告的效果并不确定,甚至不一致。这些差异归因于许多参数,如供体年龄、体外培养和储存时间以及急性髓损伤后的注射时间窗,这些都会改变间充质干细胞的治疗特性。就急性心肌梗死而言,未来的方向将是产生具有更强特性的间充质干细胞,以限制心肌组织中的细胞死亡,从而缩小梗死面积,并改善愈合阶段以提高梗死后心肌的功能。
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引用次数: 0
CD36 as a gatekeeper of myocardial lipid metabolism and therapeutic target for metabolic disease. CD36作为心肌脂质代谢的看门人和代谢性疾病的治疗靶点。
IF 33.6 1区 医学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-01 Epub Date: 2023-10-26 DOI: 10.1152/physrev.00011.2023
Jan F C Glatz, Lisa C Heather, Joost J F P Luiken

The multifunctional membrane glycoprotein CD36 is expressed in different types of cells and plays a key regulatory role in cellular lipid metabolism, especially in cardiac muscle. CD36 facilitates the cellular uptake of long-chain fatty acids, mediates lipid signaling, and regulates storage and oxidation of lipids in various tissues with active lipid metabolism. CD36 deficiency leads to marked impairments in peripheral lipid metabolism, which consequently impact on the cellular utilization of multiple different fuels because of the integrated nature of metabolism. The functional presence of CD36 at the plasma membrane is regulated by its reversible subcellular recycling from and to endosomes and is under the control of mechanical, hormonal, and nutritional factors. Aberrations in this dynamic role of CD36 are causally associated with various metabolic diseases, in particular insulin resistance, diabetic cardiomyopathy, and cardiac hypertrophy. Recent research in cardiac muscle has disclosed the endosomal proton pump vacuolar-type H+-ATPase (v-ATPase) as a key enzyme regulating subcellular CD36 recycling and being the site of interaction between various substrates to determine cellular substrate preference. In addition, evidence is accumulating that interventions targeting CD36 directly or modulating its subcellular recycling are effective for the treatment of metabolic diseases. In conclusion, subcellular CD36 localization is the major adaptive regulator of cellular uptake and metabolism of long-chain fatty acids and appears a suitable target for metabolic modulation therapy to mend failing hearts.

多功能膜糖蛋白CD36在不同类型的细胞中表达,并在细胞脂质代谢中发挥关键的调节作用。CD36促进长链脂肪酸的细胞摄取,介导脂质信号传导,并通过活跃的脂质代谢调节各种组织中脂质的储存和氧化。CD36缺乏导致外周脂质代谢的显著损伤,由于代谢的综合性,从而影响多种不同燃料的细胞利用。CD36在质膜上的功能性存在由其从内体到内体的可逆亚细胞循环调节,并受机械、激素和营养因素的控制。CD36这种动态作用的异常与各种代谢性疾病,特别是胰岛素抵抗、糖尿病心肌病和心肌肥大有因果关系。最近对心肌的研究揭示了内体质子泵v-ATP酶是调节亚细胞CD36循环的关键酶,也是各种底物之间相互作用以确定细胞底物偏好的位点。此外,越来越多的证据表明,直接靶向CD36或调节其亚细胞循环的干预措施对治疗代谢性疾病是有效的。总之,亚细胞CD36定位是细胞摄取和代谢长链脂肪酸的主要适应性调节因子,是修复衰竭心脏的代谢调节疗法的合适靶点。
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引用次数: 0
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