首页 > 最新文献

Function (Oxford, England)最新文献

英文 中文
Moving Beyond Barker's Hypothesis Towards New Therapies for the Treatment of Fetal Growth Restriction. 超越巴克的假设,寻找治疗胎儿生长受限的新疗法。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-05-19 DOI: 10.1093/function/zqaf022
Laura E Coats, Barbara T Alexander
{"title":"Moving Beyond Barker's Hypothesis Towards New Therapies for the Treatment of Fetal Growth Restriction.","authors":"Laura E Coats, Barbara T Alexander","doi":"10.1093/function/zqaf022","DOIUrl":"10.1093/function/zqaf022","url":null,"abstract":"","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Activation of the Carotid Body by Kappa Opioid Receptors Mitigates Fentanyl-Induced Respiratory Depression. kappa阿片受体激活颈动脉体减轻芬太尼诱导的呼吸抑制。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-05-19 DOI: 10.1093/function/zqaf020
Ying-Jie Peng, Jayasri Nanduri, Ning Wang, Zheng Xie, Aaron P Fox, Nanduri R Prabhakar

Previous studies reported that opioids depress breathing by inhibiting respiratory neural networks in the brainstem. The effects of opioids on sensory inputs regulating breathing are less studied. This study examined the effects of fentanyl and sufentanil on carotid body neural activity, a crucial sensory regulator of breathing. Both opioids stimulated carotid body afferent nerve activity and increased glomus cell [Ca2+]i levels. RNA sequencing and immunohistochemistry revealed a high abundance of κ opioid receptors (KORs) in carotid bodies, but no µ or δ opioid receptors. A KOR agonist, like fentanyl, stimulated carotid body afferents, while a KOR antagonist blocked carotid body activation by fentanyl and KOR agonist. In unanesthetized rats, fentanyl initially stimulated breathing, followed by respiratory depression. A KOR agonist stimulated breathing without respiratory inhibition, and this effect was absent in carotid body-denervated rats. Combining fentanyl with a KOR agonist attenuated respiratory depression in rats with intact carotid body but not in carotid body-denervated rats. These findings highlight previously uncharacterized activation of carotid body afferents by fentanyl via KORs as opposed to depression of brainstem respiratory neurons by µ opioid receptors and suggest that KOR agonists might counteract the central depressive effects of opioids on breathing.

先前的研究报道阿片类药物通过抑制脑干的呼吸神经网络来抑制呼吸。阿片类药物对调节呼吸的感觉输入的影响研究较少。这项研究检查了芬太尼和舒芬太尼对颈动脉体神经活动的影响,颈动脉体神经活动是呼吸的关键感觉调节器。两种阿片类药物均刺激颈动脉体传入神经活动并增加血管球细胞[Ca2+]i水平。RNA测序和免疫组化结果显示,颈动脉小体中κ类阿片受体(KORs)丰度高,但μ或δ类阿片受体不存在。像芬太尼一样,KOR激动剂刺激颈动脉体传入,而KOR拮抗剂通过芬太尼和KOR激动剂阻断颈动脉体激活。在未麻醉的大鼠中,芬太尼最初刺激呼吸,随后抑制呼吸。一种KOR激动剂刺激呼吸而无呼吸抑制,这种作用在颈动脉体去神经大鼠中不存在。芬太尼联合KOR激动剂可减轻颈动脉体完整大鼠的呼吸抑制,但不能减轻颈动脉体失神经大鼠的呼吸抑制。这些发现强调了芬太尼通过KORs激活颈动脉体传入,而不是通过µ阿片受体抑制脑干呼吸神经元,并表明KOR激动剂可能抵消阿片样物质对呼吸的中枢抑制作用。
{"title":"Activation of the Carotid Body by Kappa Opioid Receptors Mitigates Fentanyl-Induced Respiratory Depression.","authors":"Ying-Jie Peng, Jayasri Nanduri, Ning Wang, Zheng Xie, Aaron P Fox, Nanduri R Prabhakar","doi":"10.1093/function/zqaf020","DOIUrl":"10.1093/function/zqaf020","url":null,"abstract":"<p><p>Previous studies reported that opioids depress breathing by inhibiting respiratory neural networks in the brainstem. The effects of opioids on sensory inputs regulating breathing are less studied. This study examined the effects of fentanyl and sufentanil on carotid body neural activity, a crucial sensory regulator of breathing. Both opioids stimulated carotid body afferent nerve activity and increased glomus cell [Ca2+]i levels. RNA sequencing and immunohistochemistry revealed a high abundance of κ opioid receptors (KORs) in carotid bodies, but no µ or δ opioid receptors. A KOR agonist, like fentanyl, stimulated carotid body afferents, while a KOR antagonist blocked carotid body activation by fentanyl and KOR agonist. In unanesthetized rats, fentanyl initially stimulated breathing, followed by respiratory depression. A KOR agonist stimulated breathing without respiratory inhibition, and this effect was absent in carotid body-denervated rats. Combining fentanyl with a KOR agonist attenuated respiratory depression in rats with intact carotid body but not in carotid body-denervated rats. These findings highlight previously uncharacterized activation of carotid body afferents by fentanyl via KORs as opposed to depression of brainstem respiratory neurons by µ opioid receptors and suggest that KOR agonists might counteract the central depressive effects of opioids on breathing.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Aerobic Capacity and Exercise Mediate Protection Against Hepatic Steatosis via Enhanced Bile Acid Metabolism. 有氧能力和运动通过增强胆汁酸代谢介导对肝脂肪变性的保护。
IF 3.8 Q2 CELL BIOLOGY Pub Date : 2025-05-19 DOI: 10.1093/function/zqaf019
Benjamin A Kugler, Adrianna Maurer, Xiaorong Fu, Edziu Franczak, Nick Ernst, Kevin Schwartze, Julie Allen, Tiangang Li, Peter A Crawford, Lauren G Koch, Steven L Britton, Kartik Shankar, Shawn C Burgess, John P Thyfault

High cardiorespiratory fitness and exercise show evidence of altering bile acid (BA) metabolism and are known to protect or treat diet-induced hepatic steatosis, respectively. Here, we tested the hypothesis that high intrinsic aerobic capacity and exercise both increase hepatic BA synthesis measured by the incorporation of 2H2O. We also leveraged mice with inducible liver-specific deletion of Cyp7a1 (LCyp7a1KO), which encodes the rate-limiting enzyme for BA synthesis, to test if exercise-induced BA synthesis is critical for exercise to reduce hepatic steatosis. The synthesis of hepatic BA, cholesterol, and de novo lipogenesis was measured in rats bred for either high (HCR) or low (LCR) aerobic capacity consuming acute and chronic high-fat diets. HCR rats had increased synthesis of cholesterol and certain BA species in the liver compared to LCR rats. We also found that chronic exercise with voluntary wheel running (VWR) (4 weeks) increased newly synthesized BAs of specific species in male C57BL/6J mice compared to sedentary mice. Loss of Cyp7a1 resulted in fewer new BAs and increased liver triglycerides compared to controls after a 10-week high-fat diet. Additionally, exercise via VWR for 4 weeks effectively reduced hepatic triglycerides in the high-fat diet-fed control male and female mice as expected; however, exercise in LCyp7a1KO mice did not lower liver triglycerides in either sex. These results show that aerobic capacity and exercise increase hepatic BA metabolism, which may be critical for combatting hepatic steatosis.

高心肺适能和运动显示出改变胆汁酸(BA)代谢的证据,并分别保护或治疗饮食引起的肝脂肪变性。在这里,我们测试了高内在有氧能力和运动都增加肝脏BA合成的假设,通过掺入2H2O来测量。我们还利用小鼠诱导肝脏特异性缺失Cyp7a1 (lyp7a1ko),该基因编码BA合成的限速酶,以测试运动诱导的BA合成是否对运动减少肝脂肪变性至关重要。在高(HCR)和低(LCR)有氧能力饲养的大鼠中,分别摄入急性和慢性高脂肪饮食,测量了肝脏BA的合成、胆固醇和新生脂肪生成。与LCR大鼠相比,HCR大鼠肝脏中胆固醇和某些BA物质的合成增加。我们还发现,与久坐不动的小鼠相比,C57BL/ 6j雄性小鼠慢性运动与自愿轮跑(VWR)(4周)增加了特定物种的新合成BAs。在10周的高脂饮食后,与对照组相比,Cyp7a1的缺失导致新的BAs减少,肝脏甘油三酯增加。此外,通过VWR进行4周的运动可以有效降低高脂肪饮食喂养的对照雄性和雌性小鼠的肝脏甘油三酯,正如预期的那样;然而,lyp7a1ko小鼠的运动并没有降低肝脏甘油三酯。这些结果表明,有氧能力和运动增加了肝脏BA代谢,这可能是对抗肝脂肪变性的关键。
{"title":"Aerobic Capacity and Exercise Mediate Protection Against Hepatic Steatosis via Enhanced Bile Acid Metabolism.","authors":"Benjamin A Kugler, Adrianna Maurer, Xiaorong Fu, Edziu Franczak, Nick Ernst, Kevin Schwartze, Julie Allen, Tiangang Li, Peter A Crawford, Lauren G Koch, Steven L Britton, Kartik Shankar, Shawn C Burgess, John P Thyfault","doi":"10.1093/function/zqaf019","DOIUrl":"10.1093/function/zqaf019","url":null,"abstract":"<p><p>High cardiorespiratory fitness and exercise show evidence of altering bile acid (BA) metabolism and are known to protect or treat diet-induced hepatic steatosis, respectively. Here, we tested the hypothesis that high intrinsic aerobic capacity and exercise both increase hepatic BA synthesis measured by the incorporation of 2H2O. We also leveraged mice with inducible liver-specific deletion of Cyp7a1 (LCyp7a1KO), which encodes the rate-limiting enzyme for BA synthesis, to test if exercise-induced BA synthesis is critical for exercise to reduce hepatic steatosis. The synthesis of hepatic BA, cholesterol, and de novo lipogenesis was measured in rats bred for either high (HCR) or low (LCR) aerobic capacity consuming acute and chronic high-fat diets. HCR rats had increased synthesis of cholesterol and certain BA species in the liver compared to LCR rats. We also found that chronic exercise with voluntary wheel running (VWR) (4 weeks) increased newly synthesized BAs of specific species in male C57BL/6J mice compared to sedentary mice. Loss of Cyp7a1 resulted in fewer new BAs and increased liver triglycerides compared to controls after a 10-week high-fat diet. Additionally, exercise via VWR for 4 weeks effectively reduced hepatic triglycerides in the high-fat diet-fed control male and female mice as expected; however, exercise in LCyp7a1KO mice did not lower liver triglycerides in either sex. These results show that aerobic capacity and exercise increase hepatic BA metabolism, which may be critical for combatting hepatic steatosis.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12086534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Science Is at a Crossroads-and Physiology With It: A Statement from the APS Chief Executive Officer. 科学和生理学正处于十字路口:美国科学学会首席执行官的声明。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-05-19 DOI: 10.1093/function/zqaf025
Scott Steen
{"title":"Science Is at a Crossroads-and Physiology With It: A Statement from the APS Chief Executive Officer.","authors":"Scott Steen","doi":"10.1093/function/zqaf025","DOIUrl":"10.1093/function/zqaf025","url":null,"abstract":"","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12199138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Perspective on "Signal Transduction Pathway Mediating Carotid Body Dependent Sympathetic Activation and Hypertension by Chronic Intermittent Hypoxia". 关于 "介导颈动脉体依赖性交感神经激活和慢性间歇性缺氧引起的高血压的信号转导途径 "的观点。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqaf012
Gary C Sieck
{"title":"A Perspective on \"Signal Transduction Pathway Mediating Carotid Body Dependent Sympathetic Activation and Hypertension by Chronic Intermittent Hypoxia\".","authors":"Gary C Sieck","doi":"10.1093/function/zqaf012","DOIUrl":"10.1093/function/zqaf012","url":null,"abstract":"","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
KATP Channels as Target for Remodeling Connectivity in Type 2 Diabetes. KATP 通道是重塑 2 型糖尿病患者连接性的目标。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqaf013
Fei Kang, Herbert Y Gaisano
{"title":"KATP Channels as Target for Remodeling Connectivity in Type 2 Diabetes.","authors":"Fei Kang, Herbert Y Gaisano","doi":"10.1093/function/zqaf013","DOIUrl":"10.1093/function/zqaf013","url":null,"abstract":"","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Aryl Hydrocarbon Receptor Activation Promotes Effector CD4+ T Cell Homeostasis and Restrains Salt-Sensitive Hypertension. 芳烃受体激活促进效应CD4+ T细胞稳态和抑制盐敏感性高血压。
IF 3.8 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqaf001
Patrick A Molina, Claudia J Edell, Luke S Dunaway, Cailin E Kellum, Rachel Q Muir, Melissa S Jennings, Jackson C Colson, Carmen De Miguel, Megan K Rhoads, Ashlyn A Buzzelli, Laurie E Harrington, Selene Meza-Perez, Troy D Randall, Davide Botta, Dominik N Müller, David M Pollock, Craig L Maynard, Jennifer S Pollock

Excess dietary salt and salt-sensitivity contribute to cardiovascular disease. Distinct T cell phenotypic responses to high salt and hypertension, as well as influences from environmental cues, are not well understood. The aryl hydrocarbon receptor (AhR) is activated by dietary ligands, promoting T cell and systemic homeostasis. We hypothesized that activating AhR supports CD4+ homeostatic functions, such as cytokine production and mobilization, in response to high salt intake while mitigating salt-sensitive hypertension. In the intestinal mucosa, we demonstrate that a high-salt diet (HSD) is a key driving factor, independent of hypertension, in diminishing interleukin 17A (IL-17A) production by CD4+ T (Th17) cells without disrupting circulating cytokines associated with Th17 function. Previous studies suggest that hypertensive patients and individuals on a HSD are deficient in AhR ligands or agonistic metabolites. We found that activating AhR augments Th17 cells during experimental salt-sensitive hypertension. Further, we demonstrate that activating AhR in vitro contributes to sustaining Th17 cells in the setting of excess salt. Using photoconvertible Kikume Green-Red mice, we also revealed that HSD drives CD4+ T cell mobilization. Next, we found that excess salt augments T cell mobilization markers, validating HSD-driven T cell migration. Also, we found that activating AhR mitigates HSD-induced T cell migration markers. Using telemetry in a model of experimental salt-sensitivity, we found that activating AhR prevents the development of salt-sensitive hypertension. Collectively, stimulating AhR through dietary ligands facilitates immunologic and systemic functions amid excess salt intake and restrains the development of salt-sensitive hypertension.

饮食中盐过量和盐敏感会导致心血管疾病。不同的T细胞对高盐和高血压的表型反应以及环境因素的影响尚不清楚。芳烃受体(AhR)被膳食配体激活,促进T细胞和系统的稳态。我们假设激活AhR支持CD4+稳态功能,如细胞因子的产生和动员,以应对高盐摄入,同时减轻盐敏感性高血压。在肠粘膜中,我们证明高盐饮食(HSD)是一个独立于高血压的关键驱动因素,在不破坏与Th17功能相关的循环细胞因子的情况下,减少CD4+ T (Th17)细胞产生白细胞介素17A (IL-17A)。先前的研究表明,高血压患者和高盐饮食的个体缺乏AhR配体或激动性代谢物。我们发现,在实验性盐敏感性高血压中,激活AhR可增强Th17细胞。此外,我们证明在体外激活AhR有助于维持过量盐环境下的Th17细胞。在光转换的Kikume GreenRed小鼠中,我们还发现HSD可以促进CD4+ T细胞的动员。接下来,我们发现过量的盐增加了T细胞动员标记物,验证了hsd驱动的T细胞迁移。此外,我们发现激活AhR可以减轻hsd诱导的T细胞迁移标记物。在实验盐敏感性模型中使用遥测技术,我们发现激活AhR可以防止盐敏感性高血压的发展。总的来说,通过饮食配体刺激AhR可促进过量盐摄入时的免疫和系统功能,并抑制盐敏感性高血压的发展。
{"title":"Aryl Hydrocarbon Receptor Activation Promotes Effector CD4+ T Cell Homeostasis and Restrains Salt-Sensitive Hypertension.","authors":"Patrick A Molina, Claudia J Edell, Luke S Dunaway, Cailin E Kellum, Rachel Q Muir, Melissa S Jennings, Jackson C Colson, Carmen De Miguel, Megan K Rhoads, Ashlyn A Buzzelli, Laurie E Harrington, Selene Meza-Perez, Troy D Randall, Davide Botta, Dominik N Müller, David M Pollock, Craig L Maynard, Jennifer S Pollock","doi":"10.1093/function/zqaf001","DOIUrl":"10.1093/function/zqaf001","url":null,"abstract":"<p><p>Excess dietary salt and salt-sensitivity contribute to cardiovascular disease. Distinct T cell phenotypic responses to high salt and hypertension, as well as influences from environmental cues, are not well understood. The aryl hydrocarbon receptor (AhR) is activated by dietary ligands, promoting T cell and systemic homeostasis. We hypothesized that activating AhR supports CD4+ homeostatic functions, such as cytokine production and mobilization, in response to high salt intake while mitigating salt-sensitive hypertension. In the intestinal mucosa, we demonstrate that a high-salt diet (HSD) is a key driving factor, independent of hypertension, in diminishing interleukin 17A (IL-17A) production by CD4+ T (Th17) cells without disrupting circulating cytokines associated with Th17 function. Previous studies suggest that hypertensive patients and individuals on a HSD are deficient in AhR ligands or agonistic metabolites. We found that activating AhR augments Th17 cells during experimental salt-sensitive hypertension. Further, we demonstrate that activating AhR in vitro contributes to sustaining Th17 cells in the setting of excess salt. Using photoconvertible Kikume Green-Red mice, we also revealed that HSD drives CD4+ T cell mobilization. Next, we found that excess salt augments T cell mobilization markers, validating HSD-driven T cell migration. Also, we found that activating AhR mitigates HSD-induced T cell migration markers. Using telemetry in a model of experimental salt-sensitivity, we found that activating AhR prevents the development of salt-sensitive hypertension. Collectively, stimulating AhR through dietary ligands facilitates immunologic and systemic functions amid excess salt intake and restrains the development of salt-sensitive hypertension.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Hands-On Introduction to Data Analytics for Biomedical Research. 生物医学研究数据分析的动手介绍。
IF 3.8 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqaf015
Joshua Pickard, Victoria E Sturgess, Katherine O McDonald, Nicholas Rossiter, Kelly B Arnold, Yatrik M Shah, Indika Rajapakse, Daniel A Beard

Artificial intelligence (AI) applications are having increasing impacts in the biomedical sciences. Modern AI tools enable uncovering hidden patterns in large datasets, forecasting outcomes, and numerous other applications. Despite the availability and power of these tools, the rapid expansion and complexity of AI applications can be daunting, and there is a conspicuous absence of consensus on their ethical and responsible use. Misapplication of AI can result in invalid, unclear, or biased outcomes, exacerbated by the unfamiliarity of many biomedical researchers with the underlying mathematical and computational principles. To address these challenges, this review and tutorial paper aims to achieve three primary objectives: (1) highlight prevalent data science applications in biomedical research, including data visualization, dimensionality reduction, missing data imputation, and predictive model training and evaluation; (2) provide comprehensible explanations of the mathematical foundations underpinning these methodologies; and (3) guide readers on the effective use and interpretation of software tools for implementing these methods in biomedical contexts. While introductory, this guide covers core principles essential for understanding advanced applications, empowering readers to critically interpret results, assess tools, and explore the potential and limitations of machine learning in their research. Ultimately, this paper serves as a practical foundation for biomedical researchers to confidently navigate the growing intersection of AI and biomedicine.

人工智能(AI)应用对生物医学科学的影响越来越大。现代人工智能工具能够揭示大型数据集中隐藏的模式、预测结果以及许多其他应用。尽管这些工具可用性强、功能强大,但人工智能应用的快速扩展和复杂性可能令人望而生畏,而且在道德和负责任地使用这些工具方面明显缺乏共识。人工智能的错误应用可能会导致无效、不明确或有偏见的结果,而许多生物医学研究人员对基本数学和计算原理的不熟悉更加剧了这种情况。为了应对这些挑战,这篇综述和教程论文旨在实现三个主要目标:(1) 强调数据科学在生物医学研究中的普遍应用,包括数据可视化、降维、缺失数据估算以及预测模型的训练和评估;(2) 对支撑这些方法的数学基础提供易懂的解释;(3) 指导读者有效使用和解释软件工具,以便在生物医学环境中实施这些方法。本指南虽然是入门级的,但涵盖了理解高级应用所必需的核心原则,使读者有能力批判性地解释结果、评估工具并探索机器学习在其研究中的潜力和局限性。最终,本文将为生物医学研究人员自信地驾驭人工智能与生物医学日益增长的交叉学科奠定实用的基础。
{"title":"A Hands-On Introduction to Data Analytics for Biomedical Research.","authors":"Joshua Pickard, Victoria E Sturgess, Katherine O McDonald, Nicholas Rossiter, Kelly B Arnold, Yatrik M Shah, Indika Rajapakse, Daniel A Beard","doi":"10.1093/function/zqaf015","DOIUrl":"10.1093/function/zqaf015","url":null,"abstract":"<p><p>Artificial intelligence (AI) applications are having increasing impacts in the biomedical sciences. Modern AI tools enable uncovering hidden patterns in large datasets, forecasting outcomes, and numerous other applications. Despite the availability and power of these tools, the rapid expansion and complexity of AI applications can be daunting, and there is a conspicuous absence of consensus on their ethical and responsible use. Misapplication of AI can result in invalid, unclear, or biased outcomes, exacerbated by the unfamiliarity of many biomedical researchers with the underlying mathematical and computational principles. To address these challenges, this review and tutorial paper aims to achieve three primary objectives: (1) highlight prevalent data science applications in biomedical research, including data visualization, dimensionality reduction, missing data imputation, and predictive model training and evaluation; (2) provide comprehensible explanations of the mathematical foundations underpinning these methodologies; and (3) guide readers on the effective use and interpretation of software tools for implementing these methods in biomedical contexts. While introductory, this guide covers core principles essential for understanding advanced applications, empowering readers to critically interpret results, assess tools, and explore the potential and limitations of machine learning in their research. Ultimately, this paper serves as a practical foundation for biomedical researchers to confidently navigate the growing intersection of AI and biomedicine.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11999024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Response of the Nephron Arterial Network and Its Interactions to Acute Hypertension: A Simulation. 肾动脉网络及其相互作用对急性高血压的反应:模拟。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqae049
Donald J Marsh, Niels-Henrik Holstein-Rathlou

We simulated the dynamics of a group of 10 nephrons supplied from an arterial network and subjected to acute increases in blood pressure. Arterial lengths and topology were based on measurements of a vascular cast. The model builds on a previous version exercised at a single blood pressure with 2 additional features: pressure diuresis and the effect of blood pressure on efferent arteriolar vascular resistance. The new version simulates autoregulation, and reproduces tubule pressure oscillations. Individual nephron dynamics depended on mean arterial pressure and the axial pressure gradient required to cause blood flow through the arteries. Rhythmic blood withdrawal into afferent arterioles caused blood flow fluctuations in downstream vessels. Blood pressure dependent changes in nephron dynamics affected synchronization metrics. The combination of vascular pressure gradients and oscillations created a range of arterial pressures at the origins of the 10 afferent arterioles. Because arterial blood pressure in conscious animals has ${1}/{f}$ dynamics, we applied an arterial pressure pattern with such dynamics to the model. Amplitude of tubule pressure oscillations were affected by the ${1}/{f}$ blood pressure fluctuations, but the oscillation frequencies did not change. The pressure gradients required to deliver blood to all afferent arterioles impose a complexity that affects nephrons according to their locations in the network, but other interactions compensate to ensure the stability of the system. The sensitivity of nephron response to location on the network, and the constancy of the tubular oscillation frequency provide a spatial and time context.

我们模拟了一组由 10 个肾小球组成的动脉网络在血压急剧升高时的动态变化。动脉长度和拓扑结构基于血管铸模的测量结果。该模型是在单一血压下运行的前一版本的基础上增加了两个功能:压力利尿和血压对传出动脉血管阻力的影响。新版本模拟了自动调节,并再现了肾小管压力振荡。单个肾小球的动态取决于平均动脉压和动脉血流所需的轴压梯度。有节奏地将血液抽入传入动脉血管会引起下游血管的血流波动。肾小球动力学中与血压相关的变化影响了同步指标。血管压力梯度和振荡的结合在 10 个传入动脉血管的起源处产生了一系列动脉压力。由于有意识动物的动脉血压具有 1/f 动态变化,因此我们在模型中应用了具有这种动态变化的动脉压力模式。肾小管压力振荡的振幅受到 1/f 血压波动的影响,但振荡频率没有变化。将血液输送到所有传入动脉血管所需的压力梯度带来了复杂性,根据肾小管在网络中的位置对其产生影响,但其他相互作用起到了补偿作用,确保了系统的稳定性。肾小球的反应对网络中位置的敏感性以及肾小管振荡频率的恒定性提供了一个空间和时间背景。
{"title":"Response of the Nephron Arterial Network and Its Interactions to Acute Hypertension: A Simulation.","authors":"Donald J Marsh, Niels-Henrik Holstein-Rathlou","doi":"10.1093/function/zqae049","DOIUrl":"10.1093/function/zqae049","url":null,"abstract":"<p><p>We simulated the dynamics of a group of 10 nephrons supplied from an arterial network and subjected to acute increases in blood pressure. Arterial lengths and topology were based on measurements of a vascular cast. The model builds on a previous version exercised at a single blood pressure with 2 additional features: pressure diuresis and the effect of blood pressure on efferent arteriolar vascular resistance. The new version simulates autoregulation, and reproduces tubule pressure oscillations. Individual nephron dynamics depended on mean arterial pressure and the axial pressure gradient required to cause blood flow through the arteries. Rhythmic blood withdrawal into afferent arterioles caused blood flow fluctuations in downstream vessels. Blood pressure dependent changes in nephron dynamics affected synchronization metrics. The combination of vascular pressure gradients and oscillations created a range of arterial pressures at the origins of the 10 afferent arterioles. Because arterial blood pressure in conscious animals has ${1}/{f}$ dynamics, we applied an arterial pressure pattern with such dynamics to the model. Amplitude of tubule pressure oscillations were affected by the ${1}/{f}$ blood pressure fluctuations, but the oscillation frequencies did not change. The pressure gradients required to deliver blood to all afferent arterioles impose a complexity that affects nephrons according to their locations in the network, but other interactions compensate to ensure the stability of the system. The sensitivity of nephron response to location on the network, and the constancy of the tubular oscillation frequency provide a spatial and time context.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142636214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phosphatases Control the Duration and Range of cAMP/PKA Microdomains. 磷酸酶控制cAMP/PKA微域的持续时间和范围。
IF 5.1 Q2 CELL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1093/function/zqaf007
Filippo Conca, Doruk Kaan Bayburtlu, Mauro Vismara, Nicoletta C Surdo, Alessandra Tavoni, Leonardo Nogara, Adamo Sarra, Stefano Ciciliot, Giulietta Di Benedetto, Liliana F Iannucci, Konstantinos Lefkimmiatis

The spatiotemporal interplay between the second messenger cyclic AMP (cAMP) and its main effector, protein kinase A (PKA), is crucial for the pleiotropic nature of this cascade. To maintain a high degree of specificity, the cAMP/PKA axis is organised into functional units called microdomains, precisely distributed within the cell. While the subcellular allocation of PKA is guaranteed by a family of tethers called A-Kinase-anchoring Proteins (AKAPs), the mechanisms underlying the efficient confinement of a microdomain's functional effects are not fully understood. Here, we used FRET-based sensors to detect cAMP levels and PKA-dependent phosphorylation within specific subcellular compartments. We find that cellular cAMP levels may depend on different mechanisms and are responsible for the activation of local PKA enzymes. On the other hand, the dephosphorylating actions of phosphatases dictate the duration of the microdomain's effects. To test the range of action of PKA microdomains, we used rigid aminoacidic nanorulers to distance our FRET sensors from their original location for 10 or 30 nm. Interestingly, we established that cAMP levels do not affect the spatial range of the microdomain while on the contrary, phosphatase activity provides a functional boundary for phosphorylated PKA targets. Finally, using the same strategy to distance phosphatases from the mitochondria, we found that enzymes close to the outer mitochondrial membrane produced a fragmented phenotype that was not observed when phosphatases were moved to 30 nm from the organelle's surface. Our findings contribute to the design of a picture where 2 microdomain-forming events have distinct roles. Cyclic AMP elevations trigger the initial activation of subcellular PKA moieties, while the temporal and spatial extent of the PKA's actions are regulated by phosphatases.

第二信使环AMP (cAMP)与其主要效应物蛋白激酶A (PKA)之间的时空相互作用对于该级联的多效性至关重要。为了保持高度特异性,cAMP/PKA轴被组织成称为微域的功能单元,精确地分布在细胞内。虽然PKA的亚细胞分配是由一种称为a -激酶锚定蛋白(AKAPs)的系链家族保证的,但有效限制微结构域功能效应的机制尚不完全清楚。在这里,我们使用基于fret的传感器来检测特定亚细胞区室内cAMP水平和pka依赖性磷酸化。我们发现细胞cAMP水平可能依赖于不同的机制,并负责局部PKA酶的激活。另一方面,磷酸酶的去磷酸化作用决定了微结构域作用的持续时间。为了测试PKA微域的作用范围,我们使用刚性氨基酸纳米尺将FRET传感器与原始位置距离10或30 nm。有趣的是,我们发现cAMP水平不影响微结构域的空间范围,相反,磷酸酶活性为磷酸化的PKA靶点提供了一个功能边界。最后,使用相同的策略使磷酸酶远离线粒体,我们发现靠近线粒体外膜的酶产生了碎片化的表型,当磷酸酶移动到离细胞器表面30 nm处时,没有观察到这种表型。我们的发现有助于设计两个微畴形成事件具有不同作用的图像。循环AMP升高触发亚细胞PKA片段的初始激活,而PKA作用的时间和空间范围由磷酸酶调节。
{"title":"Phosphatases Control the Duration and Range of cAMP/PKA Microdomains.","authors":"Filippo Conca, Doruk Kaan Bayburtlu, Mauro Vismara, Nicoletta C Surdo, Alessandra Tavoni, Leonardo Nogara, Adamo Sarra, Stefano Ciciliot, Giulietta Di Benedetto, Liliana F Iannucci, Konstantinos Lefkimmiatis","doi":"10.1093/function/zqaf007","DOIUrl":"10.1093/function/zqaf007","url":null,"abstract":"<p><p>The spatiotemporal interplay between the second messenger cyclic AMP (cAMP) and its main effector, protein kinase A (PKA), is crucial for the pleiotropic nature of this cascade. To maintain a high degree of specificity, the cAMP/PKA axis is organised into functional units called microdomains, precisely distributed within the cell. While the subcellular allocation of PKA is guaranteed by a family of tethers called A-Kinase-anchoring Proteins (AKAPs), the mechanisms underlying the efficient confinement of a microdomain's functional effects are not fully understood. Here, we used FRET-based sensors to detect cAMP levels and PKA-dependent phosphorylation within specific subcellular compartments. We find that cellular cAMP levels may depend on different mechanisms and are responsible for the activation of local PKA enzymes. On the other hand, the dephosphorylating actions of phosphatases dictate the duration of the microdomain's effects. To test the range of action of PKA microdomains, we used rigid aminoacidic nanorulers to distance our FRET sensors from their original location for 10 or 30 nm. Interestingly, we established that cAMP levels do not affect the spatial range of the microdomain while on the contrary, phosphatase activity provides a functional boundary for phosphorylated PKA targets. Finally, using the same strategy to distance phosphatases from the mitochondria, we found that enzymes close to the outer mitochondrial membrane produced a fragmented phenotype that was not observed when phosphatases were moved to 30 nm from the organelle's surface. Our findings contribute to the design of a picture where 2 microdomain-forming events have distinct roles. Cyclic AMP elevations trigger the initial activation of subcellular PKA moieties, while the temporal and spatial extent of the PKA's actions are regulated by phosphatases.</p>","PeriodicalId":73119,"journal":{"name":"Function (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Function (Oxford, England)
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1