Wiley Interdisciplinary Reviews-Systems Biology and Medicine最新文献_第10页

Computational models of the neural control of breathing 呼吸神经控制的计算模型

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-03-01 DOI: 10.1002/wsbm.1371

Y. Molkov, J. Rubin, I. Rybak, Jeffrey C. Smith

{"title":"Computational models of the neural control of breathing","authors":"Y. Molkov, J. Rubin, I. Rybak, Jeffrey C. Smith","doi":"10.1002/wsbm.1371","DOIUrl":"https://doi.org/10.1002/wsbm.1371","url":null,"abstract":"The ongoing process of breathing underlies the gas exchange essential for mammalian life. Each respiratory cycle ensues from the activity of rhythmic neural circuits in the brainstem, shaped by various modulatory signals, including mechanoreceptor feedback sensitive to lung inflation and chemoreceptor feedback dependent on gas composition in blood and tissues. This paper reviews a variety of computational models designed to reproduce experimental findings related to the neural control of breathing and generate predictions for future experimental testing. The review starts from the description of the core respiratory network in the brainstem, representing the central pattern generator (CPG) responsible for producing rhythmic respiratory activity, and progresses to encompass additional complexities needed to simulate different metabolic challenges, closed‐loop feedback control including the lungs, and interactions between the respiratory and autonomic nervous systems. The integrated models considered in this review share a common framework including a distributed CPG core network responsible for generating the baseline three‐phase pattern of rhythmic neural activity underlying normal breathing. WIREs Syst Biol Med 2017, 9:e1371. doi: 10.1002/wsbm.1371","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"22 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84773163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 53

Cancer and inflammation 癌症和炎症

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-03-01 DOI: 10.1002/wsbm.1370

L. Munn

{"title":"Cancer and inflammation","authors":"L. Munn","doi":"10.1002/wsbm.1370","DOIUrl":"https://doi.org/10.1002/wsbm.1370","url":null,"abstract":"The relationship between inflammation and cancer has been recognized since the 17th century,1 and we now know much about the cells, cytokines and physiological processes that are central to both inflammation and cancer.2-9 Chronic inflammation can induce certain cancers,10-17 and solid tumors, in turn, can initiate and perpetuate local inflammatory processes that foster tumor growth and dissemination.5,18-20 Consequently, inflammatory pathways have been targeted in attempts to control cancer.21-23 Inflammation is a central aspect of the innate immune system's response to tissue damage or infection, and also facilitates the recruitment of circulating cells and antibodies of the adaptive immune response to the tissue. Components of the innate immune response carry out a robust, but sometimes overly‐conservative response, sacrificing specificity for the sake of preservation. Thus, when innate immunity goes awry, it can have profound implications. How the innate and adaptive immune systems cooperate to neutralize pathogens and repair damaged tissues is still an area of intense investigation. Further, how these systems can respond to cancer, which arises from normal ‘self’ cells that undergo an oncogenic transformation, has profound implications for cancer therapy. Recently, immunotherapies that activate adaptive immunity have shown unprecedented promise in the clinic, producing durable responses and dramatic increases in survival rate in patients with advanced stage melanoma.24-26 Consequently, the relationship between cancer and inflammation has now returned to the forefront of clinical oncology. WIREs Syst Biol Med 2017, 9:e1370. doi: 10.1002/wsbm.1370","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"23 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84353504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 181

Toward modeling locomotion using electromyography‐informed 3D models: application to cerebral palsy 利用肌电图三维模型建模运动:在脑瘫中的应用

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-03-01 DOI: 10.1002/wsbm.1368

Massimo Sartori, J. Fernàndez, L. Modenese, C. Carty, L. Barber, K. Oberhofer, Jianwei Zhang, G. Handsfield, N. Stott, T. Besier, D. Farina, D. Lloyd

{"title":"Toward modeling locomotion using electromyography‐informed 3D models: application to cerebral palsy","authors":"Massimo Sartori, J. Fernàndez, L. Modenese, C. Carty, L. Barber, K. Oberhofer, Jianwei Zhang, G. Handsfield, N. Stott, T. Besier, D. Farina, D. Lloyd","doi":"10.1002/wsbm.1368","DOIUrl":"https://doi.org/10.1002/wsbm.1368","url":null,"abstract":"This position paper proposes a modeling pipeline to develop clinically relevant neuromusculoskeletal models to understand and treat complex neurological disorders. Although applicable to a variety of neurological conditions, we provide direct pipeline applicative examples in the context of cerebral palsy (CP). This paper highlights technologies in: (1) patient‐specific segmental rigid body models developed from magnetic resonance imaging for use in inverse kinematics and inverse dynamics pipelines; (2) efficient population‐based approaches to derive skeletal models and muscle origins/insertions that are useful for population statistics and consistent creation of continuum models; (3) continuum muscle descriptions to account for complex muscle architecture including spatially varying material properties with muscle wrapping; (4) muscle and tendon properties specific to CP; and (5) neural‐based electromyography‐informed methods for muscle force prediction. This represents a novel modeling pipeline that couples for the first time electromyography extracted features of disrupted neuromuscular behavior with advanced numerical methods for modeling CP‐specific musculoskeletal morphology and function. The translation of such pipeline to the clinical level will provide a new class of biomarkers that objectively describe the neuromusculoskeletal determinants of pathological locomotion and complement current clinical assessment techniques, which often rely on subjective judgment. WIREs Syst Biol Med 2017, 9:e1368. doi: 10.1002/wsbm.1368","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"64 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86882941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 36

Systems biology of oxygen homeostasis 氧稳态的系统生物学

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-02-21 DOI: 10.1002/wsbm.1382

Debangshu Samanta, N. Prabhakar, G. Semenza

引用次数: 45

Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms 极端嗜热微生物的生理、代谢和生物技术特征

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-02-16 DOI: 10.1002/wsbm.1377

James A. Counts, Benjamin Zeldes, Laura L. Lee, Christopher T. Straub, M. Adams, R. M. Kelly

{"title":"Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms","authors":"James A. Counts, Benjamin Zeldes, Laura L. Lee, Christopher T. Straub, M. Adams, R. M. Kelly","doi":"10.1002/wsbm.1377","DOIUrl":"https://doi.org/10.1002/wsbm.1377","url":null,"abstract":"The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs—basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology‐based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"151 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79542937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 29

Mathematical modeling of the female reproductive system: from oocyte to delivery. 女性生殖系统的数学建模:从卵母细胞到分娩。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-01-01 Epub Date: 2016-09-09 DOI: 10.1002/wsbm.1353

Alys R Clark, Jennifer A Kruger

{"title":"Mathematical modeling of the female reproductive system: from oocyte to delivery.","authors":"Alys R Clark, Jennifer A Kruger","doi":"10.1002/wsbm.1353","DOIUrl":"https://doi.org/10.1002/wsbm.1353","url":null,"abstract":"From ovulation to delivery, and through the menstrual cycle, the female reproductive system undergoes many dynamic changes to provide an optimal environment for the embryo to implant, and to develop successfully. It is difficult ethically and practically to observe the system over the timescales involved in growth and development (often hours to days). Even in carefully monitored conditions clinicians and biologists can only see snapshots of the development process. Mathematical models are emerging as a key means to supplement our knowledge of the reproductive process, and to tease apart complexity in the reproductive system. These models have been used successfully to test existing hypotheses regarding the mechanisms of female infertility and pathological fetal development, and also to provide new experimentally testable hypotheses regarding the process of development. This new knowledge has allowed for improvements in assisted reproductive technologies and is moving toward translation to clinical practice via multiscale assessments of the dynamics of ovulation, development in pregnancy, and the timing and mechanics of delivery. WIREs Syst Biol Med 2017, 9:e1353. doi: 10.1002/wsbm.1353 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1353","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34375858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Network dynamics: quantitative analysis of complex behavior in metabolism, organelles, and cells, from experiments to models and back. 网络动力学:代谢、细胞器和细胞中复杂行为的定量分析，从实验到模型再返回。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-01-01 Epub Date: 2016-09-07 DOI: 10.1002/wsbm.1352

Felix T Kurz, Jackelyn M Kembro, Ana G Flesia, Antonis A Armoundas, Sonia Cortassa, Miguel A Aon, David Lloyd

{"title":"Network dynamics: quantitative analysis of complex behavior in metabolism, organelles, and cells, from experiments to models and back.","authors":"Felix T Kurz, Jackelyn M Kembro, Ana G Flesia, Antonis A Armoundas, Sonia Cortassa, Miguel A Aon, David Lloyd","doi":"10.1002/wsbm.1352","DOIUrl":"https://doi.org/10.1002/wsbm.1352","url":null,"abstract":"Advancing from two core traits of biological systems: multilevel network organization and nonlinearity, we review a host of novel and readily available techniques to explore and analyze their complex dynamic behavior within the framework of experimental-computational synergy. In the context of concrete biological examples, analytical methods such as wavelet, power spectra, and metabolomics-fluxomics analyses, are presented, discussed, and their strengths and limitations highlighted. Further shown is how time series from stationary and nonstationary biological variables and signals, such as membrane potential, high-throughput metabolomics, O2 and CO2 levels, bird locomotion, at the molecular, (sub)cellular, tissue, and whole organ and animal levels, can reveal important information on the properties of the underlying biological networks. Systems biology-inspired computational methods start to pave the way for addressing the integrated functional dynamics of metabolic, organelle and organ networks. As our capacity to unravel the control and regulatory properties of these networks and their dynamics under normal or pathological conditions broadens, so is our ability to address endogenous rhythms and clocks to improve health-span in human aging, and to manage complex metabolic disorders, neurodegeneration, and cancer. WIREs Syst Biol Med 2017, 9:e1352. doi: 10.1002/wsbm.1352 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1352","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34420722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 32

Regulatory elements in molecular networks 分子网络中的调控元件

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-01-01 DOI: 10.1002/wsbm.1374

A. Doane, O. Elemento

引用次数: 16

Behavioral epigenetics 行为实验胚胎学

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-01-01 DOI: 10.1002/wsbm.1333

David Moore

{"title":"Behavioral epigenetics","authors":"David Moore","doi":"10.1002/wsbm.1333","DOIUrl":"https://doi.org/10.1002/wsbm.1333","url":null,"abstract":"Why do we grow up to have the traits we do? Most 20th century scientists answered this question by referring only to our genes and our environments. But recent discoveries in the emerging field of behavioral epigenetics have revealed factors at the interface between genes and environments that also play crucial roles in development. These factors affect how genes work; scientists now know that what matters as much as which genes you have (and what environments you encounter) is how your genes are affected by their contexts. The discovery that what our genes do depends in part on our experiences has shed light on how Nature and Nurture interact at the molecular level inside of our bodies. Data emerging from the world's behavioral epigenetics laboratories support the idea that a person's genes alone cannot determine if, for example, he or she will end up shy, suffering from cardiovascular disease, or extremely smart. Among the environmental factors that can influence genetic activity are parenting styles, diets, and social statuses. In addition to influencing how doctors treat diseases, discoveries about behavioral epigenetics are likely to alter how biologists think about evolution, because some epigenetic effects of experience appear to be transmissible from generation to generation. This domain of research will likely change how we think about the origins of human nature. WIREs Syst Biol Med 2017, 9:e1333. doi: 10.1002/wsbm.1333","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"16 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87137422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 78

Modified mRNA as a therapeutic tool to induce cardiac regeneration in ischemic heart disease 修饰mRNA作为诱导缺血性心脏病心脏再生的治疗工具

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-01-01 DOI: 10.1002/wsbm.1367

Y. Hadas, M. Katz, C. Bridges, L. Zangi

{"title":"Modified mRNA as a therapeutic tool to induce cardiac regeneration in ischemic heart disease","authors":"Y. Hadas, M. Katz, C. Bridges, L. Zangi","doi":"10.1002/wsbm.1367","DOIUrl":"https://doi.org/10.1002/wsbm.1367","url":null,"abstract":"Ischemic heart disease (IHD) is a leading cause of morbidity and mortality in developed countries. Current pharmacological and interventional therapies provide significant improvement in the life quality of patient; however, they are mostly symptom‐oriented and not curative. A high disease and economic burden of IHD requires the search for new therapeutic strategies to significantly improve patients’ prognosis and quality of life. One of the main challenges during IHD is the massive loss of cardiomyocytes that possess minimal regenerative capacity. Recent understanding of the pathophysiological mechanisms underlying IHD, as well as new therapeutic approaches provide new hope for patients suffering from IHD. Synthetic modified mRNA (modRNA) is a new gene delivery vector that is increasingly used in in vivo applications. modRNA is a relatively stable, non‐immunogenic, highly‐expressed molecule that has been shown to mediate high and transient expression of proteins in different type of cells and tissues including cardiomyocytes. modRNA properties, together with its expression kinetics in the heart make it an attractive option for the treatment of IHD, especially after myocardial infarction. In this review we discuss the role of gene therapy in cardiac regeneration as an approach to treat IHD; traditional and innovative gene delivery methods; and focus specifically on modRNA structure, mode of delivery, and its use for the induction of endogenous regenerative capacity, mainly in the context of IHD. WIREs Syst Biol Med 2017, 9:e1367. doi: 10.1002/wsbm.1367","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"123 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76151536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 31