Abstract:
:Recent progress in high-throughput data acquisition has shifted the focus from data generation to processing and understanding of how to integrate collected information. Context specific reconstruction based on generic genome scale models like ReconX or HMR has the potential to become a diagnostic and treatment tool tailored to the analysis of specific individuals. The respective computational algorithms require a high level of predictive power, robustness and sensitivity. Although multiple context specific reconstruction algorithms were published in the last 10 years, only a fraction of them is suitable for model building based on human high-throughput data. Beside other reasons, this might be due to problems arising from the limitation to only one metabolic target function or arbitrary thresholding. This review describes and analyses common validation methods used for testing model building algorithms. Two major methods can be distinguished: consistency testing and comparison based testing. The first is concerned with robustness against noise, e.g., missing data due to the impossibility to distinguish between the signal and the background of non-specific binding of probes in a microarray experiment, and whether distinct sets of input expressed genes corresponding to i.e., different tissues yield distinct models. The latter covers methods comparing sets of functionalities, comparison with existing networks or additional databases. We test those methods on several available algorithms and deduce properties of these algorithms that can be compared with future developments. The set of tests performed, can therefore serve as a benchmarking procedure for future algorithms.
journal_name
Front Physioljournal_title
Frontiers in physiologyauthors
Pacheco MP,Pfau T,Sauter Tdoi
10.3389/fphys.2015.00410subject
Has Abstractpub_date
2016-01-22 00:00:00pages
410issn
1664-042Xjournal_volume
6pub_type
杂志文章abstract::Background: Hypoxia represents both an outcome of cardiopulmonary diseases and a trigger for severe pulmonary complications as pulmonary hypertension. Because nitric oxide (NO) is a critical mediator in the development of pulmonary hypertension, the modulators of its downstream function may become target of pharmacolo...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00289
更新日期:2018-03-27 00:00:00
abstract::Most sense organs of arthropods are ensconced in small exoskeletal compartments that hinder direct access to plasma membranes. We have developed a method for exposing live sensory and supporting cells in such structures. The technique uses a viscous light cured resin to embed and support the structure, which is then s...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2016.00398
更新日期:2016-09-12 00:00:00
abstract::Reactive Oxygen Species (ROS) can cause oxidative damage and have been proposed to be the main cause of aging and age-related diseases including cancer, diabetes and Parkinson's disease. Accordingly, mitochondria from old individuals have higher levels of ROS. However, ROS also participate in cellular signaling, are i...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2017.00428
更新日期:2017-06-27 00:00:00
abstract::Bone morphogenetic proteins (BMPs) not only play essential roles in bone development but also are involved in embryonic growth, organogenesis cell proliferation and differentiation. However, the previous studies on the functions of shellfish BMPs genes are still very limited. To better understand its molecular structu...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.01059
更新日期:2020-08-28 00:00:00
abstract::Recent strategies to treat peripheral arterial disease (PAD) have focused on stem cell based therapies, which are believed to result in local secretion of vascular growth factors. Little is known, however, about the role of ischemic endogenous cells in this context. We hypothesized that ischemic muscle cells (MC) are ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2015.00161
更新日期:2015-05-19 00:00:00
abstract::Many disease fighting strategies have focused on the generation of NK cells, since they constitute the main immune barrier against cancer and intracellular pathogens such as viruses. Therefore, a predictive model for the development of NK cells would constitute a useful tool to test several hypotheses regarding the pr...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01029
更新日期:2018-08-02 00:00:00
abstract::Actual theaters of operations require fast actions from special operations units with a high level of readiness and survival. Mission accomplishment depends on their psychological and physiological performance. The aim of the present study was to analyze: (1) the physical parameters related with success in a special o...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.00867
更新日期:2019-07-10 00:00:00
abstract::Surface electromyography (sEMG) is a popular research tool in sport and rehabilitation sciences. Common study designs include the comparison of sEMG amplitudes collected from different muscles as participants perform various exercises and techniques under different loads. Based on such comparisons, researchers attempt...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2017.00985
更新日期:2018-01-04 00:00:00
abstract::The fluid transport and mixing induced by beating cilia, present in the bronchial airways, are studied using a coupled lattice Boltzmann-Immersed Boundary solver. This solver allows the simulation of both single and multi-component fluid flows around moving solid boundaries. The cilia are modeled by a set of Lagrangia...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00161
更新日期:2018-03-06 00:00:00
abstract::Global environmental change is leading to an increase in the frequency, intensity, and duration of extreme weather events, so effective environmental management requires an understanding not only of the physiological response of organisms to increased mean temperatures, but also to extreme environmental conditions. To...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.01405
更新日期:2019-11-20 00:00:00
abstract::Atherosclerosis is considered as a chronic disease of arterial wall, with a strong contribution of inflammation. Dendritic cells (DCs) play a crucial role in the initiation of proatherogenic inflammatory response. Mature DCs present self-antigens thereby supporting differentiation of naïve T cells to effector cells th...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2014.00196
更新日期:2014-05-27 00:00:00
abstract::During formation of the secondary palate in mammalian embryos, two vertically oriented palatal shelves rapidly elevate into a horizontal position above the tongue, meet at the midline, and fuse to form a single entity. Previous observations suggested that elevation occurs by a simple 90° rotation of the palatal shelve...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2016.00392
更新日期:2016-09-07 00:00:00
abstract::Apolipophorin III (ApoLp-III) is a well-known hemolymph protein having a functional role in lipid transport and immune responses of insects. Here we report the molecular and functional characterization of Anopheles stephensi Apolipophorin-III (AsApoLp-III) gene. This gene consists of 679 nucleotides arranged into two ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2017.00185
更新日期:2017-04-07 00:00:00
abstract::Vascular calcification is the deposition of calcium phosphate minerals in vascular tissue. Vascular calcification occurs by both active and passive processes. Extent and tissue-specific patterns of vascular calcification are predictors of cardiovascular morbidity and mortality. The placenta is a highly vascularized or...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01044
更新日期:2018-08-07 00:00:00
abstract:Background:Nav1.5 cardiac Na+ channel mutations can cause arrhythmogenic syndromes. Some of these mutations exert a dominant negative effect on wild-type channels. Recent studies showed that Na+ channels can dimerize, allowing coupled gating. This leads to the hypothesis that allosteric interactions between Na+ channel...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.589386
更新日期:2020-11-05 00:00:00
abstract::Athletes should achieve event-specific physiological requirements through careful periodization of training, underpinned by individualized and targeted nutrition strategies. However, evidence of whether, and how, elite endurance athletes periodize nutrition is scarce. Accordingly, elite international female (n = 67) a...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01732
更新日期:2018-12-03 00:00:00
abstract:UNLABELLED:Limitations of current methods: Normalization of resting energy expenditure (REE) for body composition using the 2-compartment model fat mass (FM), and fat-free mass (FFM) has inherent limitations for the interpretation of REE and may lead to erroneous conclusions when comparing people with a wide range of a...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2013.00047
更新日期:2013-03-25 00:00:00
abstract::Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefiting from the tr...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2012.00143
更新日期:2012-05-18 00:00:00
abstract:Background:Perturbation of endothelial function in people with cystic fibrosis (CF) has been reported, which may be associated with endothelial cell expression of the cystic fibrosis transmembrane conductance regulator (CFTR). Previous reports indicate that CFTR activity upregulates endothelial barrier function, endoth...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.00879
更新日期:2020-07-29 00:00:00
abstract::Cotton rats are one of the experimental rodents used for testing different infectious and non-infectious diseases, including gastrointestinal tract pathology. However, their intestinal morphological characteristics are still poorly understood. Here, we clarified the anatomical and histological characteristics of the c...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.587214
更新日期:2020-10-26 00:00:00
abstract::Muscle tone represents one of the important concepts for characterizing changes in the state of the developing nervous system. It can be manifested in the level of activity of flexors and extensors and in muscle reactions to its passive stretching (StR) or shortening (ShR). Here we investigated such reactions in a coh...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.01158
更新日期:2019-09-13 00:00:00
abstract::The generation of neural network dynamics relies on the interactions between the intrinsic and synaptic properties of their neural components. Moreover, neuromodulators allow networks to change these properties and adjust their activity to specific challenges. Endogenous continuous ("tonic") neuromodulation can regula...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2012.00253
更新日期:2012-07-20 00:00:00
abstract::Pancreatic cancer shows a characteristic tissue structure called desmoplasia, which consists of dense fibrotic stroma surrounding cancer cells. Interactions between pancreatic cancer cells and stromal cells promote invasive growth of cancer cells and establish a specific microenvironment such as hypoxia which further ...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2013.00318
更新日期:2013-11-01 00:00:00
abstract::To fully unravel the ixodid ticks' role as vectors of viral pathogens, their susceptibility to new control measures, and their ability to develop acaricide resistance, acclimatization of ticks under laboratory conditions is greatly needed. However, the unique and complicated feeding behavior of these ticks compared to...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2018.01728
更新日期:2018-12-04 00:00:00
abstract::We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a contr...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00198
更新日期:2018-03-13 00:00:00
abstract::The luminal endoplasmic reticulum (ER) protein of 29 kDa (ERp29) is a ubiquitously expressed cellular agent with multiple critical roles. ERp29 regulates the biosynthesis and trafficking of several transmembrane and secretory proteins, including the cystic fibrosis transmembrane conductance regulator (CFTR), the epith...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.574339
更新日期:2020-09-08 00:00:00
abstract::Sleep inertia, the transitional state of reduced alertness and impaired cognitive performance upon waking, is a safety risk for on-call personnel who can be required to perform critical tasks soon after waking. Sleep inertia countermeasures have previously been investigated; however, none have successfully dissipated ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.00254
更新日期:2020-04-07 00:00:00
abstract::Alpine skiing has been an Olympic event since the first Winter Games in 1936. Nowadays, skiers compete in four main events: slalom, giant slalom, super-G and downhill. Here, we present an update on the biomechanics of alpine ski racers and their equipment. The technical and tactical ability of today's world-class skie...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.00111
更新日期:2019-02-20 00:00:00
abstract::Length-dependent activation of calcium-dependent myocardial force generation provides the basis for the Frank-Starling mechanism. To directly compare the effects of mutations associated with hypertrophic cardiomyopathy and dilated cardiomyopathy, the native troponin complex in skinned trabecular fibers of guinea pigs ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.00516
更新日期:2020-06-03 00:00:00
abstract::Tumor cells alter their metabolism to maintain unregulated cellular proliferation and survival, but this transformation leaves them reliant on constant supply of nutrients and energy. In addition to the widely studied dysregulated glucose metabolism to fuel tumor cell growth, accumulating evidences suggest that utiliz...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2015.00382
更新日期:2015-12-16 00:00:00