Abstract:
:The detailed behavior of many molecular processes in the cell, such as protein folding, protein complex assembly, and gene regulation, transcription and translation, can often be accurately captured by stochastic chemical kinetic models. We investigate a novel computational problem involving these models - that of finding the most-probable sequence of reactions that connects two or more states of the system observed at different times. We describe an efficient method for computing the probability of a given reaction sequence, but argue that computing most-probable reaction sequences is EXPSPACE-hard. We develop exact (exhaustive) and approximate algorithms for finding most-probable reaction sequences. We evaluate these methods on test problems relating to a recently-proposed stochastic model of folding of the Trp-cage peptide. Our results provide new computational tools for analyzing stochastic chemical models, and demonstrate their utility in illuminating the behavior of real-world systems.
journal_name
Front Physioljournal_title
Frontiers in physiologyauthors
Salehi M,Perkins TJdoi
10.3389/fphys.2010.00170subject
Has Abstractpub_date
2010-10-19 00:00:00pages
170issn
1664-042Xjournal_volume
1pub_type
杂志文章abstract::Extracellular ATP acts on the P2X family of ligand-gated ion channels and several members of the P2Y family of G protein-coupled receptors to mediate intercellular communication among many cell types including bone-forming osteoblasts. It is known that multiple P2 receptors are expressed on osteoblasts (P2X2,5,6,7 and...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2016.00294
更新日期:2016-07-13 00:00:00
abstract::The effect of Withania somnifera a medicinal plant seed extract was tested against lesser mulberry pyralid, a potential pest of mulberry. The mulberry leaves were used for silk production in rural areas of northern Iran. The extract was administered orally by leaf dipping method in two lower (5%W/V) and higher (15%W/V...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.00908
更新日期:2020-08-07 00:00:00
abstract:Objective:Develop an automated approach to detect flash (<1.0 s) or prolonged (>2.0 s) capillary refill time (CRT) that correlates with clinician judgment by applying several supervised machine learning (ML) techniques to pulse oximeter plethysmography data. Materials and Methods:Data was collected in the Pediatric In...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.564589
更新日期:2020-10-06 00:00:00
abstract::Defects in mitochondrial ribosomal proteins (MRPs) cause various diseases in humans. Because of the essential role of MRPs in synthesizing the essential subunits of oxidative phosphorylation (OXPHOS) complexes, identifying all of the protein components involved in the mitochondrial translational machinery is critical....
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2013.00183
更新日期:2013-07-30 00:00:00
abstract::A number of years ago we reported that ventral Lateral Neurons (LNvs), which are essential in the control of rest-activity cycles in Drosophila, undergo circadian remodeling of their axonal projections. This structural plasticity gives rise to changes in the degree of connectivity, which could provide a means of trans...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2017.00918
更新日期:2017-11-14 00:00:00
abstract::Domestic pig molars provide an interesting system to study the biomineralization process. The large size, thick enamel and complex crown morphology make pig molars relatively similar to human molars. However, compared to human molars, pig molars develop considerably faster. Here we use microCT to image the developing ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00071
更新日期:2018-02-09 00:00:00
abstract::Submaximal vertical hopping capitalizes on the strain energy storage-recovery mechanism associated with the stretch-shortening cycle and is emerging as an important component of progressive rehabilitation protocols in Achilles tendon injury and a determinant of readiness to return to sport. This study explored the rel...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.567641
更新日期:2020-12-03 00:00:00
abstract::Unlike other marine teleosts, the Plotosidae catfishes reportedly have an extra-branchial salt secreting dendritic organ (DO). Salinity acclimation [brackishwater (BW) 3aaa, seawater (SWcontrol) 34aaa, and hypersaline water (HSW) 60aaa] for 14 days was used to investigate the osmoregulatory abilities of Plotosus linea...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00761
更新日期:2018-07-03 00:00:00
abstract::Productivity in science has increased and it is becoming more important for scientists to publish, to publish frequently, and to accumulate citations to their work. However, the peer review system may not only promote and advance but also hinder, prevent, or delay publication. In this personal perspective, confirmator...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.01073
更新日期:2020-09-04 00:00:00
abstract::Singlet oxygen generated in a type II photodynamic action, due to its limited lifetime (1 μs) and reactive distance (<10 nm), could regulate live cell function nanoscopically. The genetically-encoded protein photosensitizers (engineered fluorescent proteins such as KillerRed, TagRFP, and flavin-binding proteins such a...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2017.00191
更新日期:2017-04-04 00:00:00
abstract::Natural reward is an essential element of any organism's ability to adapt to environmental variation. Its underlying circuits and mechanisms guide the learning process as they help associate an event, or cue, with the perception of an outcome's value. More generally, natural reward serves as the fundamental generator ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00433
更新日期:2018-05-14 00:00:00
abstract::Nicotinamide nucleotide transhydrogenase (TH) is an enzyme complex in animal mitochondria and bacteria that utilizes the electrochemical proton gradient across membranes to drive the production of NADPH. The enzyme plays an important role in maintaining the redox balance of cells with implications in aging and a numbe...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2017.01089
更新日期:2017-12-19 00:00:00
abstract::Oxidative modification of proteins in photosystem II (PSII) exposed to high light has been studied for a few decades, but the characterization of protein radicals formed by protein oxidation is largely unknown. Protein oxidation is induced by the direct reaction of proteins with reactive oxygen species known to form h...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.00958
更新日期:2019-08-13 00:00:00
abstract::This review details the manner in which the central nervous system regulates metabolic homeostasis in normal weight and obese rodents and humans. It includes a review of the homeostatic contributions of neurons located in the hypothalamus, the midbrain and limbic structures, the pons and the medullary area postrema, n...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2018.00574
更新日期:2018-05-17 00:00:00
abstract:BACKGROUND:Recent findings strongly promoted the hypothesis that common pelvic gynecological diseases including endometriosis and ovarian neoplasia may develop de novo from ectopic endometrial-like glands and/or embryonic epithelial remnants. To verify the frequency, the anatomical localization and the phenotype of mis...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2012.00444
更新日期:2012-12-03 00:00:00
abstract::Swimming induced pulmonary edema (SIPE) is a complication that can occur during exercise with the possibility of misdiagnosis and can quickly become life threatening; however, medical literature infrequently describes SIPE. Therefore, the aim of this review was to analyse all individual cases diagnosed with SIPE as re...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2017.00652
更新日期:2017-08-31 00:00:00
abstract::Objective: Neuromuscular injury prevention programs (IPP) can reduce injury rate by about 40% in youth sport. Multimodal IPP include, for instance, balance, strength, power, and agility exercises. Our systematic review and meta-analysis aimed to evaluate the effects of multimodal IPP on neuromuscular performance in yo...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2017.00791
更新日期:2017-10-12 00:00:00
abstract::[This corrects the article DOI: 10.3389/fphys.2020.00302.]. ...
journal_title:Frontiers in physiology
pub_type: 已发布勘误
doi:10.3389/fphys.2020.00672
更新日期:2020-07-03 00:00:00
abstract::Introduction: Baroreflex sensitivity (BRS) is essential to ensure rapid adjustment to variations in blood pressure (BP). Little is known concerning the adaptive responses of BRS during acclimatization to high altitude at rest and during exercise. Methods: Twenty-one healthy sea-level residents were tested near sea lev...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00767
更新日期:2018-06-21 00:00:00
abstract::Several studies have highlighted the interplay between metabolism, immunity and inflammation. Both tissue resident and infiltrating immune cells play a major role in the inflammatory process of rheumatoid arthritis (RA) via the production of cytokines, adipo-cytokines and metabolic intermediates. These functions are m...
journal_title:Frontiers in physiology
pub_type: 杂志文章,评审
doi:10.3389/fphys.2020.00347
更新日期:2020-04-17 00:00:00
abstract::Stable gait requires active control of the mediolateral (ML) kinematics of the body center of mass (CoM) and the base of support (BoS) in relation to each other. Stance leg hip abductor (HA) muscle spindle afference may be used to guide contralateral swing foot placement and adequately position the BoS in relation to ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01134
更新日期:2018-08-21 00:00:00
abstract::Muscle and tendon stiffness are related to sports performance, tendinopathy, and tendon degeneration. However, the effects of habitual loading on muscle and tendon mechanical properties are unclear. Using amateur basketball players as examples, we investigated the effects of mechanical loading on the stiffness of the ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2020.606706
更新日期:2020-12-10 00:00:00
abstract:Background:The aim of presented cross-sectional study was to determine the association of different types of physical activity (PA) with metabolic control in people with type 1 diabetes. Materials and Methods:A total of 109 adult subjects with type 1 diabetes were asked to complete the non-exercise activity thermogene...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.01210
更新日期:2019-09-24 00:00:00
abstract::Unlike most excitable cells, certain syncytial smooth muscle cells are known to exhibit spontaneous action potentials of varying shapes and sizes. These differences in shape are observed even in electrophysiological recordings obtained from a single cell. The origin and physiological relevance of this phenomenon are c...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01300
更新日期:2018-09-20 00:00:00
abstract::Aim: Tea is usually consumed at two temperatures (as hot tea or as iced tea). However, the importance of drink temperature on the cardiovascular system and on metabolism has not been thoroughly investigated. The purpose of this study was to compare the cardiovascular, metabolic and cutaneous responses to the ingestion...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00315
更新日期:2018-04-06 00:00:00
abstract::Liver cirrhosis (LC) is the final usual outcome of liver damage induced by various chronic liver diseases. Because of asymptomatic nature of LC, it is usually diagnosed at late and advanced stages, and patients are easy to miss the best timing for treatment. Thus, the early detection of LC is needed. In the prospectiv...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2019.01421
更新日期:2019-11-19 00:00:00
abstract::The detection of error information is an essential prerequisite of a feedback-based movement. This study investigated the differential behavior and neurophysiological mechanisms of a cyclic force-tracking task using error-reducing and error-enhancing feedback. The discharge patterns of a relatively large number of mot...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2017.00140
更新日期:2017-03-13 00:00:00
abstract::The integrated pest management (IPM) strategy was developed and used in combination with pesticides and beneficial biological control agents. To further develop IPM efficiency, it is important to evaluate the side effects of pesticides on biological control agents. Aphidius gifuensis is one of the most important aphid...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.01729
更新日期:2018-12-11 00:00:00
abstract::We investigate analytically the production of entropy during a breathing cycle in healthy and diseased lungs. First, we calculate entropy production in healthy lungs by applying the laws of thermodynamics to the well-known transpulmonary pressure-volume (P-V) curves of the lung under the assumption that lung tissue be...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2016.00073
更新日期:2016-03-01 00:00:00
abstract::The aim of this study is to detect the effects of C60 fullerenes, which possess pronounced antioxidant properties, in comparison with the actions of the known exogenous antioxidants N-acetylcysteine (NAC) and β-Alanine in terms of exercise tolerance and contractile property changes of the m. triceps surae (TS) during ...
journal_title:Frontiers in physiology
pub_type: 杂志文章
doi:10.3389/fphys.2018.00517
更新日期:2018-05-15 00:00:00