Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

BACKGROUND: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. RESULTS: We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from . BioNetS also can be run as a stand alone package. All the required files are accessible from . CONCLUSIONS: We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems

Self-heated fiber Bragg grating sensors

This letter demonstrates an approach for tuning fiber Bragg grating sensors with optical energy carried in the same optical fiber. Optical energy carried in the optical fiber was used to heat in-fiber Bragg gratings in order to alter the grating's optical response to surrounding media. The functional enhancement of optically heated Bragg gratings as sensor devices is demonstrated by a dual-function Bragg grating temperature and level sensing array for liquid at room and cryogenic temperatures. © 2005 American Institute of Physics

The motion of whips and chains

We study the motion of an inextensible string (a whip) fixed at one point in the absence of gravity, satisfying the equations $$\eta_{tt} = \partial_s(\sigma \eta_s), \qquad \sigma_{ss}-\lvert \eta_{ss}\rvert^2 = -\lvert \eta_{st}\rvert^2, \qquad \lvert \eta_s\rvert^2 \equiv 1$$ with boundary conditions $\eta(t,1)=0$ and $\sigma(t,0)=0$. We prove local existence and uniqueness in the space defined by the weighted Sobolev energy $$\sum_{\ell=0}^m \int_0^1 s^{\ell} \lvert \partial_s^{\ell}\eta_t\rvert^2 \, ds + \int_0^1 s^{\ell+1} \lvert \partial_s^{\ell+1}\eta\rvert^2 \, ds,$$ when $m\ge 3$. In addition we show persistence of smooth solutions as long as the energy for $m=3$ remains bounded. We do this via the method of lines, approximating with a discrete system of coupled pendula (a chain) for which the same estimates hold.Comment: 47 pages, 8 figure

Early restriction of placental growth results in placental structural and gene expression changes in late gestation independent of fetal hypoxemia

Placental restriction and insufficiency are associated with altered patterns of placental growth, morphology, substrate transport capacity, growth factor expression, and glucocorticoid exposure. We have used a pregnant sheep model in which the intrauterine environment has been perturbed by uterine carunclectomy (Cx). This procedure results in early restriction of placental growth and either the development of chronic fetal hypoxemia (PaO₂≤17 mmHg) in late gestation or in compensatory placental growth and the maintenance of fetal normoxemia (PaO2>17 mmHg). Based on fetal PaO₂, Cx, and Control ewes were assigned to either a normoxemic fetal group (Nx) or a hypoxemic fetal group (Hx) in late gestation, resulting in 4 groups. Cx resulted in a decrease in the volumes of fetal and maternal connective tissues in the placenta and increased placental mRNA expression of IGF2, vascular endothelial growth factor (VEGF), VEGFR-2, ANGPT2, and TIE2 There were reduced volumes of trophoblast, maternal epithelium, and maternal connective tissues in the placenta and a decrease in placental GLUT1 and 11βHSD2 mRNA expression in the Hx compared to Nx groups. Our data show that early restriction of placental growth has effects on morphological and functional characteristics of the placenta in late gestation, independent of whether the fetus becomes hypoxemic. Similarly, there is a distinct set of placental changes that are only present in fetuses that were hypoxemic in late gestation, independent of whether Cx occurred. Thus, we provide further understanding of the different placental cellular and molecular mechanisms that are present in early placental restriction and in the emergence of later placental insufficiency.Song Zhang, Paige Barker, Kimberley J. Botting, Claire T. Roberts, Christine M. McMillan, Isabella Caroline McMillen, Janna L. Morriso

Fiber Bragg grating vacuum sensors

This letter demonstrates functional enhancements of fiber Bragg grating sensors powered by in-fiber light. High-power laser light transmitted in double-clad optical fiber was extracted from the fiber core to heat an on-fiber metal coating. When the power-laser is turned off, the fiber Bragg grating is used as a passive component for temperature sensing. When the laser is turned on, the thermal response of the optically heated grating was used to monitor ambient air pressure. The sensitivity and dynamic range of optically powered fiber sensors can be actively adjusted by in-fiber light to measure vacuum pressures over four orders of magnitude. © 2005 American Institute of Physics

Knowledge of and Attitudes toward Behavioral Health Services among Older Youth in the Foster Care System

This study examined knowledge of and attitudes toward services among 268 17-year olds with psychiatric diagnoses preparing to exit foster care. A structured interview assessed knowledge of services with vignette scenarios and attitudes with a standardized scale. Descriptive statistics described the extent of knowledge and attitudes among this population and regression analyses examined predictors of these dimensions of literacy. Most youth suggested a help source, but responses often lacked specificity. Gender and depression were the strongest predictors of knowledge and attitudes, respectively. Knowing which aspects of literacy are low, and for whom, can inform education efforts to improve access to care in adulthood

Sensitivity enhancement of fiber Bragg gratings to transverse stress by using microstructural fibers

We present simulation and experimental results of fiber Bragg grating responses to transverse stress in microstructure fibers. The grating wavelength shifts and peak splits are studied as a function of external load and fiber orientation. Both simulation and measurement results indicate that the sensitivity of grating sensors to the transverse stress can be enhanced by a factor of eight in a two-hole fiber over that in a standard fiber. © 2006 Optical Society of America

A monolithic micro-tensile tester for investigating silica micromechanics, fabricated and fully operated using a femtosecond laser Citation for published version (APA)

. (2014). A monolithic micro-tensile tester for investigating silica micromechanics, fabricated and fully operated using a femtosecond laser

Placental adaptations in growth restriction

The placenta is the primary interface between the fetus and mother and plays an important role in maintaining fetal development and growth by facilitating the transfer of substrates and participating in modulating the maternal immune response to prevent immunological rejection of the conceptus. The major substrates required for fetal growth include oxygen, glucose, amino acids and fatty acids, and their transport processes depend on morphological characteristics of the placenta, such as placental size, morphology, blood flow and vascularity. Other factors including insulin-like growth factors, apoptosis, autophagy and glucocorticoid exposure also affect placental growth and substrate transport capacity. Intrauterine growth restriction (IUGR) is often a consequence of insufficiency, and is associated with a high incidence of perinatal morbidity and mortality, as well as increased risk of cardiovascular and metabolic diseases in later life. Several different experimental methods have been used to induce placental insufficiency and IUGR in animal models and a range of factors that regulate placental growth and substrate transport capacity have been demonstrated. While no model system completely recapitulates human IUGR, these animal models allow us to carefully dissect cellular and molecular mechanisms to improve our understanding and facilitate development of therapeutic interventions