The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

LetterThis is the final version of the article. Available from SAGE Publications via the DOI in this record.Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.K.S. was supported by the UK BBSRC grant BB/E015263/1. SynthSys Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1

A New Operation on Sequences: the Boustrouphedon Transform

A generalization of the Seidel-Entringer-Arnold method for calculating the alternating permutation numbers (or secant-tangent numbers) leads to a new operation on integer sequences, the Boustrophedon transform.Comment: very minor change: corrected typo in author list. June 24 2002: correction to a proof; additional reference

Axion-photon conversion caused by dielectric interfaces: quantum field calculation

Axion-photon conversion at dielectric interfaces, immersed in a near-homogeneous magnetic field, is the basis for the dielectric haloscope method to search for axion dark matter. In analogy to transition radiation, this process is possible because the photon wave function is modified by the dielectric layers ("Garibian wave function") and is no longer an eigenstate of momentum. A conventional first-order perturbative calculation of the transition probability between a quantized axion state and these distorted photon states provides the microwave production rate. It agrees with previous results based on solving the classical Maxwell equations for the combined system of axions and electromagnetic fields. We argue that in general the average photon production rate is given by our result, independently of the detailed quantum state of the axion field. Moreover, our result provides a new perspective on axion-photon conversion in dielectric haloscopes because the rate is based on an overlap integral between unperturbed axion and photon wave functions, in analogy to the usual treatment of microwave-cavity haloscopes.Comment: 15 pages, 2 figures; v2: minor changes to match published versio

Study of volatile contaminants in reclaimed water

Different methods were evaluated for reducing the volatile contaminants found in water recovered from urine by distillation. The use of activated carbon, addition of potassium permanganate, and the use of oxidation catalyst are described along with laboratory tests. It is concluded that catalytic decomposition appears to be feasible, and further investigation is recommended

A model to define operational irrigation frequency for maximum yield of crops.

Se describe un modelo para definir la frecuencia operacional de riego para obtener maxima produccion de los cultivos. El modelo usa como informacion basica la respuesta de la planta e las condiciones de humedad en el suelo, caracteristicas de retencion y movimiento del agua en el suelo, evapotranspiracion y demanda atmosferica. Se presentan los resultados de la aplicacion del modelo en cultivos de tomate y frijol, en un suelo franco arenoso. Se discute el uso de la informacion mundial de la relacion entre rendimiento de los cultivos y el potencial matricial de agua en el suelo

Reduced lethality in mice receiving a combined dose of cyclophosphamide and busulphan.

Animals treated with a sufficiently high dose of busulphan die about 14 days later from bone marrow failure. A single, appropriately timed injection of cyclophosphamide can save these mice. The nature of this protection is shown to be the cyclophosphamide induced elaboration of a humoral factor which stimulates haemopoietic recovery

Abnormal oxygen homeostasis in the nucleus tractus solitarius of the spontaneously hypertensive rat

The effects of arterial hypertension on cerebral blood flow remain poorly understood. Hemodynamic responses within the somatosensory cortex have been shown to be impaired in the spontaneously hypertensive rat (SHR) model. However, it is unknown whether arterial hypertension affects oxygen homeostasis in vital brainstem areas that control cardiovascular reflexes. In this study, we assessed vagus nerve stimulation-induced changes in local tissue PO2 (Pt O2 ) in the caudal nucleus tractus solitarius (cNTS) of SHRs and normotensive Wistar rats. Pt O2 measurements were performed using a novel application of fast cyclic voltammetry, which allows higher temporal resolution of O2 changes than traditional optical fluorescence techniques. Electrical stimulation of the central-cut end of the vagus nerve (ESVN) caused profound arterial blood pressure decreases along with biphasic Pt O2 changes in the cNTS, characterised by a rapid decrease in Pt O2 ("initial dip") followed by a post-stimulus overshoot above baseline. The initial dip was found to be significantly smaller in SHRs compared to normotensive Wistar rats even after ganglionic blockade. Post-ESVN overshoot was similar in both groups but was reduced in Wistar rats after ganglionic blockade. In conclusion, neural activity-dependent changes in tissue oxygen in brainstem cardiovascular autonomic centres are significantly impaired in animals with arterial hypertension

Effects of Aerobic Training in Adolescents with Down Syndrome

The purpose of this study was to evaluate the effects that aerobic training has on adolescents and young adults with Down syndrome. Fourteen individuals with Down syndrome (mean age = 17.7 yr) participated in a 10-wk walking/jogging exercise training study. A pre- and post-training walking treadmill test was performed to determine the following parameters: peak oxygen uptake (VO2, absolute and relative), minute ventilation (VE, l•min-1), heart rate HR, b•min-1), RER (VCO2/VO2), and time and grade to exhaustion. Following the pre-training evaluations, subjects were assigned to a control group (N = 4) or an exercise group (N= 10). The exercise group underwent a 10-wk walk/jog training program at a frequency of 3 times per week, for a duration of 30 min, and at an intensity, of approximately 65-75% peak HR. Following training, both control and experimental groups showed no changes in peak VO2 (absolute and relative), VE, HR, and RER. The exercise group, however, did demonstrate a significant improvement in peak exercise time (and grade). Although the training program did not produce improvements in aerobic capacity, it did produce gains in walking capacity. It was concluded that the adolescents and young adults may not be able to improve their aerobic capacity when performing a walk/jog training program. © 1993 by the American College of Sports Medicine