Parameter estimation and determinability analysis applied to Drosophila gap gene circuits.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. RESULTS: In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. CONCLUSION: Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous

Correction for respiration artifact in pulmonary blood pressure signals of ventilated patients

Objective. To develop an algorithm that corrects pulmonary artery pressure signals of ventilated patients for the respiration artifact. The algorithm should test the validity of the pulmonary pressure signal and differentiate between the cyclic respiration artifact and true measurement artifacts. Methods. The shape of each pulmonary pressure beat is described by eight characteristic features, including mean pressure value and the systolic and diastolic timing and pressure values. The features are corrected for the respiration artifact by fitting them in a least-squares sense on the first and second harmonica of the ventilator frequency. The corrected features are used by a signal validation algorithm, which adds a validity flag to each pressure beat. The validation algorithm rejects pressure beats with sudden changes in their shape but adapts itself when the changes persist. Results. The performance of the correction and validation technique was evaluated using pulmonary artery pressure signals of 30 patients who were scheduled for open heart surgery. The algorithm correctly recognized as invalid data those pressure signals disturbed by coagulation, surgical manipulations, or flushes of the pressure line. The algorithm marked on average 77 ± 11 % of the pulmonary pressure beats as valid. Conclusions. The validation algorithm marked sufficient pressure beats as valid to update a trend display every 5 sec. The correction algorithm enabled the validation algorithm to differentiate between true measurement artifacts and the respiration artifact

ATK-ForceField: A New Generation Molecular Dynamics Software Package

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.Comment: 28 pages, 9 figure

Treatment of chronically depressed patients: A multisite randomized controlled trial testing the effectiveness of \u27Cognitive Behavioral Analysis System of Psychotherapy\u27 (CBASP) for chronic depressions versus usual secondary care

Background \u27Cognitive Behavioral Analysis System of Psychotherapy\u27 (CBASP) is a form of psychotherapy specifically developed for patients with chronic depression. In a study in the U.S., remarkable favorable effects of CBASP have been demonstrated. However, no other studies have as yet replicated these findings and CBASP has not been tested outside the United States. This protocol describes a randomized controlled trial on the effectiveness of CBASP in the Netherlands. Methods/Design The purpose of the present paper is to report the study protocol of a multisite randomized controlled trial testing the effectiveness of \u27Cognitive Behavioral Analysis System of Psychotherapy\u27 (CBASP) for chronic depression in the Netherlands. In this study, CBASP in combination with medication, will be tested versus usual secondary care in combination with medication. The aim is to recruit 160 patients from three mental health care organizations. Depressive symptoms will be assessed at baseline, after 8 weeks, 16 weeks, 32 weeks and 52 weeks, using the 28-item Inventory for Depressive Symptomatology (IDS). Effect modification by co morbid anxiety, alcohol consumption, general and social functioning and working alliance will be tested. GEE analyses of covariance, controlling for baseline value and center will be used to estimate the overall treatment effectiveness (difference in IDS score) at post-treatment and follow up. The primary analysis will be by \u27intention to treat\u27 using double sided tests. An economic analysis will compare the two groups in terms of mean costs and cost-effectiveness from a societal perspective. Discussion The study will provide an answer to the question whether the favorable effects of CBASP can be replicated outside the US. Trial Registration The Dutch Cochrane Center, NTR1090

Data2Game: Towards an Integrated Demonstrator

The Data2Game project investigates how the efficacy of computerized training games can be enhanced by tailoring training scenarios to the individual player. The research is centered around three research innovations: (1) techniques for the automated modelling of players’ affective states, based on exhibited social signals, (2) techniques for the automated generation of in-game narratives tailored to the learning needs of the player, and (3) validated studies on the relation of the player behavior and game properties to learning performance. This paper describes the integration of the main results into a joint prototype

Ventricular function and biomarkers in relation to repair and pulmonary valve replacement for tetralogy of Fallot

Objective Cardiac surgery may cause temporarily impaired ventricular performance and myocardial injury. We aim to characterise the response to perioperative injury for patients undergoing repair or pulmonary valve replacement (PVR) for tetralogy of Fallot (ToF). Methods We enrolled children undergoing ToF repair or PVR from four tertiary centres in a prospective observational study. Assessment - including blood sampling and speckle tracking echocardiography - occurred before surgery (T1), at the first follow-up (T2) and 1 year after the procedures (T3). Ninety-two serum biomarkers were expressed as principal components to reduce multiple statistical testing. RNA Sequencing was performed on right ventricular (RV) outflow tract samples. Results We included 45 patients with ToF repair aged 4.3 (3.4 - 6.5) months and 16 patients with PVR aged 10.4 (7.8 - 12.7) years. Ventricular function following ToF repair showed a fall-and-rise pattern for left ventricular global longitudinal strain (GLS) (-18±4 to -13±4 to -20±2, p &lt; 0.001 for each comparison) and RV GLS (-19±5 to -14±4 to 20±4, p &lt; 0.002 for each comparison). This pattern was not seen for patients undergoing PVR. Serum biomarkers were expressed as three principal components. These phenotypes are related to: (1) surgery type, (2) uncorrected ToF and (3) early postoperative status. Principal component 3 scores were increased at T2. This increase was higher for ToF repair than PVR. The transcriptomes of RV outflow tract tissue are related to patients' sex, rather than ToF-related phenotypes in a subset of the study population. Conclusions The response to perioperative injury following ToF repair and PVR is characterised by specific functional and immunological responses. However, we did not identify factors relating to (dis)advantageous recovery from perioperative injury. Trial registration number Netherlands Trial Register: NL5129.</p

A family history of breast cancer will not predict female early onset breast cancer in a population-based setting

ABSTRACT: BACKGROUND: An increased risk of breast cancer for relatives of breast cancer patients has been demonstrated in many studies, and having a relative diagnosed with breast cancer at an early age is an indication for breast cancer screening. This indication has been derived from estimates based on data from cancer-prone families or from BRCA1/2 mutation families, and might be biased because BRCA1/2 mutations explain only a small proportion of the familial clustering of breast cancer. The aim of the current study was to determine the predictive value of a family history of cancer with regard to early onset of female breast cancer in a population based setting. METHODS: An unselected sample of 1,987 women with and without breast cancer was studied with regard to the age of diagnosis of breast cancer. RESULTS: The risk of early-onset breast cancer was increased when there were: (1) at least 2 cases of female breast cancer in first-degree relatives (yes/no; HR at age 30: 3.09; 95% CI: 128-7.44), (2) at least 2 cases of female breast cancer in first or second-degree relatives under the age of 50 (yes/no; HR at age 30: 3.36; 95% CI: 1.12-10.08), (3) at least 1 case of female breast cancer under the age of 40 in a first- or second-degree relative (yes/no; HR at age 30: 2.06; 95% CI: 0.83-5.12) and (4) any case of bilateral breast cancer (yes/no; HR at age 30: 3.47; 95%: 1.33-9.05). The positive predictive value of having 2 or more of these characteristics was 13% for breast cancer before the age of 70, 11% for breast cancer before the age of 50, and 1% for breast cancer before the age of 30. CONCLUSION: Applying family history related criteria in an unselected population could result in the screening of many women who will not develop breast cancer at an early age

Functional Echocardiographic and Serum Biomarker Changes Following Surgical and Percutaneous Atrial Septal Defect Closure in Children

BACKGROUND: Ventricular performance is temporarily reduced following surgical atrial septa! defect closure. Cardiopulmonary bypass and changes in loading conditions are considered important factors, but this phenomenon is incompletely understood. We aim to characterize biventricular performance following surgical and percutaneous atrial septal defect closure and to relate biomarkers to ventricular performance following intervention. METHODS AND RESULTS: In this multicenter prospective study, children scheduled for surgical or percutaneous atrial septal defect closure were included. Subjects were assessed preoperatively, in the second week postintervention (at 2-weeks follow-up), and 1-year postintervention (1-year follow-up). At each time point, an echocardiographic study and a panel of biomarkers were obtained. Sixty-three patients (median age, 4.1 [interquartile range, 3.1-6.1] years) were included. Forty-three patients underwent surgery. At 2-weeks follow-up, right ventricular global longitudinal strain was decreased for the surgical, but not the percutaneous, group (-17.6 +/- 4.1 versus -27.1 +/- 3.4; P CONCLUSIONS: Right, and to a lesser degree left, ventricular performance was reduced early after surgical atrial septal defect closure. Right ventricular performance at 1-year follow-up remained below baseline levels. Several biomarkers showed a pattern over time similar to ventricular performance. These biomarkers may provide insight into the processes that affect ventricular function