Setting Parameters for Biological Models With ANIMO

ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entities in form of a graph, while the parameters determine the speed of occurrence of such interactions. When a mismatch is observed between the behavior of an ANIMO model and experimental data, we want to update the model so that it explains the new data. In general, the topology of a model can be expanded with new (known or hypothetical) nodes, and enables it to match experimental data. However, the unrestrained addition of new parts to a model causes two problems: models can become too complex too fast, to the point of being intractable, and too many parts marked as "hypothetical" or "not known" make a model unrealistic. Even if changing the topology is normally the easier task, these problems push us to try a better parameter fit as a first step, and resort to modifying the model topology only as a last resource. In this paper we show the support added in ANIMO to ease the task of expanding the knowledge on biological networks, concentrating in particular on the parameter settings

Change in environmental barriers experienced over a 5-year period by people living with spinal cord injury in Switzerland:a prospective cohort study

STUDY DESIGN: Cohort study with two measurement occasions. OBJECTIVES: To investigate change in environmental barriers experienced by people living with spinal cord injury (SCI) over a 5-year period. SETTING: Community, Switzerland. METHODS: Data were from the Swiss spinal cord injury (SwiSCI) survey. Main outcome measure was the Nottwil Environmental Factors Inventory-Short Form. Random-effects Poisson regression featuring between-within estimation was used to examine predictors of the number of environmental barriers and of its change over time. RESULTS: One thousand five hundred and forty-nine persons participated in Survey 2012 and 1530 participated in Survey 2017; 761 participated in both surveys. In both surveys most participants reported at least three barriers. Leading issues were unfavorable climate, inaccessibility of buildings and public spaces, and lack of or insufficiently adapted means of transportation. Reporting of barriers related to climate, finances, and state services declined over time. Between subjects, having more health problems, lesser physical independence, poorer mental health, and a lower household income were related to a higher number of barriers experienced. Within subjects, improvements in income, physical independence, and mental health over time were related to a reduction in barriers. CONCLUSIONS: Inaccessibility of buildings and places and problems with transportation remained major barriers over a 5-year period and should be priorities of Swiss disability policy. People with reduced mental and physical health, and those with lower income are vulnerable groups deserving specific attention. Policies targeting income and life-long rehabilitation targeting health promotion and maintenance may be suitable means to reduce the experience of environmental barriers

Cross-cultural validity of four quality of life scales in persons with spinal cord injury

<p>Abstract</p> <p>Background</p> <p>Quality of life (QoL) in persons with spinal cord injury (SCI) has been found to differ across countries. However, comparability of measurement results between countries depends on the cross-cultural validity of the applied instruments. The study examined the metric quality and cross-cultural validity of the Satisfaction with Life Scale (SWLS), the Life Satisfaction Questionnaire (LISAT-9), the Personal Well-Being Index (PWI) and the 5-item World Health Organization Quality of Life Assessment (WHOQoL-5) across six countries in a sample of persons with spinal cord injury (SCI).</p> <p>Methods</p> <p>A cross-sectional multi-centre study was conducted and the data of 243 out-patients with SCI from study centers in Australia, Brazil, Canada, Israel, South Africa, and the United States were analyzed using Rasch-based methods.</p> <p>Results</p> <p>The analyses showed high reliability for all 4 instruments (person reliability index .78-.92). Unidimensionality of measurement was supported for the WHOQoL-5 (Chi²= 16.43, df = 10, p = .088), partially supported for the PWI (Chi²= 15.62, df = 16, p = .480), but rejected for the LISAT-9 (Chi²= 50.60, df = 18, p = .000) and the SWLS (Chi²= 78.54, df = 10, p = .000) based on overall and item-wise Chi²tests, principal components analyses and independent t-tests. The response scales showed the expected ordering for the WHOQoL-5 and the PWI, but not for the other two instruments. Using differential item functioning (DIF) analyses potential cross-country bias was found in two items of the SWLS and the WHOQoL-5, three items of the LISAT-9 and four items of the PWI. However, applying Rasch-based statistical methods, especially subtest analyses, it was possible to identify optimal strategies to enhance the metric properties and the cross-country equivalence of the instruments post-hoc. Following the post-hoc procedures the WHOQOL-5 and the PWI worked in a consistent and expected way in all countries.</p> <p>Conclusions</p> <p>QoL assessment using the summary scores of the WHOQOL-5 and the PWI appeared cross-culturally valid in persons with SCI. In contrast, summary scores of the LISAT-9 and the SWLS have to be interpreted with caution. The findings of the current study can be especially helpful to select instruments for international research projects in SCI.</p

Measurement Properties of the Full and Brief Version of the Work Rehabilitation Questionnaire in Persons with Physical Disabilities

Purpose The Work Rehabilitation Questionnaire (WORQ) is a self-report vocational rehabilitation assessment. A comprehensive (WORQ-FULL) and a brief version (WORQ-BRIEF) are available. The purpose of this study was to investigate measurement properties of both versions in persons with physical disabilities. Methods Cross sectional and test-retest design. Adults with physical disabilities in vocational rehabilitation were included. Internal consistency (Cronbach's alpha), test-retest reliability (intra-class correlation; ICC), agreement between sessions (Bland-Altman Plots), criterion validity (ICC and agreement with Bland-Altman Plots between WORQ-FULL and WORQ-BRIEF) and convergent validity with the Work Ability Index -Single item (WAS) and the EuroQOL 5D-5L were analyzed. Results Out of the 91 individuals who agreed to participate, 74 (81%) returned questionnaire T1 and 49 (54%) participants returned questionnaire T2 within the maximum time interval (= 27 days). At T2, 28 (57%) participants reported no medical changes compared to T1. Median age was 49 (IQR 40-60), 57% were male, 47% had experienced a stroke and 27% a spinal cord injury (n = 49). Internal consistency was good: 0.95/0.95/0.94 for the WORQ-FULL and 0.88/0.89/0.85 for the WORQ-BRIEF (n = 74/n = 48/n = 28, respectively). Test-retest reliabilitywas good: ICC = 0.86/0.85 for the WORQ-FULL and ICC = 0.87/0.86 for the WORQ-BRIEF (n = 49/ n = 28). Bland Altman plots suggested a higher score at T1. As for criterion validity of the WORQ-FULL versus the WORQ-BRIEF, ICC was good (ICC = 0.84; n = 74), however Bland Altman plots indicated potential bias. Correlations with the WAS/EuroQOL 5D-5L were variable: r = -0.24/r = -0.57 (WORQ-FULL) and r = -0.28/-0.65 (WORQ-BRIEF). Conclusions The WORQ showed good internal consistency and test-retest reliability. Agreement demonstrated large score differences are needed to indicate change beyond random chance at individual level, whereas small changes are sufficient at group level. Criterion validity of the WORQ-FULL versus the WORQ-BRIEF was supported, however, agreement demonstrated moderate to large score differences are needed to indicate change beyond random chance at individual level, whereas small changes are sufficient at group level. This indicates the WORQ-FULL and WORQ-BRIEF are better not used interchangeably. Correlation analyses provided better insight in the validity of the WORQ. Convergent validity was supported for the WORQ-BRIEF with the EuroQoL 5D-5L (r = -0.65)