Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes

The human salivary amylase genes display extensive copy number variation (CNV), and recent work has implicated this variation in adaptation to starch-rich diets, and in association with body mass index. In this work, we use paralogue ratio tests, microsatellite analysis, read depth and fibre-FISH to demonstrate that human amylase CNV is not a smooth continuum, but is instead partitioned into distinct haplotype classes. There is a fundamental structural distinction between haplotypes containing odd or even numbers of AMY1 gene units, in turn coupled to CNV in pancreatic amylase genes AMY2A and AMY2B. Most haplotypes have one copy each of AMY2A and AMY2B and contain an odd number of copies of AMY1; consequently, most individuals have an even total number of AMY1. In contrast, haplotypes carrying an even number of AMY1 genes have rearrangements leading to CNVs ofAMY2A/AMY2B. Read-depth and experimental data showthat different populations harbour different proportions of these basic haplotype classes. In Europeans, the copy numbers of AMY1 and AMY2A are correlated, so that phenotypic associations caused by variation in pancreatic amylase copy number could be detected indirectly as weak association with AMY1 copy number.We showthat the quantitative polymerase chain reaction (qPCR) assay previously applied to the high-throughput measurement of AMY1 copy number is less accurate than the measures we use and that qPCR data in other studies have been further compromised by systematic miscalibration. Our results uncover new patterns in human amylase variation and imply a potential role for AMY2 CNV in functional associations

Organizational-level strategies with or without an activity tracker to reduce office workers' sitting time: Rationale and study design of a pilot cluster-randomized trial

Background: The office workplace is a key setting in which to address excessive sitting time and inadequate physical activity. One major influence on workplace sitting is the organizational environment. However, the impact of organizational-level strategies on individual level activity change is unknown. Further, the emergence of sophisticated, consumer-targeted wearable activity trackers that facilitate real-time self-monitoring of activity, may be a useful adjunct to support organizational-level strategies, but to date have received little evaluation in this workplace setting. Objective: The aim of this study is to evaluate the feasibility, acceptability, and effectiveness of organizational-level strategies with or without an activity tracker on sitting, standing, and stepping in office workers in the short (3 months, primary aim) and long-term (12 months, secondary aim). Methods: This study is a pilot, cluster-randomized trial (with work teams as the unit of clustering) of two interventions in office workers: organizational-level support strategies (eg, visible management support, emails) or organizational-level strategies plus the use of a waist-worn activity tracker (the LUMOback) that enables self-monitoring of sitting, standing, and stepping time and enables users to set sitting and posture alerts. The key intervention message is to ‘Stand Up, Sit Less, and Move More.’ Intervention elements will be implemented from within the organization by the Head of Workplace Wellbeing. Participants will be recruited via email and enrolled face-to-face. Assessments will occur at baseline, 3, and 12 months. Time spent sitting, sitting in prolonged (≥30 minute) bouts, standing, and stepping during work hours and across the day will be measured with activPAL3 activity monitors (7 days, 24 hours/day protocol), with total sitting time and sitting time during work hours the primary outcomes. Web-based questionnaires, LUMOback recorded data, telephone interviews, and focus groups will measure the feasibility and acceptability of both interventions and potential predictors of behavior change. Results: Baseline and follow-up data collection has finished. Results are expected in 2016. Conclusions: This pilot, cluster-randomized trial will evaluate the feasibility, acceptability, and effectiveness of two interventions targeting reductions in sitting and increases in standing and stepping in office workers. Few studies have evaluated these intervention strategies and this study has the potential to contribute both short and long-term findings

Use of organic inputs by arable farmers in six agro-ecological zones across Europe: Drivers and barriers

Soil organic matter (SOM) in agricultural soils builds up via – among others - the use of organic inputs such as straw, compost, farmyard manure or the cultivation of green manures or cover crops. SOM has benefits for long-term soil fertility and can provide ecosystem services. Farmer behaviour is however known to be motivated by a larger number of factors. Using the theory of planned behaviour, we aimed to disentangle these factors. We addressed the following research question: What are currently the main drivers and barriers for arable farmers in Europe to use organic inputs? Our study focuses on six agro-ecological zones in four European countries (Austria, Flanders [Belgium], Italy and the Netherlands) and four practices (straw incorporation, green manure or cover crops, compost and farmyard manure). In a first step, relevant factors were identified for each practice with farmers using 5 to ten semi-structured interviews per agro-ecological zone. In a second step, the relevance of these factors was quantified and they were classified as either drivers or barriers in a large scale farm survey with 1263 farmers. In the semi-structured interviews, 110 factors that influenced farmer decisions to use an organic input were identified. In the larger farm survey, 60% of the factors included were evaluated as drivers, while 40% were evaluated as barriers for the use of organic inputs. Major drivers to use organic inputs were related to the perceived effects on soil quality (such as improved soil structure or reduced erosion) and the positive influence from social referents (such as fellow farmers or agricultural advisors). Major barriers to use organic inputs were financial (increased costs or foregone income) and perceived effects on crop protection (such as increased weeds, pests and diseases, or increased pesticide use). Our study shows that motivating farmers to use organic inputs requires specific guidance on how to adapt cultivation practices to reduce weeds, pests and diseases for specific soil types, weather conditions, and crops. In addition, more research is needed on the long-term financial consequences of using organic inputs

Severity of left ventricular remodeling defines outcomes and response to therapy in heart failure Valsartan heart failure trial (Val-HeFT) echocardiographic data

AbstractObjectivesThe objective of this study was to test the hypothesis that the severity of left ventricular remodeling predicts the response to treatment and outcomes in chronic heart failure.BackgroundReversal of remodeling should produce the most favorable outcome in patients with the most severe remodeling.MethodsIn 5,010 heart failure patients on background therapy and randomized to valsartan and placebo, serial recordings of left ventricular internal diastolic diameter (LVIDd) and ejection fraction (EF) were read at sites that had to meet qualifying standards before participating. Baseline LVIDd and EF were pooled across treatments and retrospectively grouped by quartiles Q1 to Q4, representing best to worst. Kaplan-Meier survival curves were obtained by the log-rank test. Q1 was compared with Q4 for mortality and combined mortality and morbidity (M + M) from Cox regression risk ratios (RRs). Valsartan versus placebo changes from baseline in LVIDd and EF were analyzed by quartiles from analysis of covariance. Valsartan and placebo were compared by RRs for M + M.ResultsSurvival rates were greater in the better quartiles for LVIDd and EF (p < 0.00001). The RR for Q1 versus Q4 in events approached 0.5 for both LVIDd and EF (p < 0.0001). An LVIDd decrease and EF increase were quartile-dependent and greater with valsartan than placebo at virtually all time points. The RR for M + M outcomes favored valsartan in the worse quartiles.ConclusionsStratification by baseline severity of remodeling showed that patients with worse LVIDd and EF are at highest risk for an event, yet appear to gain the most anti-remodeling effect and clinical benefit with valsartan treatment

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

Lipid membranes for membrane proteins

Andreas Kukol, ‘Lipid membranes for membrane proteins in Molecular Modeling of Proteins (Clifton: Humana Press/Sringer, 2015), ISBN: 978-1-4939-1464-7, e-BOOK ISBN: 978-1-4939-1465-4Peer reviewe

Associations between daily sitting time and the combinations of lifestyle risk factors in men

Background: Understanding the reciprocal role that multiple problematic behaviours play in men's health is important for intervention delivery and for reducing the healthcare burden. Data regarding the concurrence of problematic health behaviours is currently limited but offers insights into risk profiles, and should now include total time spent sitting/day. Methods: Self-reported data on lifestyle health behaviours was collected from 232 men aged ≥18 years who engaged in a men's health promotion programme delivered by 16 English Premier League Clubs. Results: Men at risk due to high sitting display multiple concurrent lifestyle risk factors, 88.6% displayed at least two ancillary risk factors and were three times more likely to report ≥2 lifestyle risk factors (OR. =3.13, 95% confidence interval (CI). =1.52-6.42) than those with low sitting risk. Significant differences in the mean number of risk factors reported between those participants in the higher risk (2.43. ±. 0.90) and lower risk (2.13. ±. 0.96) sitting categories were also found (P=0.015). Conclusions: Hard-to-reach men displayed multiple problematic concurrent behaviours, strongly linked to total sitting time. © 2012 WPMH GmbH

Applying systems thinking to unravel the mechanisms underlying orthostatic hypotension related fall risk

Orthostatic hypotension (OH) is an established and common cardiovascular risk factor for falls. An in-depth understanding of the various interacting pathophysiological pathways contributing to OH-related falls is essential to guide improvements in diagnostic and treatment opportunities. We applied systems thinking to multidisciplinary map out causal mechanisms and risk factors. For this, we used group model building (GMB) to develop a causal loop diagram (CLD). The GMB was based on the input of experts from multiple domains related to OH and falls and all proposed mechanisms were supported by scientific literature. Our CLD is a conceptual representation of factors involved in OH-related falls, and their interrelatedness. Network analysis and feedback loops were applied to analyze and interpret the CLD, and quantitatively summarize the function and relative importance of the variables. Our CLD contains 50 variables distributed over three intrinsic domains (cerebral, cardiovascular, and musculoskeletal), and an extrinsic domain (e.g., medications). Between the variables, 181 connections and 65 feedback loops were identified. Decreased cerebral blood flow, low blood pressure, impaired baroreflex activity, and physical inactivity were identified as key factors involved in OH-related falls, based on their high centralities. Our CLD reflects the multifactorial pathophysiology of OH-related falls. It enables us to identify key elements, suggesting their potential for new diagnostic and treatment approaches in fall prevention. The interactive online CLD renders it suitable for both research and educational purposes and this CLD is the first step in the development of a computational model for simulating the effects of risk factors on falls