Structural identifiability of dynamic systems biology models

22 páginas, 5 figuras, 2 tablas.-- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areasAFV acknowledges funding from the Galician government (Xunta de Galiza, Consellería de Cultura, Educación e Ordenación Universitaria http://www.edu.xunta.es/portal/taxonomy/term/206) through the I2C postdoctoral program, fellowship ED481B2014/133-0. AB and AFV were partially supported by grant DPI2013-47100-C2-2-P from the Spanish Ministry of Economy and Competitiveness (MINECO). AFV acknowledges additional funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 686282 (CanPathPro). AP was partially supported through EPSRC projects EP/M002454/1 and EP/J012041/1.Peer reviewe

Riorganizzazione istituzionale e pianificazione del territorio. Riflessioni a partire dalle prossime riforme e dall’esperienza torinese

The DdL 1542/2013, known as Ddl “Delrio”, because of the name of the minister that has promoted this new law, represents a further step in the long and complex history of the Italian reorganisation of local authorities. Its peculiarity is on the clearly reformist approach that foresee an organisational model of local autonomies that is based on two levels of government that are directly elected (Regions and Municipalities) and a level of governance for sub-regional areas. The latter can refer to both metropolitan and non-metropolitan areas. In the Italian panorama, this law could represent a complete change taking into account opportunities arising from the shortened decision-making chain and from the possibility to concretely proceed in co-planning among different institutions. The Ddl “Delrio”, on another hand, has shifted also the on-going process of institution of metropolitan cities from the spending review perspective (as in the previous law 135/2012) to a more complete and coherent reform. In this framework, the Torino experience is interesting for at least two characteristics: the territorial specificity of the Provincia di Torino, a province with 315 municipalities – a larger part of which are in mountain and national border areas – that will become the metropolitan city from the 1st of January 2014; the simultaneous strategic planning process for the core area of the province and not for the whole territory

Comment on “minimal and maximal models to quantitate glucose metabolism : tools to measure, to simulate and to run in silico clinical trials"

Comment on “Minimal and Maximal Models to Quantitate Glucose Metabolism: Tools to Measure, to Simulate and to Run in Silico Clinical Trials

Foreign body ingestion in children: Definition of a nomogram to predict surgical or endoscopic intervention

Background and aims: Foreign body ingestion (FBI) in children requires early identification to prevent adverse outcomes and may necessitate endoscopic or surgical intervention. This study aims to develop a nomogram that identifies children who require urgent surgical or endoscopic intervention by using the patient's medical history and clinical parameters collected at admission. Methods: This study is a retrospective review (01/2015-12/2020) of a multicenter case series of children admitted for FBI. Data from 5864 records from 24 hospitals in Italy were analyzed. Logistic regression models were used to establish the probability of requiring surgical or endoscopic intervention based on patient history and clinical characteristics. The nomogram representing the results from the multivariable model was reported to examine the propensity for surgery/endoscopy. Results: The study identified a significant association between intervention and various factors, including type of foreign body (blunt: reference category, disk battery (odds ratio OR:4.89), food bolus (OR:1.88), magnets (OR:2.61), sharp-pointed (OR:1.65), unknown (OR:1.02)), pre-existing diseases or conditions (OR 3.42), drooling (OR 10.91), dysphagia (OR 5.58), vomiting (OR 3.30), retrosternal pain (OR 5.59), abdominal pain (OR 1.58), hematemesis (OR 2.82), food refusal/poor feeding (OR 2.99), and unexplained crying (OR 2.01). The multivariable regression model showed good calibration and discrimination ability, with an area under the ROC curve of 0.77. Conclusions: This study developed the first nomogram to predict the probability of the need for surgical or endoscopic intervention in children with FBI, based on the information collected at admission. The nomogram will aid clinicians in identifying children who require early intervention to prevent adverse outcomes

Brace related stress in scoliosis patients – Comparison of different concepts of bracing

<p>Abstract</p> <p>Background</p> <p>The BSSQbrace questionnaire has been shown to be reliable with good internal consistency and reproducibility estimating the stress scoliosis patients have whilst wearing their brace. Eight questions are provided focussing on this topic. A max. score of 24 can be achieved (from 0 for most stress to 24 for no stress). The subdivision of the score values is: 0–8 (strong stress), 9–16 (medium stress) and 17–24 (little stress).</p> <p>Study design</p> <p>Two BSSQbrace questionnaires have been posted to 65 patients under brace treatment from our Cheneau light data base. All patients had another kind of brace prior to the Cheneau light. The patients have been asked to rate their stress level using one questionnaire for the current brace and the other for the previous one.</p> <p>Results</p> <p>63 Patients (59 girls and 4 boys) returned their fully completed questionnaires (average age 13,6 years, average Cobb angle 43,7 degrees). Stress level in the previous brace was 11,04 and in the Cheneau light(r) 13,87. The differences were highly significant in the t-test; t = -4,67; p < 0,001.</p> <p>Conclusion</p> <p>The use of the Cheneau light^®brace leads to reduced stress and/or impairment for the patients under treatment compared to heavier brace models used so far.</p

The relationship between quality of life and compliance to a brace protocol in adolescents with idiopathic scoliosis: a comparative study

<p>Abstract</p> <p>Background</p> <p>Corrective bracing for adolescent idiopathic scoliosis (AIS) has favourable outcomes when patients are compliant. However, bracing may be a stressful and traumatic experience and compliance with a bracing protocol is likely to be dependent upon patients' physical, emotional and social wellbeing. The Brace Questionnaire (BrQ), a recently-developed, condition-specific tool to measure quality of life (QOL) has enabled clinicians to study relationships between QOL and compliance.</p> <p>Methods</p> <p>The BrQ was administered to 31 AIS patients after a minimum of 1 year of wearing a brace. Subjects were 13–16 year old South African girls with Cobb angles of 25–40 degrees. Participants were divided into two groups according to their level of compliance with the bracing protocol. Brace Questionnaire sub- and total scores were compared between the two groups using the t-test for comparison of means.</p> <p>Results</p> <p>Twenty participants were classified as compliant and 11 as non-compliant. Mean total BrQ scores (expressed as a percentage) were 83.7 for the compliant group and 64.4 for the non-compliant group (p < 0.001), and on analysis of the 8 domains that make up the BrQ, the compliant group scored significantly higher in the 6 domains that measured vitality and social, emotional and physical functioning.</p> <p>Conclusion</p> <p>Poor compliance with a brace protocol is associated with poorer QOL, with non-compliant patients lacking vitality and functioning poorly physically, emotionally and socially. Quality of life for adolescents with idiopathic scoliosis may relate more to psychosocial coping mechanisms than to physical deformity and its consequences. It is important to establish whether remedial programmes are capable of addressing personal, group and family issues, improving QOL and promoting compliance.</p

Determination of quality of life in adolescents with idiopathic scoliosis subjected to conservative treatment.

<p>Abstract</p> <p>Introduction and objectives</p> <p>Physical deformities caused by adolescent idiopathic scoliosis (AIS) coupled with conservative treatment of AIS with orthesis unavoidably impacts on patients' quality of life (QoL). The present study aimed at evaluating the QoL in patients affected by AIS treated with brace. The study also sought to determine the ability of different QoL questionnaires to monitor QoL over the course of treatment.</p> <p>Materials and methods</p> <p>Data were collected in 108 consecutive patients (96 females, 16 males) affected by AIS admitted to the outpatient orthopaedic clinic of the Catholic University of the Sacred Heart in Rome (Italy). Patients were subjected to full-time (i.e., 22 hrs per day) conservative treatment with the progressive action short brace (PASB), the Lyon brace or a combination of PASB + Lyon brace. Three instruments were used for QoL determination: the Scoliosis Research Society 22 (SRS-22), Bad Sobernheim Stress Questionnaire (BSSQ) and the Brace Questionnaire (BrQ).</p> <p>Results</p> <p>A significant correlation was detected among the 3 scores (p < 0.001). The BrQ possesses a higher capacity to detect changes in QoL in relation to the patient gender, type of brace, curve severity at baseline and at the completion of treatment, and curve type. Overall, boys displayed a higher QoL than girls. In all 3 questionnaires, higher QoL scores were determined in patients treated with the PASB compared with those using the Lyon brace. QoL scores were significantly correlated with the curve severity. Higher QoL scores were obtained by participants with thoraco-lumbar curves as compared with those with other curves.</p> <p>Conclusions</p> <p>The 3 questionnaires are effective in capturing changes in QoL in AIS patients subjected to conservative treatment. However, the BrQ possesses a higher discriminatory capacity compared with the other questionnaires tested. PASB-based treatment is associated with better QoL than the Lyon bracing.</p

Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research.</p> <p>Results</p> <p>We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient F_iswas 0.282 ± 0.124, but it varied widely among marker loci, from F_is= +0.876 (heterozygote deficiency) to F_is= -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (F_st= 0.232 ± 0.027). Among triploid varieties the genetic differentiation was much lower (F_st= 0.100 ± 0.010). The overall genetic differentiation between diploid and triploid varieties was F_st= 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was F_st= 0.063.</p> <p>Conclusions</p> <p>Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.</p

Drugs in focus: Botulinum toxin in the therapy of gastrointestinal disorders in children

What is Known Botulinum toxin (BoNT) causes muscle relaxation by inhibiting acetylcholine release from presynaptic motor neurons at the neuromuscular junction. What is New In children with achalasia, BoNT can be considered only in patients in whom rapid weight gain is important to improve surgical outcomes. BoNT has been suggested for treating cricopharyngeal achalasia and delayed gastric emptying. Anal achalasia and constipation after Hirschsprung disease corrective surgery are very promising indications for BoNT use. In selected children with resistant type of functional constipation and chronic anal fissure, BoNT is a viable option for treating