Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kB signaling pathway

Mathematical modelling offers a variety of useful techniques to help in understanding the intrinsic behaviour of complex signal transduction networks. From the system engineering point of view, the dynamics of metabolic and signal transduction models can always be described by nonlinear ordinary differential equations (ODEs) following mass balance principles. Based on the state-space formulation, many methods from the area of automatic control can conveniently be applied to the modelling, analysis and design of cell networks. In the present study, dynamic sensitivity analysis is performed on a model of the IB-NF-B signal pathway system. Univariate analysis of the Euclidean-form overall sensitivities shows that only 8 out of the 64 parameters in the model have major influence on the nuclear NF-B oscillations. The sensitivity matrix is then used to address correlation analysis, identifiability assessment and measurement set selection within the framework of least squares estimation and multivariate analysis. It is shown that certain pairs of parameters are exactly or highly correlated to each other in terms of their effects on the measured variables. The experimental design strategy provides guidance on which proteins should best be considered for measurement such that the unknown parameters can be estimated with the best statistical precision. The whole analysis scheme we describe provides efficient parameter estimation techniques for complex cell networks

An investigation of the impact of bounded rationality on the decarbonisation of Kenya's power system

How can we transition to a low-carbon energy supply to limit the effects of climate change? The methodology of quantitative energy models can have an impact on the advice inferred. We compare Kenya’s electricity system transition to 2050 with a 2-model inter-comparison. To explore the uncertainty, we use an agent-based simulation model (MUSE) and an optimisation model (OSeMOSYS)

Mpemba effect and phase transitions in the adiabatic cooling of water before freezing

An accurate experimental investigation on the Mpemba effect (that is, the freezing of initially hot water before cold one) is carried out, showing that in the adiabatic cooling of water a relevant role is played by supercooling as well as by phase transitions taking place at 6 +/- 1 oC, 3.5 +/- 0.5 oC and 1.3 +/- 0.6 oC, respectively. The last transition, occurring with a non negligible probability of 0.21, has not been detected earlier. Supported by the experimental results achieved, a thorough theoretical analysis of supercooling and such phase transitions, which are interpreted in terms of different ordering of clusters of molecules in water, is given.Comment: revtex, 4 pages, 2 figure

CWRML: representing crop wild relative conservation and use data in XML

Background Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Results Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. Conclusion CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data

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A prioritised inventory of crop wild relatives and wild harvested plants of Tunisia

An inventory of crop wild relatives (CWR) and wild harvested plants (WHP) occurring in Tunisia, based on the integration of the last available floristic checklists, is presented. The taxa were prioritised according to economic value of the related crop, potential for crop improvement, threat status, endemism, inclusion in the ITPGRFA (Annex I) and average annual contributions to dietary energy (kilocalories) per capita per day by applying a scoring system based on 4 priority levels. Of a total of 2912 taxa belonging to the Tunisian Flora, 2504 CWR and/or WHP (86% of the total), from 143 families and 686 genera, were identified, 2445 of which are CWR and 847 are WHP. In detail, 1654 are solely CWR and 59 are WHP only, whereas 788 are both CWR and WHP. The final priority list for active conservation includes 1036 CWR (43% of the total CWR taxa), with 139 taxa rated as high priority, 660 medium priority and 237 low priority. The final priority list for WHP is composed of 344 taxa and includes eight high priority, 254 medium priority and 82 low priority taxa. Our results confirm Tunisia as a hotspot of CWR and WHP diversity in the Mediterranean area. The inventory here proposed provides the basis for the development and implementation of a more targeted national CWR/WHP conservation strategy for Tunisia

International Conference Enhanced Genepool Utilization - Capturing wild relative and landrace diversity for crop improvement, Cambridge, United Kingdom, 16-20 June 2014. Book of Abstracts

This conference presents the culmination of the PGR Secure project (www.pgrsecure.org) – a collaborative project involving eleven partners funded under the EU Seventh Framework Programme, THEME KBBE.2010.1.1-03, 'Characterization of biodiversity resources for wild crop relatives to improve crops by breeding', Grant agreement no. 266394. It is jointly organized with the section on genetic resources of the European Association for Research on Plant Breeding (EUCARPIA). This international conference showcases innovative and potential novel characterization techniques and conservation strategies to identify and safeguard crop wild relative (CWR) and landrace (LR) genetic diversity to increase potential options for crop improvement as a means of underpinning food security in the face of climate change. The conference brings together a wide range of biodiversity expertise from the international community to debate current and future enhanced conservation and utilization of CWR and LR diversity for improving agricultural production, increasing food security and sustaining the environment for better livelihoods. The conference represents a landmark in the plant genetic resources science arena, highlighting exotic plant germplasm as a potentially critical but neglected resource for crop improvement. Part 1 of the book of abstracts contains the abstracts of the oral presentations and Part 2, those of the posters. They are organized under the four conference themes, viz. characterization techniques, conservation strategies, facilitating CWR and LR use and informatics development. The oral presentations will be the subject of a book entitled “Enhancing Crop Genepool Use: Capturing wild relative and landrace diversity for crop improvement” that will be published by CABI as the conference proceedings. All duly registered participants will be receiving a copy of the book when it is published

Paper and electronic versions of HM-PRO, a novel patient-reported outcome measure for hematology: an equivalence study.

© 2019 Goswami, Oliva, Ionova et al.Aim:To determine measurement equivalence of paper and electronic application of the hematologi-cal malignancy-patient-reported outcome (HM-PRO), a specific measure for the evaluation of patient-reported outcomes in HMs.Patients & methods:Following International Society of Pharmacoeconomicsand Outcomes Research ePRO Good Research Practice Task Force guidelines, a total of 193 adult patientswith different HMs were recruited into a multicenter prospective study. The paper and the electronic ver-sion of the instrument were completed in the outpatient clinics in a randomized crossover design with a30-min time interval to minimize the learning effect. Those who completed the paper version first, com-pleted the electronic version after 30 min and vice versa. Instrument version and order effects were testedon total score of the two parts of the HM-PRO (Part A: quality of life and Part B: signs & symptoms) in atwo-way ANOVA with patients as random effects. Intraclass correlation coefficients (95% CI) and Spear-man’s rank correlation coefficients were used to evaluate test–retest reliability and reproducibility. Theeffects of instrument version and order were tested on total score of the two parts of HM-PRO.Results:The questionnaire version and administration order effects were not significant at the 5% level. Therewere no interactions found between these two factors for HM-PRO (Part A [quality of life]; p=0.95); and(part B [signs and symptoms]; p=0.72]. Spearman’s rank correlation coefficients were greater than 0.9, andintraclass correlation coefficients ranged from 0.94 to 0.98; furthermore, the scores were not statisticallydifferent between the two versions, showing acceptable reliability indexes. Noteworthy, the differencebetween the completion time for both paper (mean=6:38 min) and electronic version (mean=7:29 min)was not statistically significant (n=100; p=0.11). Patients did not report any difficulty in completing theelectronic version during cognitive interviews and were able to understand and respond spontaneously.Conclusion:Measurement equivalence has been demonstrated for the paper and electronic applicationof the HM-PRO.Peer reviewe