Discrete time piecewise affine models of genetic regulatory networks

We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. When compared to other models of regulatory networks, these models have an additional parameter which is identified as quantifying interaction delays. In spite of their simplicity, their dynamics presents a rich variety of behaviours. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle -- with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.Comment: 34 page

Changes in cocoa properties induced by the alkalization process: A review

[EN] Alkalization, also known as "Dutching," is an optional, but very useful, step taken in the production chain of cocoa to darken its color, modify its taste, and increase natural cocoa solubility. Over the years, various attempts have been made to design new and more effective alkalization methods. Moreover, different authors have attempted to elucidate the impact of alkalization on the physicochemical, nutritional, functional, microbiological, and sensory characteristics of alkalized cocoa. The aim of this review is to provide a clear guide about not only the conditions that can be applied to alkalize cocoa, but also the reported effects of alkalization on the nutritional, functional, microbiological, and sensory characteristics of cocoa. The first part of this review describes different cocoa alkalization systems and how they can be tuned to induce specific changes in cocoa properties. The second part is a holistic analysis of the effects of the alkalization process on different cocoa features, performed by emphasizing the biochemistry behind all these transformations.European Regional Development Fund, Grant/Award Number: Project RTC-2016-5241-2; Ministerio deEconomia y Competitividad, Grant/Award Number: Project RTC-2016-5241-2Valverde-Garcia, D.; Pérez-Esteve, É.; Barat Baviera, JM. (2020). Changes in cocoa properties induced by the alkalization process: A review. Comprehensive Reviews in Food Science and Food Safety. 19(4):2200-2221. https://doi.org/10.1111/1541-4337.12581S22002221194Ilesanmi Adeyeye, E. (2016). Proximate, Mineral And Antinutrient Compositions Of Natural Cocoa Cake, Cocoa Liquor And Alkalized Cocoa Powders. Journal of Advanced Pharmaceutical Science And Technology, 1(3), 12-28. doi:10.14302/issn.2328-0182.japst-15-855Ajandouz, E. H., Tchiakpe, L. S., Ore, F. D., Benajiba, A., & Puigserver, A. (2001). 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International Journal of Food Science & Technology, 46(9), 1793-1800. doi:10.1111/j.1365-2621.2011.02670.xKofink, M., Papagiannopoulos, M., & Galensa, R. (2007). (-)-Catechin in Cocoa and Chocolate: Occurence and Analysis of an Atypical Flavan-3-ol Enantiomer. Molecules, 12(7), 1274-1288. doi:10.3390/12071274Kongor, J. E., Hinneh, M., de Walle, D. V., Afoakwa, E. O., Boeckx, P., & Dewettinck, K. (2016). Factors influencing quality variation in cocoa (Theobroma cacao) bean flavour profile — A review. Food Research International, 82, 44-52. doi:10.1016/j.foodres.2016.01.012Kopp G. M. Hennen J. C. Seyller M. &Brandstetter B.(2010).Process for producing high flavour cocoa. EP2241190A1.Kruszewski, B., & Obiedziński, M. W. (2020). Impact of Raw Materials and Production Processes on Furan and Acrylamide Contents in Dark Chocolate. Journal of Agricultural and Food Chemistry, 68(8), 2562-2569. doi:10.1021/acs.jafc.0c00412Lan, X., Liu, P., Xia, S., Jia, C., Mukunzi, D., Zhang, X., … Xiao, Z. (2010). Temperature effect on the non-volatile compounds of Maillard reaction products derived from xylose–soybean peptide system: Further insights into thermal degradation and cross-linking. Food Chemistry, 120(4), 967-972. doi:10.1016/j.foodchem.2009.11.033Li, Y., Feng, Y., Zhu, S., Luo, C., Ma, J., & Zhong, F. (2012). The effect of alkalization on the bioactive and flavor related components in commercial cocoa powder. Journal of Food Composition and Analysis, 25(1), 17-23. doi:10.1016/j.jfca.2011.04.010Li, Y., Zhu, S., Feng, Y., Xu, F., Ma, J., & Zhong, F. (2013). Influence of alkalization treatment on the color quality and the total phenolic and anthocyanin contents in cocoa powder. Food Science and Biotechnology, 23(1), 59-63. doi:10.1007/s10068-014-0008-5Lima, L. J. R., Kamphuis, H. J., Nout, M. J. R., & Zwietering, M. H. (2011). Microbiota of cocoa powder with particular reference to aerobic thermoresistant spore-formers. Food Microbiology, 28(3), 573-582. doi:10.1016/j.fm.2010.11.011MALEYKI, M. J. A., & ISMAIL, A. (2010). ANTIOXIDANT PROPERTIES OF COCOA POWDER. Journal of Food Biochemistry, 34(1), 111-128. doi:10.1111/j.1745-4514.2009.00268.xMartín, M. Á., & Ramos, S. (2017). Health beneficial effects of cocoa phenolic compounds: a mini-review. Current Opinion in Food Science, 14, 20-25. doi:10.1016/j.cofs.2016.12.002Martin, M. A., Goya, L., & Ramos, S. (2013). Potential for preventive effects of cocoa and cocoa polyphenols in cancer. Food and Chemical Toxicology, 56, 336-351. doi:10.1016/j.fct.2013.02.020Méndez-Albores, A., De Jesús-Flores, F., Castañeda-Roldan, E., Arámbula-Villa, G., & Moreno-Martı́nez, E. (2004). The effect of toasting and boiling on the fate of B-aflatoxins during pinole preparation. Journal of Food Engineering, 65(4), 585-589. doi:10.1016/j.jfoodeng.2004.02.024Miller, K. B., Hurst, W. J., Payne, M. J., Stuart, D. A., Apgar, J., Sweigart, D. S., & Ou, B. (2008). Impact of Alkalization on the Antioxidant and Flavanol Content of Commercial Cocoa Powders. Journal of Agricultural and Food Chemistry, 56(18), 8527-8533. doi:10.1021/jf801670pOlam. (2017).The De Zaan cocoa manual. The Netherlands: Archer Daniels Midland Company BV.ODUNS, A. A., & LONGE, O. G. (1998). Nutritive value of hot water- or cocoa-pod ash solution-treated cocoa bean cake for broiler chicks. British Poultry Science, 39(4), 519-525. doi:10.1080/00071669888700Ofosu, I. W., Ankar-Brewoo, G. M., Lutterodt, H. E., Benefo, E. O., & Menyah, C. A. (2019). Estimated daily intake and risk of prevailing acrylamide content of alkalized roasted cocoa beans. Scientific African, 6, e00176. doi:10.1016/j.sciaf.2019.e00176Okiyama, D. C. G., Navarro, S. L. B., & Rodrigues, C. E. C. (2017). Cocoa shell and its compounds: Applications in the food industry. 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A., Lerma‐García, M. J., Pérez‐Esteve, É., Talens, P., & Barat, J. M. (2020). Roadmap of cocoa quality and authenticity control in the industry: A review of conventional and alternative methods. Comprehensive Reviews in Food Science and Food Safety, 19(2), 448-478. doi:10.1111/1541-4337.12522Razzaque, M. A., Saud, Z. A., Absar, N., Karim, M. R., & Hashinaga, F. (2000). Purification and Characterization of Polyphenoloxidase from Guava Infected with Fruit-rot Disease. Pakistan Journal of Biological Sciences, 3(3), 407-410. doi:10.3923/pjbs.2000.407.410Rimbach, G., Melchin, M., Moehring, J., & Wagner, A. (2009). Polyphenols from Cocoa and Vascular Health—A Critical Review. International Journal of Molecular Sciences, 10(10), 4290-4309. doi:10.3390/ijms10104290Rodríguez, P., Pérez, E., & Guzmán, R. (2009). Effect of the types and concentrations of alkali on the color of cocoa liquor. 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The emergence of international food safety standards and guidelines: understanding the current landscape through a historical approach

Following the Second World War, the Food and Agriculture Organization (FAO) and the World Health Organization (WHO) teamed up to construct an International Codex Alimentarius (or 'food code') which emerged in 1963. The Codex Committee on Food Hygiene (CCFH) was charged with the task of developing microbial hygiene standards, although it found itself embroiled in debate with the WHO over the nature these standards should take. The WHO was increasingly relying upon the input of biometricians and especially the International Commission on Microbial Specifications for Foods (ICMSF) which had developed statistical sampling plans for determining the microbial counts in the final end products. The CCFH, however, was initially more focused on a qualitative approach which looked at the entire food production system and developed codes of practice as well as more descriptive end-product specifications which the WHO argued were 'not scientifically correct'. Drawing upon historical archival material (correspondence and reports) from the WHO and FAO, this article examines this debate over microbial hygiene standards and suggests that there are many lessons from history which could shed light upon current debates and efforts in international food safety management systems and approaches

Expert opinion as 'validation' of risk assessment applied to calf welfare

<p>Abstract</p> <p>Background</p> <p>Recently, a Risk Assessment methodology was applied to animal welfare issues in a report of the European Food Safety Authority (EFSA) on intensively housed calves.</p> <p>Methods</p> <p>Because this is a new and potentially influential approach to derive conclusions on animal welfare issues, a so-called semantic-modelling type 'validation' study was conducted by asking expert scientists, who had been involved or quoted in the report, to give welfare scores for housing systems and for welfare hazards.</p> <p>Results</p> <p>Kendall's coefficient of concordance among experts (n = 24) was highly significant (P < 0.001), but low (0.29 and 0.18 for housing systems and hazards respectively). Overall correlations with EFSA scores were significant only for experts with a veterinary or mixed (veterinary and applied ethological) background. Significant differences in welfare scores were found between housing systems, between hazards, and between experts with different backgrounds. For example, veterinarians gave higher overall welfare scores for housing systems than ethologists did, probably reflecting a difference in their perception of animal welfare.</p> <p>Systems with the lowest scores were veal calves kept individually in so-called "baby boxes" (veal crates) or in small groups, and feedlots. A suckler herd on pasture was rated as the best for calf welfare. The main hazards were related to underfeeding, inadequate colostrum intake, poor stockperson education, insufficient space, inadequate roughage, iron deficiency, inadequate ventilation, poor floor conditions and no bedding. Points for improvement of the Risk Assessment applied to animal welfare include linking information, reporting uncertainty and transparency about underlying values.</p> <p>Conclusion</p> <p>The study provides novel information on expert opinion in relation to calf welfare and shows that Risk Assessment applied to animal welfare can benefit from a semantic modelling approach.</p

Population exposure to trace elements in the Kilembe copper mine area, Western Uganda: a pilot study

The mining and processing of copper in Kilembe, Western Uganda, from 1956 to 1982 left over 15 Mt. of tailings containing cupriferous and cobaltiferous pyrite dumped within a mountain river valley. This pilot study was conducted to assess the nature and extent of risk to local populations from metal contamination arising from those mining activities. We determined trace element concentrations in mine tailings, soils, locally cultivated foods,house dust, drinking water and human biomarkers (toenails) using ICP-MS analysis of acid digested samples. The results showed that tailings, containing higher concentrations of Co, Cu, Ni and As compared with world average crust values had eroded and contaminated local soils. Pollution load indices revealed that 51% of agricultural soils sampled were contaminated with trace elements. Local water supplies were contaminated, with Co concentrations that exceeded Wisconsin (US) thresholds in 25% of domestic water supplies and 40% of Nyamwamba river water samples. Zinc exceeded WHO/FAO thresholds of 99.4 mg kg−1 in 36% of Amaranthus vegetable samples, Cu exceeded EC thresholds of 20 mg kg−1 in 19% of Amaranthus while Pb exceeded WHO thresholds of 0.3 mg kg−1 in 47% of Amaranthus vegetables. In bananas, 20% of samples contained Pb concentrations that exceeded the WHO/FAO recommended threshold of 0.3 mg kg−1. However, risk assessment of local foods and water, based on hazard quotients (HQ values) revealed no potential health effects. The high external contamination of volunteers' toenails with some elements (even after a washing process) calls into question their use as a biomarker for metal exposure in human populations where feet are frequently exposed to soil

Can we define a level of protection for allergic consumers that everyone can accept?

Substantial progress has been made in characterising the risk associated with exposure to allergens in food. However, absence of agreement on what risk is tolerable has made it difficult to set quantitative limits to manage that risk and protect allergic consumers effectively. This paper reviews scientific progress in the area and the diverse status of allergen management approaches and lack of common standards across different jurisdictions, including within the EU. This lack of regulation largely explains why allergic consumers find Precautionary Allergen Labelling confusing and cannot rely on it. We reviewed approaches to setting quantitative limits for a broad range of food safety hazards to identify the reasoning leading to their adoption. This revealed a diversity of approaches from pragmatic to risk-based, but we could not find clear evidence of the process leading to the decision on risk acceptability. We propose a framework built around the criteria suggested by Murphy and Gardoni (2008) for approaches to defining tolerable risks. Applying these criteria to food allergy, we concluded that sufficient knowledge exists to implement the framework, including sufficient expertise across the whole range of stakeholders to allow opinions to be heard and respected, and a consensus to be achieved