A Computational Algebra Approach to the Reverse Engineering of Gene Regulatory Networks

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have only two possible states. The use of a larger number of possible states allows a finer discretization of experimental data and more than one possible mode of action for the variables, depending on threshold values. Furthermore, with a suitable choice of state set, one can employ powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. To perform well, the algorithm requires wildtype together with perturbation time courses. This makes it suitable for small to meso-scale networks rather than networks on a genome-wide scale. The complexity of the algorithm is quadratic in the number of variables and cubic in the number of time points. The algorithm is validated on a recently published Boolean network model of segment polarity development in Drosophila melanogaster.Comment: 28 pages, 5 EPS figures, uses elsart.cl

Effect of curing conditions and harvesting stage of maturity on Ethiopian onion bulb drying properties

The study was conducted to investigate the impact of curing conditions and harvesting stageson the drying quality of onion bulbs. The onion bulbs (Bombay Red cultivar) were harvested at three harvesting stages (early, optimum, and late maturity) and cured at three different temperatures (30, 40 and 50 oC) and relative humidity (30, 50 and 70%). The results revealed that curing temperature, RH, and maturity stage had significant effects on all measuredattributesexcept total soluble solids

Roadmap of cocoa quality and authenticity control in the industry: a review of conventional and alternative methods

[EN] Cocoa (Theobroma cacao L.) and its derivatives are appreciated for their aroma, color, and healthy properties, and are commodities of high economic value worldwide. Wide ranges of conventional methods have been used for years to guarantee cocoa quality. Recently, however, demand for global cocoa and the requirements of sensory, functional, and safety cocoa attributes have changed. On the one hand, society and health authorities are increasingly demanding new more accurate quality control tests, including not only the analysis of physicochemical and sensory parameters, but also determinations of functional compounds and contaminants (some of which come in trace quantities). On the other hand, increased production forces industries to seek quality control techniques based on fast, nondestructive online methods. Finally, an increase in global cocoa demand and a consequent rise in prices can lead to future cases of fraud. For this reason, new analytes, technologies, and ways to analyze data are being researched, developed, and implemented into research or quality laboratories to control cocoa quality and authenticity. The main advances made in destructive techniques focus on developing new and more sensitive methods such as chromatographic analysis to detect metabolites and contaminants in trace quantities. These methods are used to assess cocoa quality; study new functional properties; control cocoa authenticity; or detect frequent emerging frauds. Regarding nondestructive methods, spectroscopy is the most explored technique, which is conducted within the near infrared range, and also within the medium infrared range to a lesser extent. It is applied mainly in the postharvest stage of cocoa beans to analyze different biochemical parameters or to assess the authenticity of cocoa and its derivatives.The authors wish to acknowledge the financial assistance provided by the Spanish Government and European Regional Development Fund (Project RTC-2016-5241-2). Maribel Quelal Vásconez thanks the Ministry Higher Education, Science, Technology, and Innovation (SENESCYT) of the Republic of Ecuador for her PhD grant.Quelal-Vásconez, MA.; Lerma-García, MJ.; Pérez-Esteve, É.; Talens Oliag, P.; Barat Baviera, JM. (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. https://doi.org/10.1111/1541-4337.12522S448478192Abdullahi, G., Muhamad, R., Dzolkhifli, O., & Sinniah, U. R. (2018). Analysis of quality retentions in cocoa beans exposed to solar heat treatment in cardboard solar heater box. Cogent Food & Agriculture, 4(1), 1483061. doi:10.1080/23311932.2018.1483061Abt, E., Fong Sam, J., Gray, P., & Robin, L. P. (2018). Cadmium and lead in cocoa powder and chocolate products in the US Market. Food Additives & Contaminants: Part B, 11(2), 92-102. doi:10.1080/19393210.2017.1420700Acierno, V., Alewijn, M., Zomer, P., & van Ruth, S. M. (2018). Making cocoa origin traceable: Fingerprints of chocolates using Flow Infusion - Electro Spray Ionization - Mass Spectrometry. Food Control, 85, 245-252. doi:10.1016/j.foodcont.2017.10.002Aculey, P. C., Snitkjaer, P., Owusu, M., Bassompiere, M., Takrama, J., Nørgaard, L., … Nielsen, D. S. (2010). Ghanaian Cocoa Bean Fermentation Characterized by Spectroscopic and Chromatographic Methods and Chemometrics. Journal of Food Science, 75(6), S300-S307. doi:10.1111/j.1750-3841.2010.01710.xAfoakwa, E. O., Paterson, A., Fowler, M., & Ryan, A. (2009). Matrix effects on flavour volatiles release in dark chocolates varying in particle size distribution and fat content using GC–mass spectrometry and GC–olfactometry. Food Chemistry, 113(1), 208-215. doi:10.1016/j.foodchem.2008.07.088Afoakwa, E. O., Quao, J., Takrama, J., Budu, A. S., & Saalia, F. K. (2011). Chemical composition and physical quality characteristics of Ghanaian cocoa beans as affected by pulp pre-conditioning and fermentation. Journal of Food Science and Technology, 50(6), 1097-1105. doi:10.1007/s13197-011-0446-5Alander, J. T., Bochko, V., Martinkauppi, B., Saranwong, S., & Mantere, T. (2013). A Review of Optical Nondestructive Visual and Near-Infrared Methods for Food Quality and Safety. International Journal of Spectroscopy, 2013, 1-36. doi:10.1155/2013/341402Álvarez, C., Pérez, E., Cros, E., Lares, M., Assemat, S., Boulanger, R., & Davrieux, F. (2012). The Use of near Infrared Spectroscopy to Determine the Fat, Caffeine, Theobromine and (−)-Epicatechin Contents in Unfermented and Sun-Dried Beans of Criollo Cocoa. Journal of Near Infrared Spectroscopy, 20(2), 307-315. doi:10.1255/jnirs.990Agricultural and Processed Food Products Export Development Authority (APEDA). (2015).Export statement. Retrieved fromhttp://agriexchange.apeda.gov.in/indexp/exportstatement.aspxAprotosoaie, A. C., Luca, S. V., & Miron, A. (2015). Flavor Chemistry of Cocoa and Cocoa Products-An Overview. Comprehensive Reviews in Food Science and Food Safety, 15(1), 73-91. doi:10.1111/1541-4337.12180Arévalo-Gardini, E., Arévalo-Hernández, C. O., Baligar, V. C., & He, Z. L. (2017). Heavy metal accumulation in leaves and beans of cacao (Theobroma cacao L.) in major cacao growing regions in Peru. Science of The Total Environment, 605-606, 792-800. doi:10.1016/j.scitotenv.2017.06.122Assa, A., Noor, A., Yunus, M. R., Misnawi, & Djide, M. N. (2018). 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Food capillary suspensions

When a small amount of a secondary immiscible fluid is added to a particle suspension, the rheological properties of the suspension can alter dramatically. The secondary liquid can create a sample-spanning network due to capillary bridges formed between the particles, inducing a transition from a fluid-like to a gel-like state. In this thesis it has been investigated how capillary suspensions can be used to create novel food products from suspensions with oil and water as bulk fluids

Integrated assessment of ecosystem connectivity and functioning: coastal forest avifauna of northeast Australia

The extraordinary diversity of species-environment relationships that occur across space and time can engender a deep curiosity of their mechanistic underpinnings. Moreover, the rapid rate of ecosystem change associated with anthropogenic and climatic pressures makes information regarding species' landscape and resource use ever more important. Without this information, we will be unable to effectively protect landscapes and their constituent species. The coastal ecosystem mosaic of northeast Australia, which is comprised of a high diversity of habitat types, provides a suitable region for investigating how species respond to heterogeneity in habitat and resource availability. The present thesis examined ecosystem functioning in heterogeneous coastal landscapes of northeast Australia for forest avifauna. An array of analytical approaches were employed to establish a comprehensive understanding: 1) spatial assessment to determine relationships between regional landscape connectivity and coastal forest bird assemblages, 2) isotopic assessment to evaluate the local foraging ecology of mangrove bird assemblages, and 3) nutrient assessment of cross-ecosystem connectivity provided by a migratory coastal forest bird species (i.e. the Pied Imperial-Pigeon (Ducula bicolor)). Within the coastal ecosystem mosaic, mangrove forests sit at the land-sea interface. Therefore, to effectively 'set the scene' I review how mangrove birds require and facilitate connectivity through their use of the broader coastal landscape. Next, to specifically assess regional landscape patterns and processes influencing northeast Australia's coastal forest avifauna, I surveyed the composition of bird assemblages in four of the major coastal forest types occurring throughout the region (i.e. Eucalypt, Melaleuca, mangrove, and rainforest). Following this, spatial patterns of habitat configuration within the coastal landscape (i.e. structural connectivity) were quantified to understand broad relationships between coastal forest bird assemblage composition and landscape heterogeneity at multiple spatial scales. Most bird species in coastal northeast Australia occurred in multiple forest types. Spatial assessment suggested that Melaleuca woodlands are a keystone structure that supports use of the entire coastal landscape mosaic by coastal forest generalist species. However, the species composition of mangrove bird assemblages was distinct relative to other coastal forest types. Therefore, to provide more detailed information regarding the response of coastal forest generalists and mangrove specialists to specific forest attributes, functionally connected forest networks were developed to assess the relative importance of forest area, availability, and connectivity to their compositional turnover. This revealed that mangrove specialists and coastal generalists differ in the forest attributes they require (i.e. area vs. availability) to maintain regional beta diversity. Understanding landscape pattern-process relationships that drive bird assemblage composition and turnover can inform the prioritization of regional-scale landscape features for protection. However, species' responses to local-scale spatiotemporal variability in resource availability may also play a role in these relationships. I used isotopic analysis to better understand the foraging ecology of coastal forest birds in a highly dynamic mangrove forest environment. This demonstrated that flexible and opportunistic foraging strategies were prevalent among coastal forest generalist species. However, specialized foraging strategies were employed by some species, primarily for resources that were uniquely available in mangrove forests (i.e. estuarine fish and crabs). Mobile species not only respond to landscape patterns and processes, but can also facilitate connectivity processes through their movement (e.g. nutrient transfer, pollination, genetic linking, etc.). To determine the implications of avian mobility for ecosystem functioning in northeast Australia, I focused on a migratory coastal forest bird species, the Pied Imperial-Pigeon (Ducula bicolor). Nutrient measurements demonstrated that Pied Imperial-Pigeons provide mainland-derived nutrient subsidies to island forests, highlighting their important role as an avian mobile-link species. The integrated analytical approach used in this thesis has provided insight to the complexity of coastal landscapes and their use by forest avifauna. This has broadened our understanding of coastal ecosystem functioning to include a hierarchy of ecosystem components that exist at local and regional scales. The ecosystem properties that emerge from interactions across coastal ecosystem components include: vegetative connectivity, compositional turnover, avian foraging strategy, and nutrient transfer. Results from this thesis can inform the holistic conservation and management strategies that are required to maintain coastal ecosystem functioning in regional northeast Australia

Oral processing of micro-aerated chocolates: a computational mechanics, rheological and tribological study

The emerging need to reduce the calorific value of foods, while simultaneously improving the consumer perception drives the quest for food structures that satisfy both criteria. Aiming to shed light on the influence that micro-aeration has on the breakdown of chocolate during the early stages of the oral processing, this study focuses on the investigation of the effect that micro-aeration has from a computational mechanics, rheological and tribological perspective. Firstly, several constitutive models are investigated and compared in both the explicit and implicit Finite Element (FE) frameworks and are calibrated using experimental results from mechanical testing conducted in a parallel PhD study. Afterwards, a non-local damage evolution law is presented providing mesh objectivity in both microscopic and macroscopic FE calculations. The constitutive model coupled with the non-local damage model, implemented in an ABAQUS VUMAT subroutine, is then applied in a micromechanical model for the prediction of the elastic, plastic, and fracture properties of micro-aerated chocolate using as input the properties of the non-aerated solid chocolate. Different boundary conditions are employed in both monodisperse and polydisperse dispersion of pores for the estimation of a representative volume element that is used for the estimation of the macroscopic properties. Overall, micro-aeration reduces the elastic, plastic and fracture properties of the chocolate, whereas the polydisperse dispersions provide a better estimation for the equivalent fracture strain at failure. The estimated values are applied in macroscopic FE simulations of the first bite, where the force-displacement FE results match the experimental data obtained by a replicate of the first bite model with 3D printed molar teeth. The forces needed for the fragmentation of chocolate reduce with micro-aeration level as shown from the experiments and validated by the FE simulations, whereas the in-vivo and in-vitro fragmentation studies show that micro-aerated chocolate breaks into more and smaller pieces. Furthermore, the effect of the micro-aeration on the rheological properties of the molten chocolate with and without the influence of artificial saliva is investigated. Micro-aeration increases viscosity values while the storage and loss moduli decrease. From a tribological perspective, a new bench test rig to measure friction in the simulated tongue-palate contact is developed. The test was applied to molten chocolate samples with and without artificial saliva. Friction was measured over the first few rubbing cycles, simulating mechanical degradation of chocolate in the tongue-palate region. The coefficient of friction increases with cocoa solids percentage and decreases with increasing micro-aeration level. The presence of artificial saliva in the contact reduced the friction for all chocolate samples, however, the relative ranking remained the same. Finally, the link between structure, material properties and sensory perception is given through a comparison with data from sensory tests. The current study can be used as a cost efficient tool for the investigation of new food structures that reduce the calorific value while enhancing the taste perception.Open Acces

2020 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Schedule and abstract book for the Twelfth Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: October 31 - November 1, 2020Location: The 2020 conference was conducted remotely due to COVID-19 concerns, utilizing the sococo platform that allows personal avatars to move between rooms and sessions, interact in small groups and also participate in zoom sessions.Keynote Speaker: Gerardo Chowell, Population Health Sciences, Georgia State Univ. School of Public Health, AtlantaFeatured Speaker: Olivia Prosper, Mathematics, Univ. of Tennessee, Knoxvill

Disease Name Extraction from Clinical Text Using Conditional Random Fields

The aim of the research done in this thesis was to extract disease and disorder names from clinical texts. We utilized Conditional Random Fields (CRF) as the main method to label diseases and disorders in clinical sentences. We used some other tools such as MetaMap and Stanford Core NLP tool to extract some crucial features. MetaMap tool was used to identify names of diseases/disorders that are already in UMLS Metathesaurus. Some other important features such as lemmatized versions of words, and POS tags were extracted using the Stanford Core NLP tool. Some more features were extracted directly from UMLS Metathesaurus, including semantic types of words. We participated in the SemEval 2014 competition\u27s Task 7 and used its provided data to train and evaluate our system. Training data contained 199 clinical texts, development data contained 99 clinical texts, and the test data contained 133 clinical texts, these included discharge summaries, echocardiogram, radiology, and ECG reports. We obtained competitive results on the disease/disorder name extraction task. We found through ablation study that while all features contributed, MetaMap matches, POS tags, and previous and next words were the most effective features

Molekulare Interaktionen in Schokolade und ihr Einfluss auf die Rheologie – eine molekulardynamische Herangehensweise

In this dissertation, different molecular interactions in chocolate are explored in order to give mechanistic explanations for the rheological behavior of chocolate. This is done by performing molecular dynamics simulations. Phospholipids are examined in terms of their strength of interaction with crystalline sucrose at the cocoa butter interface and their concentration-dependent structures in chocolate. Cocoa butter immobilization on sucrose crystal surfaces is explored by calculating its mobility on the particle surface.In dieser Dissertation werden verschiedene molekulare Interaktionen in Schokolade untersucht, um mechanistische Erklärungen für das rheologische Verhalten von Schokolade geben zu können. Dazu werden molekulardynamische Simulationen durchgeführt. Phospholipide werden hinsichtlich der Stärke ihrer Interaktion mit kristalliner Saccharose an der Grenzfläche zu Kakaobutter und ihrer konzentrationsabhängigen Strukturen in Schokolade untersucht. Kakaobutterimmobilisierung an Saccharosekristalloberflächen wird untersucht, indem die Mobilität an der Partikeloberfläche berechnet wird