Design, modelling, simulation and integration of cyber physical systems: methods and applications

The main drivers for the development and evolution of Cyber Physical Systems (CPS) are the reduction of development costs and time along with the enhancement of the designed products. The aim of this survey paper is to provide an overview of different types of system and the associated transition process from mechatronics to CPS and cloud-based (IoT) systems. It will further consider the requirement that methodologies for CPS-design should be part of a multi-disciplinary development process within which designers should focus not only on the separate physical and computational components, but also on their integration and interaction. Challenges related to CPS-design are therefore considered in the paper from the perspectives of the physical processes, computation and integration respectively. Illustrative case studies are selected from different system levels starting with the description of the overlaying concept of Cyber Physical Production Systems (CPPSs). The analysis and evaluation of the specific properties of a sub-system using a condition monitoring system, important for the maintenance purposes, is then given for a wind turbine.

Climate Change or Urbanization? Impacts on a Traditional Coffee Production System in East Africa over the Last 80 Years

Global environmental changes (GEC) such as climate change (CC) and climate variability have serious impacts in the tropics, particularly in Africa. These are compounded by changes in land use/land cover, which in turn are driven mainly by economic and population growth, and urbanization. These factors create a feedback loop, which affects ecosystems and particularly ecosystem services, for example plant-insect interactions, and by consequence agricultural productivity. We studied effects of GEC at a local level, using a traditional coffee production area in greater Nairobi, Kenya. We chose coffee, the most valuable agricultural commodity worldwide, as it generates income for 100 million people, mainly in the developing world. Using the coffee berry borer, the most serious biotic threat to global coffee production, we show how environmental changes and different production systems (shaded and sun-grown coffee) can affect the crop. We combined detailed entomological assessments with historic climate records (from 1929-2011), and spatial and demographic data, to assess GEC's impact on coffee at a local scale. Additionally, we tested the utility of an adaptation strategy that is simple and easy to implement. Our results show that while interactions between CC and migration/urbanization, with its resultant landscape modifications, create a feedback loop whereby agroecosystems such as coffee are adversely affected, bio-diverse shaded coffee proved far more resilient and productive than coffee grown in monoculture, and was significantly less harmed by its insect pest. Thus, a relatively simple strategy such as shading coffee can tremendously improve resilience of agro-ecosystems, providing small-scale farmers in Africa with an easily implemented tool to safeguard their livelihoods in a changing climate.

Energy requirements for the continuous biohydrogen production from Spirogyra biomass in a sequential batch reactor

The current energy market requires urgent revision for the introduction of renewable, less-polluting and inexpensive energy sources. Biohydrogen (bioH2) is considered to be one of the most appropriate options for this model shift, being easily produced through the anaerobic fermentation of carbohydrate-containing biomass. Ideally, the feedstock should be low-cost, widely available and convertible into a product of interest. Microalgae are considered to possess the referred properties, being also highly valued for their capability to assimilate CO2 [1]. The microalga Spirogyra sp. is able to accumulate high concentrations of intracellular starch, a preferential carbon source for some bioH2 producing bacteria such as Clostridium butyricum [2]. In the present work, Spirogyra biomass was submitted to acid hydrolysis to degrade polymeric components and increase the biomass fermentability. Initial tests of bioH2 production in 120 mL reactors with C. butyricum yielded a maximum volumetric productivity of 141 mL H2/L.h and a H2 production yield of 3.78 mol H2/mol consumed sugars. Subsequently, a sequential batch reactor (SBR) was used for the continuous H2 production from Spirogyra hydrolysate. After 3 consecutive batches, the fermentation achieved a maximum volumetric productivity of 324 mL H2/L.h, higher than most results obtained in similar production systems [3] and a potential H2 production yield of 10.4 L H2/L hydrolysate per day. The H2 yield achieved in the SBR was 2.59 mol H2/mol, a value that is comparable to those attained with several thermophilic microorganisms [3], [4]. In the present work, a detailed energy consumption of the microalgae value-chain is presented and compared with previous results from the literature. The specific energy requirements were determined and the functional unit considered was gH2 and MJH2. It was possible to identify the process stages responsible for the highest energy consumption during bioH2 production from Spirogyra biomass for further optimisation.

Guardian dogs protect sheep by guarding sheep, not by establishing territories and excluding predators

Guardian animals have been a common non-lethal method for reducing predator impacts on livestock for centuries in Europe. But elsewhere, livestock producers sometimes doubt whether such methods work or are compatible with modern livestock husbandry practices in extensive grazing systems. In this study we evaluate the hypothesis that guardian dogs primarily ‘work’ by establishing and defending territories from which canid predators are excluded. Eight maremmas and six free-ranging wild dogs of different sexes were fitted with GPS collars and monitored for 7 months on a large sheep property in north Queensland, Australia. Wild dog incursions into the territories of adjacent wild dogs and maremmas were recorded. Wild dog territories never overlapped and their home ranges infrequently overlapped. In contrast, 713 hourly locations from 120 wild dog incursions into maremma territories were recorded, mostly from three wild dogs. These three wild dogs spent a mean of 2.5–5.9 h inside maremma territories during incursions. At this location, maremmas worked by guarding sheep and prohibiting fine-scale interaction between wild dogs and sheep, not by establishing a territory respected by wild dogs. We conclude that shepherding behaviour and boisterous vocalisations of guardian dogs combined with the flocking behaviour of sheep circumvents attacks on sheep but does not prevent nor discourage wild dogs from foraging in close proximity. Certain husbandry practices and the behaviour of sheep at parturition may incur greater predation risk.

Estudo da prevalência e da gravidade da dermatite de contacto em 'frango do campo'

O sector avícola enfrenta atualmente dois desafios muito estimulantes. O primeiro decorre do aumento, que se prevê continuar a crescer, nos níveis de procura de carne de aves no mercado interno e internacional; o segundo decorre do facto da criação avícola ter adotado métodos de produção mais intensivos (kg peso vivo/m2/ano) e em maior escala, i.e. com maior concentração animal na mesma exploração. Este carácter vincadamente “industrial” tem merecido uma natural atenção das sociedades e das autoridades pecuárias no sentido desta economia de escala passar a ter num conjunto de instrumentos legais e técnicos o devido contrapeso para a salvaguarda das aves enquanto ser vivo. O presente trabalho tem como ponto de partida a Directiva 2007/43/CE do Conselho de 28 de Junho, relativa ao estabelecimento de regras mínimas para a proteção de frangos de carne. Em virtude de não existir ainda informação suficiente sobre a forma como a qualidade do maneio animal pode ser monitorizada, ao nível do abate, por médicos veterinários e auxiliares oficiais, em frangos de criação especial segundo os modelos definidos no Regulamento (CE) n.º 543/2008, urge realizar estudos neste domínio. O principal objetivo da realização do presente trabalho de campo foi o estudo da ocorrência das dermatites de contacto plantar (pododermatites) e da bolsa sinovial préesternal em frangos produzidos em sistemas de produção considerados “protetores” do bem-estar animal, designadamente os seguintes: i) ar livre; e, ii) extensivo de interior. O estudo foi efetuado num centro de abate de frangos do campo, em Oliveira de Frades, entre Maio de 20012 e Março de 2013. Os animais abatidos foram criados em explorações com contratos de integração situadas no Distrito de Viseu. Os dados foram recolhidos em 39 bandos diferentes da espécie Gallus domesticus, dos quais 1021 carcaças foram avaliadas após evisceração, o que correspondeu ao exame de uma a cada quinze aves da linha de abate. Para a avaliação da pododermatite foi utilizado o método adaptado pela DGAV, enquanto para a avaliação da bursite esternal foi efetuada tendo em conta o modelo aplicado em perus por Berk em 2002. Apesar do modelo estatístico desenvolvido para a análise dos resultados obtidos no presente trabalho exigir um maior número de observações, foi possível identificar com grande precisão alguns fatores de risco que devem ser realçados pela sua relevância no contexto dos sistemas produtivos escrutinados ou no mecanismo fisiopatológico da dermatite de contacto, nomeadamente os seguintes: (i) a idade das aves que, apesar de não ter sido identificada uma relação directa com os scores de pododermatite e bursite, verificou-se que a idade elevada que os animais tipicamente atingem nos sistemas de produção extensivos está associada a uma taxa superior de rejeições pela inspecção sanitária; (ii) o peso pré-abate que, independentemente da inconsistência defendida por diversos autores em relação à influência do peso vivo do frango industrial sobre a dermatite de contacto, nos animais produzidos em regime extensivo, esta variável pode desempenhar um fator chave para a ocorrência desta lesão. De facto, há que realçar que o peso destes animais tem uma importância fulcral na modelação da biomecânica da ave, incluindo na pressão exercida sobre a superfície plantar; (iii) o tipo de sistema de abeberamento, tendo ficado demonstrado que a selecção do tipo de bebedouro tem uma importância peculiar sobre a ocorrência de pododermatite em “frango de campo”, algo que está provavelmente relacionado com a influência exercida sobre o teor de humidade da cama. Globalmente, as frequências de pododermatite e bursite apuradas neste trabalho devem ser consideradas inquietantes. Esta preocupação eleva-se quando se toma consciência que as aves provieram de regimes considerados “amigáveis” e “sustentáveis”, pelo que urge monitorizar adequadamente aqueles sistemas produtivos, melhorar as suas condições e reanalisar os benefícios ao nível do bem-estar animal.

Wheats developed for high yield on stored soil moisture have deep vigorous root systems

Many rainfed wheat production systems are reliant on stored soil water for some or all of their water inputs. Selection and breeding for root traits could result in a yield benefit; however, breeding for root traits has traditionally been avoided due to the difficulty of phenotyping mature root systems, limited understanding of root system development and function, and the strong influence of environmental conditions on the phenotype of the mature root system. This paper outlines an international field selection program for beneficial root traits at maturity using soil coring in India and Australia. In the rainfed areas of India, wheat is sown at the end of the monsoon into hot soils with a quickly receding soil water profile; in season water inputs are minimal. We hypothesised that wheat selected and bred for high yield under these conditions would have deep, vigorous root systems, allowing them to access and utilise the stored soil water at depth around anthesis and grain-filling when surface layers were dry. The Indian trials resulted in 49 lines being sent to Australia for phenotyping. These lines were ranked against 41 high yielding Australian lines. Variation was observed for deep root traits e.g. in eastern Australia in 2012, maximum depth ranged from 118.8 to 146.3 cm. There was significant variation for root traits between sites and years, however, several Indian genotypes were identified that consistently ranked highly across sites and years for deep rooting traits.

Production responses of reproducing ewes to a by-product-based diet inoculated with the probiotic Bacillus amyloliquefaciens strain H57

The potential application of the spore-forming probiotic Bacillus amyloliquefaciens strain H57 (H57) as a novel probiotic for ruminants was evaluated in reproducing ewes. Performance responses were determined by delivering H57 in a pelleted diet based mainly on palm kernel meal (PKM) and sorghum grain. PKM is an agro-industrial by-product with a reputation for poor palatability and the availability of the starch in sorghum grain can be limited in ruminants. The hypothesis was that H57 improves the feeding value of a relatively low quality concentrate diet. Twenty-four first-parity white Dorper ewes were fed PKM-based pellets manufactured with or without H57 (109 cfu/kg pellet) in late pregnancy. During this phase of late pregnancy, the H57 ewes ate 17% more dry matter (1019 vs 874 g/day, P = 0.03), gained more weight (194 vs 30 g/day, P = 0.008) and retained more nitrogen (6.13 vs 3.34 g/day, P = 0.01), but produced lambs with a similar birthweight (4.1 vs 4.2 kg, P = 0.73). Rumen fluid collected from H57 ewes in late pregnancy had higher pH (7.1 vs 6.8, P = 0.07), acetate : propionate ratio (3.4 vs 2.7, P = 0.04), lower ammonia (69 vs 147 mmol/L, P = 0.001) and total volatile fatty acid concentrations (40 vs 61 mg/L, P = 0.02). The digestibility of dry matter, organic matter and fibre were similar between the two groups. The lambs of the H57 ewes grew faster than those of the Control ewes for the first 21 days of lactation (349 vs 272 g/day, P = 0.03), but not thereafter. H57 can improve feed intake and maternal liveweight gain in late pregnancy of first-parity ewes fed a diet based on PKM.

Impacto del uso de los sistemas de alimentación a corral como estrategia para el engorde de bovinos para carne

El confinamiento estratégico de los bovinos Argentina es una herramienta muy útil para lograr la terminación de animales destinados al consumo interno y a la exportación. La utilidad de estos encierres consiste permitir un mejor aprovechamiento del forraje y reduciendo la edad a la faena. Para su aplicación es necesario considerar los factores que afectan su resultado económico tales como la característica de las dietas utilizadas, los niveles de consumo y la eficiencia de conversión. Esto interactúa a su vez con el tipo de animal a encerrar. Son dos los sistemas de confinamiento estratégico que van a ser considerados en esta presentación: los corrales de engorde o terminación y los de recría o engorde de los terneros posdete. La actividad del engorde a corral durante los últimos años, ha estado ligada a variaciones operadas en el precio del grano y del tipo de producto logrado. Hay variaciones atribuidas al cambio en las preferencias del consumidor y también al efecto de la concentración de las ventas de carne en determinadas bocas de expendio que exigen uniformidad en la entrega de animales y del tamaño de los cortes. Se comentan entonces algunos aspectos relevantes del engorde a corral americano y de los engordes a corral en Argentina, además de algunos factores que pueden afectar el resultado económico de la actividad. En cuanto al corral de recría, tiene como objetivo la mejora de la ganancia de peso durante esta etapa frente a condiciones de recría a pasto donde pueden existir limitantes en la cantidad y calidad del forraje producido. En esta presentación se hace el comentario y el análisis de los factores a tener en cuenta en los dos tipos de manejo de los animales a corral: los de terminación o engorde final y los de recría o engorde de terneros después del destete. En el primer caso, los efectos del sexo, la edad, la eficiencia de conversión, la raza, el estado nutricional previo, así como factores de la dieta en si mismo. En el segundo caso se analizan sobre todo los distintos tipos de terneros que pueden incorporar al sistema, así como el uso de diferentes dietas. El desarrollo de los encierres de terneros permitió diseñar nuevos sistemas de producción basados en un aumento de la carga, de la ganancia de peso, la modificación del peso final y los posibles cambios en el momento de terminación. En el caso de los corrales de terminación, han sido una herramienta muy útil para lograr la terminación de animales destinados al consumo interno como exportación.

Impacto de los forrajes conservados sobre los sistemas de cria vacuna

En los sistemas ganaderos pastoriles, el manejo de excedentes y déficits estacionales e interanuales de forraje mediante el uso de reservas forrajeras impacta sobre la eficiencia de utilización las pasturas (manejo, productividad, y cosecha), y consecuentemente sobre el desempeño animal y productividad del sistema. En este trabajo se reporta información sobre la productividad y calidad de distintos recursos forrajeros que se utilizan para la confección de forrajes conservados. Se presenta información sobre la respuesta animal esperada para distintos momentos de confección, tipos de reservas (henos vs. Silos) para distintas categorías de animales. Se hace particular énfasis en los puntos críticos para lograr reservas de buena calidad y sobre el uso de las reservas como suplemento de pasturas, en dietas de recría y dietas engorde a corral. Finalmente se destacan algunas deficiencias nutricionales comunes en las reservas forrajeras y su modo de corrección. Aunque es bien conocido que la confección de reservas forrajeras - silos y henos - es una herramienta para la intensificación de los sistemas ganaderos que impacta sobre la productividad individual y por hectárea del sistema, hay que tener en cuenta aspectos claves para la obtención de una reserva de buena calidad y optimizar la ventajas de las reservas en el sistema como son la productividad del material a utilizar, el momento de corte, la conservación y la utilización.

Integrative genomic, epigenetic and metabolomic characterization of beef from grass-fed Angus steers

Beef constitutes a main component of the American diet and still represent the principal source of protein in many parts of the world. Currently, the meat market is experiencing an important transformation; consumers are increasingly switching from consuming traditional beef to grass-fed beef. People recognized products obtained from grass-fed animals as more natural and healthy. However, the true variations between these two production systems regarding various aspects remain unclear. This dissertation provides information from closely genetically related animals, in order to decrease confounding factors, to explain several confused divergences between grain-fed and grass-fed beef. First, we examined the growth curve, important economic traits and quality carcass characteristics over four consecutive years in grain-fed and grass-fed animals, generating valuable information for management decisions and economic evaluation for grass-fed cattle operations. Second, we performed the first integrated transcriptomic and metabolomic analysis in grass-fed beef, detecting alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered β-oxidation. Results suggest that grass finished beef could possibly benefit consumer health from having lower total fat content and better lipid profile than grain-fed beef. Regarding animal welfare, grass-fed animals may experience less stress than grain-fed individuals as well. Finally, we contrasted the genome-wide DNA methylation of grass-fed beef against grain-fed beef using the methyl-CpG binding domain sequencing (MBD-Seq) method, identifying 60 differentially methylated regions (DMRs). Most of DMRs were located inside or upstream of genes and displayed increased levels of methylation in grass-fed individuals, implying a global DNA methylation increment in this group. Interestingly, chromosome 14, which has been associated with large effects on ADG, marbling, back fat, ribeye area and hot carcass weight in beef cattle, allocated the largest number of DMRs (12/60). The pathway analysis identified skeletal and muscular system as the preeminent physiological system and function, and recognized carbohydrates metabolism, lipid metabolism and tissue morphology among the highest ranked networks. Therefore, although we recognize some limitations and assume that additional examination is still required, this project provides the first integrative genomic, epigenetic and metabolomics characterization of beef produced under grass-fed regimen.

Effects of light quality supplied by light emitting diodes (LEDs) on microalgal production

Dissertação de mestrado, Aquacultura, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Hydro-Physical Characterization of Media Used in Agricultural Systems to Develop the Best Management Practices for operation of an Environmentally Sustainable Agricultural Enterprise

Florida is the second leading horticulture state in the United States with a total annual industry sale of over $12 Billion. Due to its competitive nature, agricultural plant production represents an extremely intensive practice with large amounts of water and fertilizer usage. Agrochemical and water management are vital for efficient functioning of any agricultural enterprise, and the subsequent nutrient loading from such agricultural practices has been a concern for environmentalists. A thorough understanding of the agrochemical and the soil amendments used in these agricultural systems is of special interest as contamination of soils can cause surface and groundwater pollution leading to ecosystem toxicity. The presence of fragile ecosystems such as the Everglades, Biscayne Bay and Big Cypress near enterprises that use such agricultural systems makes the whole issue even more imminent. Although significant research has been conducted with soils and soil mix, there is no acceptable method for determining the hydraulic properties of mixtures that have been subjected to organic and inorganic soil amendments. Hydro-physical characterization of such mixtures can facilitate the understanding of water retention and permeation characteristics of the commonly used mix which can further allow modeling of soil water interactions. The objective of this study was to characterize some of the locally and commercially available plant growth mixtures for their hydro-physical properties and develop mathematical models to correlate these acquired basic properties to the hydraulic conductivity of the mixture. The objective was also to model the response patterns of soil amendments present in those mixtures to different water and fertilizer use scenarios using the characterized hydro-physical properties with the help of Everglades-Agro-Hydrology Model. The presence of organic amendments helps the mixtures retain more water while the inorganic amendments tend to adsorb more nutrients due to their high surface area. The results of these types of characterization can provide a scientific basis for understanding the non-point source water pollution from horticulture production systems and assist in the development of the best management practices for the operation of environmentally sustainable agricultural enterprise

ASSESSMENT OF ENERGY CONSUMPTION IN GREENHOUSE PRODUCTION IN THE WEST REGION OF PORTUGAL

Greenhouse production is a very important activity in the West region of Portugal, with an area of approximately 800 ha where the regular production consists in two crops per year, one in winter-spring and the other in summer-autumn. Many growers are now prepared to better exploit market opportunities, since they know that the big export window opportunity is from June to September, when the production is difficult in other regions of south due to high temperatures. Grower’s use new and more productive varieties, either in soil or hydroponic systems, mostly in unheated greenhouses, naturally ventilated, and equipped with modern fertigation systems. Greenhouse production causes some environmental impacts due to the high use of inputs. Several improvements in technologies and crop practices may contribute to increase the use efficiency of resources, decreasing the negative environmental impacts. Greenhouse vegetable production in Northern EU countries is based on the supply of heating and differs significantly from the production system in the Southern EU countries. In the Northern countries, direct energy inputs, mostly for heating, are predominant while in the South the indirect energy input is also important, mainly associated with fertilizers, plastic cover materials and other auxiliary materials. The main objective of this work was to characterise the greenhouse production systems in the West region of Portugal, in order to evaluate the energetic consumptions (direct and indirect), the GHH emissions, the production costs and the farmer’s income. With this work the mostly important inputs were identified, allowing proposing alternative measures to improve efficiency and sustainability. All the data was obtained by surveys performed directly with growers, previously selected to be representative of the crop practices and greenhouse type of the region. However, more research should be performed in order to develop and to test technologies capable to improve resources use efficiency in greenhouse production.

Sistemas de produção de peixes e bivalves em aquacultura: crescimento e indicadores de qualidade

O presente relatório refere-se ao estágio curricular realizado na Estação Piloto de Piscicultura de Olhão, no período compreendido entre janeiro e julho de 2016, no âmbito do Mestrado Integrado em Medicina Veterinária da Universidade de Évora. Este trabalho divide-se em duas partes. A primeira parte descreve as atividades e respetiva casuística desenvolvidas nas diferentes áreas de produção aquícola. Na segunda parte é abordado o tema “Produção Aquícola de Peixes e Ostras em regime Semi-intensivo”, onde são enquadrados os conceitos relacionados com aquacultura, sistemas de produção e pesquisa de biomarcadores na qualidade e bem-estar animal. São ainda descritas as ações de acompanhamento, durante o estágio, de um projeto de investigação em sistemas de produção em tanques de terra exteriores e um caso clínico. Este relatório atesta a importância da Medicina Preventiva em aquacultura; Abstract: Fish and bivalve aquaculture production systems: growth and quality indicators The following report was elaborated after the externship conducted at the Olhão Pilot Aquaculture Station, between January and July of 2016, in order to fulfill the requirements for a Masters degree in Veterinary Medicine at the University of Évora. This report is divided in two parts. The first part contains a description of the developed activities and the casuistic at the different aquaculture production areas. The second part will focus on the development of the theme “Fish and Oyster aquaculture production in a semi-intensive culture system”, with a theoretical framework about aquaculture concepts, production systems and identifying biomarkers in animal healthcare. At last, are presented and supported the monitoring actions taken in an investigation study case about inshore production systems and a clinic case followed during the externship. This report attests the importance of Preventive Medicine in aquaculture.

Panicum maximum cv. Tanzânia: climate trends and regional pasture production in Brazil.

Projected change in forage production under a range of climate scenarios is important for the evaluation of the impacts of global climate change on pasture-based livestock production systems in Brazil. We evaluated the effects of regional climate trends on Panicum maximum cv. Tanzânia production, predicted by agro-meteorological model considering the sum of degree days and corrected by a water availa bility index. Data from Brazilian weather stations (1963?2009) were considered as the current climate (baseline), and future scenarios, based on contrasting scenarios interms of increased temperature and atmospheric CO2 concentrations (high and low increases), were determined for 2013?2040 (2025 scenario) and for 2043?2070 (2055 scenario). Predicted baseline scenarios indicated that there are regional and seasonal variations in P. maximum production related to variation intemperature and water availability during the year. Production was lower in the Northeast region and higher in the rainforest area. Total annual productionunder future climate scenarios was predicted toincrease by up to 20% for most of the Brazilian area, mainly due to temperature increase, according to each climate model and scenario evaluated. The highest increase in forage production is expected to be in the South, Southeast and Central-west areas of Brazil. In these regions, future climate scenarios will not lead to changes in the seasonal production, with largerincreases in productivity during the summer. Climate risk is expected to decrease, as the probability of occurrence of low forage productions will be lower. Due to the predicted increase in temperature and decrease in rainfall in the Northeast area, P. maximum production is expected to decrease, mainly when considering scenarios based on the PRECIS model for the 2055 scenario.