Seawater carbonate chemistry, growth rate and PIC and POC production during experiments with Emiliania huxleyi (B92/11), 2011

The coccolithophore Emiliania huxleyi was cultured under a broad range of carbonate chemistry conditions to distinguish the effects of individual carbonate system parameters on growth, primary production, and calcification. In the first experiment, alkalinity was kept constant and the fugacity of CO2(fCO2) varied from 2 to 600 Pa (1Pa ~ 10 µatm). In the second experiment, pH was kept constant (pHfree = 8) with fCO2 varying from 4 to 370 Pa. Results of the constant-alkalinity approach revealed physiological optima for growth, calcification, and organic carbon production at fCO2 values of ~20Pa, ~40 Pa, and ~80 Pa, respectively. Comparing this with the constant-pH approach showed that growth and organic carbon production increased similarly from low to intermediate CO2 levels but started to diverge towards higher CO2 levels. In the high CO2 range, growth rates and organic carbon production decreased steadily with declining pH at constant alkalinity while remaining consistently higher at constant pH. This suggests that growth and organic carbon production rates are directly related to CO2 at low (sub-saturating) concentrations, whereas towards higher CO2 levels they are adversely affected by the associated decrease in pH. A pH dependence at high fCO2 is also indicated for calcification rates, while the key carbonate system parameter determining calcification at low fCO2 remains unclear. These results imply that key metabolic processes in coccolithophores have their optima at different carbonate chemistry conditions and are influenced by different parameters of the carbonate system at both sides of the optimum.

Artificial neural network application in short-term prediction in an oscillating water column

Oscillating Water Column (OWC) is one type of promising wave energy devices due to its obvious advantage over many other wave energy converters: no moving component in sea water. Two types of OWCs (bottom-fixed and floating) have been widely investigated, and the bottom-fixed OWCs have been very successful in several practical applications. Recently, the proposal of massive wave energy production and the availability of wave energy have pushed OWC applications from near-shore to deeper water regions where floating OWCs are a better choice. For an OWC under sea waves, the air flow driving air turbine to generate electricity is a random process. In such a working condition, single design/operation point is nonexistent. To improve energy extraction, and to optimise the performance of the device, a system capable of controlling the air turbine rotation speed is desirable. To achieve that, this paper presents a short-term prediction of the random, process by an artificial neural network (ANN), which can provide near-future information for the control system. In this research, ANN is explored and tuned for a better prediction of the airflow (as well as the device motions for a wide application). It is found that, by carefully constructing ANN platform and optimizing the relevant parameters, ANN is capable of predicting the random process a few steps ahead of the real, time with a good accuracy. More importantly, the tuned ANN works for a large range of different types of random, process.

Seawater carbonate chemistry and net ecosystem calcification and production in a coral community Kaneohe Bay, Oahu, Hawaii, 2011

Net ecosystem calcification rates (NEC) and net photosynthesis (NP) were determined from CO2 seawater parameters on the barrier coral reef of Kaneohe Bay, Oahu, Hawaii. Autosamplers were deployed to collect samples on the barrier reef every 2 hours for six 48-hour deployments, two each in June 2008, August 2009, and January/February 2010. NEC on the Kaneohe Bay barrier reef increased throughout the day and decreased at night. Net calcification continued at low rates at night except for six time periods when net dissolution was measured. The barrier reef was generally net photosynthetic (positive NP) during the day and net respiring (negative NP) at night. NP controlled the diel cycles of the partial pressure of CO2 (pCO2) and aragonite saturation state resulting in high daytime aragonite saturation state levels when calcification rates were at their peak. However, the NEC and NP diel cycles can become decoupled for short periods of time (several hours) without affecting calcification rates. On a net daily basis, net ecosystem production (NEP) of the barrier reef was found to be sometimes net photosynthetic and sometimes net respiring and ranged from -378 to 80 mmol m-2 d-1 when calculated using simple box models. Daily NEC of the barrier reef was positive (net calcification) for all deployments and ranged from 174 to 331 mmol CaCO3 m-2 d-1. Daily NEC was strongly negatively correlated with average daily pCO2 (R2 = 0.76) which ranged from 431 to 622 µatm. Daily NEC of the Kaneohe Bay barrier reef is similar to or higher than daily NEC measured on other coral reefs even though aragonite saturation state levels (mean aragonite saturation state = 2.85) are some of the lowest measured in coral reef ecosystems. It appears that while calcification rate and ?arag are correlated within a single coral reef ecosystem, this relationship does not necessarily hold between different coral reef systems. It can be expected that ocean acidification will not affect coral reefs uniformly and that some may be more sensitive to increasing pCO2 levels than others.

Seawater carbonate chemistry, Mg/Ca, Sr/Ca, oxygen production and calcification rate during experiments with coral Pocillopora damicornis, 2011

The Sr/Ca of aragonitic coral skeletons is a commonly used palaeothermometer. However skeletal Sr/Ca is typically dominated by weekly-monthly oscillations which do not reflect temperature or seawater composition and the origins of which are currently unknown. To test the impact of transcellular Ca2+ transport processes on skeletal Sr/Ca, colonies of the branching coral, Pocillopora damicornis, were cultured in the presence of inhibitors of Ca-ATPase (ruthenium red) and Ca channels (verapamil hydrochloride). The photosynthesis, respiration and calcification rates of the colonies were monitored throughout the experiment. The skeleton deposited in the presence of the inhibitors was identified (by 42Ca spike) and analysed for Sr/Ca and Mg/Ca by secondary ion mass spectrometry. The Sr/Ca of the aragonite deposited in the presence of either of the inhibitors was not significantly different from that of the solvent (dimethyl sulfoxide) control, although the coral calcification rate was reduced by up to 66% and 73% in the ruthenium red and verapamil treatments, respectively. The typical precision (95% confidence limits) of mean Sr/Ca determinations within any treatment was <±1% and differences in skeletal Sr/Ca between treatments were correspondingly small. Either Ca-ATPase and Ca channels transport Sr2+ and Ca2+ in virtually the same ratio in which they are present in seawater or transcellular processes contribute little Ca2+ to the skeleton and most Ca is derived from seawater transported directly to the calcification site. Variations in the activities of Ca-ATPase and Ca-channels are not responsible for the weekly-monthly Sr/Ca oscillations observed in skeletal chronologies, assuming that the specificities of Ca transcellular transport processes are similar between coral genera.

La ética hacker frente al capitalismo netárquíco: software libre y peer production en las iniciativas de Economía Colaborativa en Andalucía

En los últimos años el término Economía Colaborativa se ha popularizado sin que, hasta el momento, haya sido definido de manera inequívoca. Bajo esta denominación se engloban experiencias tan diversas como bancos de tiempo, huertos urbanos, startups o grandes plataformas digitales. La proliferación de este tipo de iniciativas puede relacionarse con una multiplicidad de factores tales como el desarrollo tecnológico, la recesión económica y otras crisis superpuestas (medioambiental, de cuidados, de valores, de lo político) y un cierto cambio en los valores sociales. Entre 2014-2015 se han realizado dos investigaciones en Andalucía de manera casi paralela y con una metodología similar. La primera de ellas pretendía identificar prácticas de Economía Colaborativa en el entorno universitario. La segunda investigación identificaba experiencias de emprendimiento a nivel autonómico. A luz de los resultados obtenidos se plantea la siguiente cuestión sobre la naturaleza misma de la Economía Colaborativa: ¿nos encontramos ante prácticas postcapitalistas que abren el camino a una sociedad más justa e igualitaria o, más bien, estamos ante una respuesta del capital para, una vez más, seguir extrayendo de manera privada el valor que se genera socialmente? Este artículo, partiendo del análisis del conjunto de iniciativas detentadas en Andalucía, se centra en aquellas basadas en el software libre y la producción digital concluyendo cómo, gracias a la incorporación de ciertos aspectos de la ética hacker y las lógicas del conocimiento abierto, éstas pueden situarse dentro de un escenario de fomento de los comunes globales frente a las lógicas imperantes del capitalismo netárquico. 

D6.6 – Summary, Analysis, Road-mapping and Production of Training materials

This deliverable summarizes, validates and explains the purpose and concept behind the RAGE knowledge and innovation management platform as a self-sustainable Ecosystem, supporting innovation processes in the Applied Gaming (AG) industry. The Ecosystem portal will be developed with particular consideration of the demand and requirements of small and medium sized game developing companies, education providers and related stakeholders like AG researchers and AG end-users. The innovation potential of the new platform underlies the following factors: a huge, mostly entire collection of community specific knowledge (e.g., content like media objects, software components and best practices), a structured approach of knowledge access, search and browse, collaboration tools as well as social network analysis tools to foster efficient knowledge creation and transformation processes into marketable technology assets. The deliverable provides an overview of the current status and the remaining work to come, preceding the final version in month 48 of the RAGE project.

Opportunities and constraints of transhumant small ruminant production in the Chinese Altay Mountains

This PhD thesis focuses on current livelihoods of agro-pastoral livestock keepers, their animal nutrition, herd and rangeland management strategies. It thereby aims to contribute to sustainable rangeland management, livestock production and household income in Qinghe county of the Chinese Altay Mountain region, located in Xinjiang Uyghur Autonomous Region, PR China. In its first part the study characterizes the socio-economic situation and agricultural practices of agro-pastoralists through structured household interviews. The second part provides insights into the grazing behaviour and feed intake of small ruminants on seasonal pastures in this region, and into the quantitative and qualitative biomass offer on natural rangelands. The third part analyses the reproductive performance and annual growth of the local sheep and goat herds, and, by modelling improved feeding and culling strategies, tests herd management options that potentially improve the monetary output per female herd animal without increasing the pressure onto natural rangelands. Taken together, the results of the study suggest that, despite an increase and intensification of cropping and vegetable gardening in the region of Qinghe, livestock rearing is still the major livelihood strategy both in terms of prevalence and relative importance. However, livestock keeping is challenged by low biomass production on rangelands, due to the combined impact of high climate variability and highly localized grazing pressure on the seasonal pastures. Though government regulations try to tackle the latter aspect, their implementation is sometimes difficult. Alternatives to strict regulation of grazing periods and animal numbers on seasonal pastures are, in the case of goats, more rigorous culling strategies and, in the case of sheep and goats, strategic supplementation of the animals in the winter and spring season. However, for the latter strategy to become economically viable, an improvement of live animal and meat marketing options and an investment in local meat processing facilities that add value to the carcasses is needed. As the regional cities grow rapidly, the potential market to absorb diverse and good quality meat products is there, along with the road network connecting Qinghe county to the regional capital. Such governmental measures will not only create new job opportunities in the region but also benefit the cash income of pastoralists in this westernmost region of China.

Artificial Neural Network and Neutron Aplication in a Volume Fraction Calculation in Annular and Stratified Multiphase System

Multiphase flows, type oil–water-gas are very common among different industrial activities, such as chemical industries and petroleum extraction, and its measurements show some difficulties to be taken. Precisely determining the volume fraction of each one of the elements that composes a multiphase flow is very important in chemical plants and petroleum industries. This work presents a methodology able to determine volume fraction on Annular and Stratified multiphase flow system with the use of neutrons and artificial intelligence, using the principles of transmission/scattering of fast neutrons from a 241Am-Be source and measurements of point flow that are influenced by variations of volume fractions. The proposed geometries used on the mathematical model was used to obtain a data set where the thicknesses referred of each material had been changed in order to obtain volume fraction of each phase providing 119 compositions that were used in the simulation with MCNP-X –computer code based on Monte Carlo Method that simulates the radiation transport. An artificial neural network (ANN) was trained with data obtained using the MCNP-X, and used to correlate such measurements with the respective real fractions. The ANN was able to correlate the data obtained on the simulation with MCNP-X with the volume fractions of the multiphase flows (oil-water-gas), both in the pattern of annular flow as stratified, resulting in a average relative error (%) for each production set of: annular (air= 3.85; water = 4.31; oil=1.08); stratified (air=3.10, water 2.01, oil = 1.45). The method demonstrated good efficiency in the determination of each material that composes the phases, thus demonstrating the feasibility of the technique.

Survey of food network in Ovan Lake

Lake Ovan with about 9 hectares is regarded a semi-shallow lake with an average depth 5.2 meter. It is situated in Ghazvin Province, with a 1910 m high in mountainous regime. A monthly sampling was done at 3 stations studying the physicochemical and biological parameters in water and sediment at the Lake for a year. The temperature annual was measured 12.3°C and other parameters are pH as 8.8, oxygen 10, with total mean phosphate and nitrate as 0.14 & 0.8 mg/lit respectively. The chl.a mean was also measured 1.94 mg/lit. The ratio of N to P was calculated as 1:59, indicating a limiting factor for growth. Considering the trophic statues of the lake taking into account as above parameters, it is a mesotrophic lake with medium trophy. Altogether, 53 phytoplankton species were identified mostly diatoms, green algae and cyanobacteria. Although, 14 zooplankton species were identified with daphnia dominating the group. Macrobenthoses were also surveyed and 11 families were identified comprising mainly by Annelids, Gastropod, Bivalves and Insect Larvae. Other organisms were 2 dominate water plant including Phragmites australis covering at the edge of the lake and potamogeton sp in the inner parts, and also 2 fish species, common carp and Pike Perch. The diversity Shannon—Wiener index was calculated for main taxa groups with all figures lower than 3. Regarding the fish potential production of the lake based on Bramic & Lemke and morphoedophic index, it was calculated to be 20.4 kg/ha fish and a total of about 150 kg for the entire lake.

The “handwriting brain”: a motor/linguistic network with specialized “writing-specific” areas?

International audience

New Catalysts for the Renewable Production of Monomers for Bioplastics

Terephthalic acid (PTA) is one of the monomers used for the synthesis of the polyester, polyethylene terephthalate (PET), that is used for the large-scale manufacture of synthetic fibers and plastic bottles. PTA is largely produced from the liquid-phase oxidation of petroleum-derived p-xylene (PX). However, there are now ongoing worldwide efforts exploring alternative routes for producing PTA from renewable, biomass resources.

In this thesis, I present a new route to PTA starting from the biomass-derived platform chemical, 5-hydroxymethylfurfural (HMF). This route utilizes new, selective Diels-Alder-dehydration reactions involving ethylene and is advantageous over the previously proposed Diels-Alder-dehydration route to PTA from HMF via 2,5-dimethylfuran (DMF) since the H₂ reduction of HMF to DMF is avoided. Specifically, oxidized derivatives of HMF are reacted as is, or after etherification-esterification with methanol, with ethylene over solid Lewis acid catalysts that do not contain strong Brønsted acids in order to synthesize intermediates of PTA and its equally important diester, dimethyl terephthalate (DMT). The partially oxidized HMF, 5-(hydroxymethyl)furoic acid (HMFA) is reacted with high pressure ethylene over a pure-silica molecular sieve catalyst containing framework tin (Sn-Beta) to produce the Diels-Alder-dehydration product, 4-(hydroxymethyl)benzoic acid (HMBA), with ~30% selectivity at ~20% yield. If HMFA is protected with methanol to form methyl 5-(methoxymethyl)furan-2-carboxylate (MMFC), MMFC can react with ethylene in the presence of a pure-silica molecular sieve containing framework zirconium (Zr-Beta) to produce methyl 4-(methoxymethyl)benzenecarboxylate (MMBC) with >70% selectivity at >20% yield. HMBA and MMBC can then be oxidized to produce PTA and DMT, respectively. When Lewis acid containing mesoporous silica (MCM-41) and amorphous silica, or Brønsted acid containing zeolites (Al-Beta), are used as catalysts, a significant decrease in selectivity/yield of the Diels-Alder-dehydration product is observed.

An investigation to elucidate the reaction network and side products in the conversion of MMFC to MMBC was performed, and the main side products are found to be methyl 4-formylcyclohexa-1,3-diene-1-carboxylate and the ethylene Diels-Alder adduct of this cyclohexadiene. These products presumably form by a different dehydration pathway of the MMFC/ethylene Diels-Alder adduct and should be included when determining the overall selectivity to PTA or DMT since, like MMBC, these compounds are precursors to PTA or DMT.

Fundamental physical and chemical information on the ethylene Diels-Alder-dehydration reactions catalyzed by the Lewis acid-containing molecular sieves was obtained. Madon-Boudart experiments using Zr-Beta as catalyst show that the reaction rates are limited by chemical kinetics only (physical transport limitations are not present), all the Zr⁴⁺ centers are incorporated into the framework of the molecular sieve, and the whole molecular sieve crystal is accessible for catalysis. Apparent activation energies using Zr-Beta are low, suggesting that the overall activation energy of the system may be determined by a collection of terms and is not the true activation energy of a single chemical step.

Lot production size problem and simulation of urban transport

OBJECTIVES AND STUDY METHOD: There are two subjects in this thesis: “Lot production size for a parallel machine scheduling problem with auxiliary equipment” and “Bus holding for a simulated traffic network”. Although these two themes seem unrelated, the main idea is the optimization of complex systems. The “Lot production size for a parallel machine scheduling problem with auxiliary equipment” deals with a manufacturing setting where sets of pieces form finished products. The aim is to maximize the profit of the finished products. Each piece may be processed in more than one mold. Molds must be mounted on machines with their corresponding installation setup times. The key point of our methodology is to solve the single period lot-sizing decisions for the finished products together with the piece-mold and the mold-machine assignments, relaxing the constraint that a single mold may not be used in two machines at the same time. For the “Bus holding for a simulated traffic network” we deal with One of the most annoying problems in urban bus operations is bus bunching, which happens when two or more buses arrive at a stop nose to tail. Bus bunching reflects an unreliable service that affects transit operations by increasing passenger-waiting times. This work proposes a linear mathematical programming model that establishes bus holding times at certain stops along a transit corridor to avoid bus bunching. Our approach needs real-time input, so we simulate a transit corridor and apply our mathematical model to the data generated. Thus, the inherent variability of a transit system is considered by the simulation, while the optimization model takes into account the key variables and constraints of the bus operation. CONTRIBUTIONS AND CONCLUSIONS: For the “Lot production size for a parallel machine scheduling problem with auxiliary equipment” the relaxation we propose able to find solutions more efficiently, moreover our experimental results show that most of the solutions verify that molds are non-overlapping even if they are installed on several machines. We propose an exact integer linear programming, a Relax&Fix heuristic, and a multistart greedy algorithm to solve this problem. Experimental results on instances based on real-world data show the efficiency of our approaches. The mathematical model and the algorithm for the lot production size problem, showed in this research, can be used for production planners to help in the scheduling of the manufacturing. For the “Bus holding for a simulated traffic network” most of the literature considers quadratic models that minimize passenger-waiting times, but they are harder to solve and therefore difficult to operate by real-time systems. On the other hand, our methodology reduces passenger-waiting times efficiently given our linear programming model, with the characteristic of applying control intervals just every 5 minutes.

An interaction and network perspective of horizontal relationships in the portuguese pharmaceutical industry

Doutoramento em Gestão

COMPUTATIONAL PREDICTION OF THE SPORULATION NETWORK IN CLOSTRIDIUM THERMOCELLUM

Sporulation is a process in which some bacteria divide asymmetrically to form tough protective endospores, which help them to survive in a hazardous environment for a quite long time. The factors which can trigger this process are diverse. Heat, radiation, chemicals and lacking of nutrition can all lead to the formation of endospores. This phenomenon will lead to low productivity during industrial production. However, the sporulation mechanism in a spore-forming bacterium, Clostridium theromcellum, is still unclear. Therefore, if a regulation network of sporulation can be built, we may figure out ways to inhibit this process. In this study, a computational method is applied to predict the sporulation network in Clostridium theromcellum. A working sporulation network model with 40 new predicted genes and 4 function groups is built by using a network construction program, CINPER. 5 sets of microarray expression data in Clostridium theromcellum under different conditions have been collected. The analysis shows the predicted result is reasonable.

Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network

In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat-shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors.