Search results for: tomato yield prediction

Authors: Piotr Wadolowski, Grzegorz Krzesinski, Piotr Gutowski

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The aim of the presented investigation is to recognize the possible mechanical issues of mini-plate connection used to treat mandible fractures and to check the impact of different factors for the stresses and displacements within the bone-stabilizer system. The mini-plate osteosynthesis technique is a common type of internal fixation using metal plates connected to the fractured bone parts by a set of screws. The selected two types of plate application methodology used by maxillofacial surgeons were investigated in the work. Those patterns differ in location and number of plates. The bone geometry was modeled on the base of computed tomography scans of hospitalized patient done just after mini-plate application. The solid volume geometry consisting of cortical and cancellous bone was created based on gained cloud of points. Temporomandibular joint and muscle system were simulated to imitate the real masticatory system behavior. Finite elements mesh and analysis were performed by ANSYS software. To simulate realistic connection behavior nonlinear contact conditions were used between the connecting elements and bones. The influence of the initial compression of the connected bone parts or the gap between them was analyzed. Nonlinear material properties of the bone tissues and elastic-plastic model of titanium alloy were used. The three cases of loading assuming the force of magnitude of 100N acting on the left molars, the right molars and the incisors were investigated. Stress distribution within connecting plate shows that the compression of the bone parts in the connection results in high stress concentration in the plate and the screws, however the maximum stress levels do not exceed material (titanium) yield limit. There are no significant differences between negative offset (gap) and no-offset conditions. The location of the external force influences the magnitude of stresses around both the plate and bone parts. Two-plate system gives generally lower von Misses stress under the same loading than the one-plating approach. Von Mises stress distribution within the cortical bone shows reduction of high stress field for the cases without the compression (neutral initial contact). For the initial prestressing there is a visible significant stress increase around the fixing holes at the bottom mini-plate due to the assembly stress. The local stress concentration may be the reason of bone destruction in those regions. The performed calculations prove that the bone-mini-plate system is able to properly stabilize the fractured mandible bone. There is visible strong dependency between the mini-plate location and stress distribution within the stabilizer structure and the surrounding bone tissue. The results (stresses within the bone tissues and within the devices, relative displacements of the bone parts at the interface) corresponding to different models of the connection provide a basis for the mechanical optimization of the mini-plate connections. The results of the performed numerical simulations were compared to clinical observation. They provide information helpful for better understanding of the load transfer in the mandible with the stabilizer and for improving stabilization techniques.

Keywords: finite element modeling, mandible fracture, mini-plate connection, osteosynthesis

Procedia PDF Downloads 246

Authors: Beatriz González-rodrigo, Diego Hidalgo-leiva, Omar Flores, Claudia Germoso, Maribel Jiménez-martínez, Laura Navas-sánchez, Belén Orta, Nicola Tarque, Orlando Hernández- Rubio, Miguel Marchamalo, Juan Gregorio Rejas, Belén Benito-oterino

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Cities facing seismic hazard necessitate detailed risk assessments for effective urban planning and vulnerability identification, ensuring the safety and sustainability of urban infrastructure. Comprehensive studies involving seismic hazard, vulnerability, and exposure evaluations are pivotal for estimating potential losses and guiding proactive measures against seismic events. However, broad-scale traditional risk studies limit consideration of specific local threats and identify vulnerable housing within a structural typology. Achieving precise results at neighbourhood levels demands higher resolution seismic hazard exposure, and vulnerability studies. This research aims to bolster sustainability and safety against seismic disasters in three Central American and Caribbean capitals. It integrates geospatial techniques and artificial intelligence into seismic risk studies, proposing cost-effective methods for exposure data collection and damage prediction. The methodology relies on prior seismic threat studies in pilot zones, utilizing existing exposure and vulnerability data in the region. Emphasizing detailed building attributes enables the consideration of behaviour modifiers affecting seismic response. The approach aims to generate detailed risk scenarios, facilitating prioritization of preventive actions pre-, during, and post-seismic events, enhancing decision-making certainty. Detailed risk scenarios necessitate substantial investment in fieldwork, training, research, and methodology development. Regional cooperation becomes crucial given similar seismic threats, urban planning, and construction systems among involved countries. The outcomes hold significance for emergency planning and national and regional construction regulations. The success of this methodology depends on cooperation, investment, and innovative approaches, offering insights and lessons applicable to regions facing moderate seismic threats with vulnerable constructions. Thus, this framework aims to fortify resilience in seismic-prone areas and serves as a reference for global urban planning and disaster management strategies. In conclusion, this research proposes a comprehensive framework for seismic risk assessment in high-risk urban areas, emphasizing detailed studies at finer resolutions for precise vulnerability evaluations. The approach integrates regional cooperation, geospatial technologies, and adaptive fragility curve adjustments to enhance risk assessment accuracy, guiding effective mitigation strategies and emergency management plans.

Keywords: assessment, behaviour modifiers, emergency management, mitigation strategies, resilience, vulnerability

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Authors: Shlomit Paz, Meir Broza

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Cholera is an acute intestinal infection caused by ingestion of food or water contaminated with the bacterium Vibrio cholerae. It has a short incubation period and produces an enterotoxin that causes copious, painless, watery diarrhoea that can quickly lead to severe dehydration and death if treatment is not promptly given. In an epidemic, the source of the contamination is usually the feces of an infected person. The disease can spread rapidly in areas with poor treatment of sewage and drinking water. Cholera remains a global threat and is one of the key indicators of social development. An estimated 3-5 million cases and over 100,000 deaths occur each year around the world. The relevance of climatic events as causative factors for cholera epidemics is well known. However, the examination of the involvement of winds in intra-continental disease distribution is new. The study explore the hypothesis that the spreading of cholera epidemics may be related to the dominant wind direction over land by presenting the influence of the wind direction on windborn dissemination by flying insects, which may serve as vectors. Chironomids ("non-biting midges“) exist in the majority of freshwater aquatic habitats, especially in estuarine and organic-rich water bodies typical to Vibrio cholerae. Chironomid adults emerge into the air for mating and dispersion. They are highly mobile, huge in number and found frequently in the air at various elevations. The huge number of chironomid egg masses attached to hard substrate on the water surface, serve as a reservoir for the free-living Vibrio bacteria. Both male and female, while emerging from the water, may carry the cholera bacteria. In experimental simulation, it was demonstrated that the cholera-bearing adult midges are carried by the wind, and transmit the bacteria from one body of water to another. In our previous study, the geographic diffusions of three cholera outbreaks were examined through their linkage with the wind direction: a) the progress of Vibrio cholerae O1 biotype El Tor in Africa during 1970–1971 and b) again in 2005–2006; and c) the rapid spread of Vibrio cholerae O139 over India during 1992–1993. Using data and map of cholera dissemination (WHO database) and mean monthly SLP and geopotential data (NOAA NCEP-NCAR database), analysis of air pressure data at sea level and at several altitudes over Africa, India and Bangladesh show a correspondence between the dominant wind direction and the intra-continental spread of cholera. The results support the hypothesis that aeroplankton (the tiny life forms that float in the air and that may be caught and carried upward by the wind, landing far from their origin) carry the cholera bacteria from one body of water to an adjacent one. In addition to these findings, the current follow-up study will present new results regarding the possible involvement of winds in the spreading of cholera in recent outbreaks (2010-2013). The findings may improve the understanding of how climatic factors are involved in the rapid distribution of new strains throughout a vast continental area. Awareness of the aerial transfer of Vibrio cholerae may assist health authorities by improving the prediction of the disease’s geographic dissemination.

Keywords: cholera, Vibrio cholerae, wind direction, Vibrio cholerae dissemination

Procedia PDF Downloads 367

Authors: Alex J. Summers, Jasmine P. Devadhasan, Douglas Montgomery, Brittany Fischer, Jian Gu, Frederic Zenhausern

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Immunoassays have been utilized for several applications, including the detection of pathogens. Our laboratory is in the development of a tier 1 biothreat panel utilizing Vertical Flow Assay (VFA) technology for simultaneous detection of pathogens and toxins. One method of manufacturing VFA membranes is with non-contact piezoelectric dispensing, which provides advantages, such as low-volume and rapid dispensing without compromising the structural integrity of antibody or substrate. Challenges of this processinclude premature discontinuation of dispensing and misaligned spotting. Preliminary data revealed the Yp 11C7 mAb (11C7)reagent to exhibit a large angle of failure during printing which may have contributed to variable printing outputs. A Design of Experiment (DOE) was executed using this reagent to investigate the effects of hydrostatic pressure and reagent concentration on microarray printing outputs. A Nano-plotter 2.1 (GeSIM, Germany) was used for printing antibody reagents ontonitrocellulose membrane sheets in a clean room environment. A spotting plan was executed using Spot-Front-End software to dispense volumes of 11C7 reagent (20-50 droplets; 1.5-5 mg/mL) in a 6-test spot array at 50 target membrane locations. Hydrostatic pressure was controlled by raising the Pressure Compensation Vessel (PCV) above or lowering it below our current working level. It was hypothesized that raising or lowering the PCV 6 inches would be sufficient to cause either liquid accumulation at the tip or discontinue droplet formation. After aspirating 11C7 reagent, we tested this hypothesis under stroboscope.75% of the effective raised PCV height and of our hypothesized lowered PCV height were used. Humidity (55%) was maintained using an Airwin BO-CT1 humidifier. The number and quality of membranes was assessed after staining printed membranes with dye. The droplet angle of failure was recorded before and after printing to determine a “stroboscope score” for each run. The DOE set was analyzed using JMP software. Hydrostatic pressure and reagent concentration had a significant effect on the number of membranes output. As hydrostatic pressure was increased by raising the PCV 3.75 inches or decreased by lowering the PCV -4.5 inches, membrane output decreased. However, with the hydrostatic pressure closest to equilibrium, our current working level, membrane output, reached the 50-membrane target. As the reagent concentration increased from 1.5 to 5 mg/mL, the membrane output also increased. Reagent concentration likely effected the number of membrane output due to the associated dispensing volume needed to saturate the membranes. However, only hydrostatic pressure had a significant effect on stroboscope score, which could be due to discontinuation of dispensing, and thus the stroboscope check could not find a droplet to record. Our JMP predictive model had a high degree of agreement with our observed results. The JMP model predicted that dispensing the highest concentration of 11C7 at our current PCV working level would yield the highest number of quality membranes, which correlated with our results. Acknowledgements: This work was supported by the Chemical Biological Technologies Directorate (Contract # HDTRA1-16-C-0026) and the Advanced Technology International (Contract # MCDC-18-04-09-002) from the Department of Defense Chemical and Biological Defense program through the Defense Threat Reduction Agency (DTRA).

Keywords: immunoassay, microarray, design of experiment, piezoelectric dispensing

Procedia PDF Downloads 182

Authors: Jungyeol Hong, Dongjoo Park

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The primary purpose of this study is to develop a methodological framework to predict daily subway ridership at a station-level and to examine the association between subway ridership and bus demand incorporating commercial business facility in the vicinity of each subway station. The socio-economic characteristics, land-use, and built environment as factors may have an impact on subway ridership. However, it should be considered not only the endogenous relationship between bus and subway demand but also the characteristics of commercial business within a subway station’s sphere of influence, and integrated transit network topology. Regarding a statistical approach to estimate subway ridership at a station level, therefore it should be considered endogeneity and heteroscedastic issues which might have in the subway ridership prediction model. This study focused on both discovering the impacts of bus demand, commercial business characteristics, and network topology on subway ridership and developing more precise subway ridership estimation accounting for its statistical bias. The spatial scope of the study covers entire Seoul city in South Korea and includes 243 stations with the temporal scope set at twenty-four hours with one-hour interval time panels each. The data for subway and bus ridership was collected Seoul Smart Card data from 2015 and 2016. Three-Stage Least Square(3SLS) approach was applied to develop daily subway ridership model as capturing the endogeneity and heteroscedasticity between bus and subway demand. Independent variables incorporating in the modeling process were commercial business characteristics, social-economic characteristics, safety index, transit facility attributes, and dummies for seasons and time zone. As a result, it was found that bus ridership and subway ridership were endogenous each other and they had a significantly positive sign of coefficients which means one transit mode could increase another transportation mode’s ridership. In other words, two transit modes of subway and bus have a mutual relationship instead of the competitive relationship. The commercial business characteristics are the most critical dimension among the independent variables. The variables of commercial business facility rate in the paper containing six types; medical, educational, recreational, financial, food service, and shopping. From the model result, a higher rate in medical, financial buildings, shopping, and food service facility lead to increment of subway ridership at a station, while recreational and educational facility shows lower subway ridership. The complex network theory was applied for estimating integrated network topology measures that cover the entire Seoul transit network system, and a framework for seeking an impact on subway ridership. The centrality measures were found to be significant and showed a positive sign indicating higher centrality led to more subway ridership at a station level. The results of model accuracy tests by out of samples provided that 3SLS model has less mean square error rather than OLS and showed the methodological approach for the 3SLS model was plausible to estimate more accurate subway ridership. Acknowledgement: This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Science and ICT (2017R1C1B2010175).

Keywords: subway ridership, bus ridership, commercial business characteristic, endogeneity, network topology

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Authors: Sagar Saroha, Sawan S. Sinha, Sunil Lakshmipathy

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Reynolds averaged Navier-Stokes (RANS) model is the popular computational tool for prediction of turbulent flows. Being computationally less expensive as compared to direct numerical simulation (DNS), RANS has received wide acceptance in industry and research community as well. However, for high Reynolds number flows, the traditional RANS approach based on the Boussinesq hypothesis is incapacitated to capture all the essential flow characteristics, and thus, its performance is restricted in high Reynolds number flows of practical interest. RANS performance turns out to be inadequate in regimes like flow over curved surfaces, flows with rapid changes in the mean strain rate, duct flows involving secondary streamlines and three-dimensional separated flows. In the recent decade, partially averaged Navier-Stokes (PANS) methodology has gained acceptability among seamless bridging methods of turbulence- placed between DNS and RANS. PANS methodology, being a scale resolving bridging method, is inherently more suitable than RANS for simulating turbulent flows. The superior ability of PANS method has been demonstrated for some cases like swirling flows, high-speed mixing environment, and high Reynolds number turbulent flows. In our work, we intend to evaluate PANS in case of separated turbulent flows past bluff bodies -which is of broad aerodynamic research and industrial application. PANS equations, being derived from base RANS, continue to inherit the inadequacies from the parent RANS model based on linear eddy-viscosity model (LEVM) closure. To enhance PANS’ capabilities for simulating separated flows, the shortcomings of the LEVM closure need to be addressed. Inabilities of the LEVMs have inspired the development of non-linear eddy viscosity models (NLEVM). To explore the potential improvement in PANS performance, in our study we evaluate the PANS behavior in conjugation with NLEVM. Our work can be categorized into three significant steps: (i) Extraction of PANS version of NLEVM from RANS model, (ii) testing the model in the homogeneous turbulence environment and (iii) application and evaluation of the model in the canonical case of separated non-homogeneous flow field (flow past prismatic bodies and bodies of revolution at high Reynolds number). PANS version of NLEVM shall be derived and implemented in OpenFOAM -an open source solver. Homogeneous flows evaluation will comprise the study of the influence of the PANS’ filter-width control parameter on the turbulent stresses; the homogeneous analysis performed over typical velocity fields and asymptotic analysis of Reynolds stress tensor. Non-homogeneous flow case will include the study of mean integrated quantities and various instantaneous flow field features including wake structures. Performance of PANS + NLEVM shall be compared against the LEVM based PANS and LEVM based RANS. This assessment will contribute to significant improvement of the predictive ability of the computational fluid dynamics (CFD) tools in massively separated turbulent flows past bluff bodies.

Keywords: bridging methods of turbulence, high Re-CFD, non-linear PANS, separated turbulent flows

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Authors: Mohamed Ahmed Tony, Mohamed Hamoud

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The present study was conducted to determine the effect of commercially coated slow-release sodium butyrate (CM3000®) as a feed additive on zootechnical performance, immune status and Clostridium perfringens severity after experimental infection. Three hundred 1-d-old broiler chicks (Cobb 500) were randomly distributed into 3 treatment groups (4 replicates each) using 25 chicks per replicate on floor pens. Control (C) birds were offered non-supplemented basal diets. Treatments 1 and 2 (T1 and T2) were fed diets containing CM3000® at 300 and 500 g/ton feed, respectively, during the entire experimental period (35 days). Feed and water were offered ad-libitum. Feed consumption and body weight were recorded weekly to calculate body weight gain and feed conversion. Blood samples were collected to evaluate the immune status of the birds against Newcastle disease vaccines using HI test. At the end of the experimental period, 20 birds were chosen randomly from each group (5 birds from each pen) to compare carcass yield. At day 16 of age 20 birds from each group (5 birds/replicate) were bacteriologically examined and proved to be free from Clostridium perfringens. The isolated birds were challenged orally with 1 ml buffer containing 106 CFU/ml Clostridium perfringens local isolate and prepared from necrotic enteritis (NE) diseased farms. Birds were observed on a regular basis daily for any signs of NE. Birds that died in the challenged group were necropsied to determine the cause of death. On day 28 of age, the surviving chickens were killed by cervical dislocation and necropsied immediately. Intestinal tracts were removed and intestinal lesions were scored. Tissue samples of the duodenum, jejunum, ileum and cecum for histopathological examination were collected. All collected data were statistically analyzed using IBM SPSS® version 19 software for personal computers. Means were compared by one-way ANOVA (P<0.05) followed by the Duncan Post Hoc test. The results revealed that body weight gain was significantly (P<0.05) improved in chicks fed on both doses of CM3000® compared to the control one. Final body weight gain in T1 and T2 were 2064.94 and 2141.37 g/bird, respectively, while in the control group, the weight gain showed 1952.78 g/bird. In addition, supplementation of diets with CM3000® increased significantly feed intake (P<0.05). Total feed intake in T1 and T2 were 3186.32 and 3273.29 g/bird, respectively; however, feed intake in the control group recorded 3081.95 g/bird. The best feed conversion was recorded in T2 group (1.53). Feed conversion in the control and T1 groups were 1.58 and 1.54, respectively. Dressing percentage, liver weights and the other carcasses yields were not different between treatments. The butyrate significantly enhanced immune responses measured against Newcastle disease vaccines. Sodium butyrate significantly reduced NE lesions and healthy improved the intestinal tissues in the samples collected from T1 and T2-challenged chickens versus those collected from the control group. In conclusion, exogenous administration of slow-release butyrate (CM3000®) is capable of improving performance, enhancing immunity and NE disease resistance in broiler chickens.

Keywords: sodium butyrate, broiler chicken, zootechnical performance, immunity, necrotic enteritis

Procedia PDF Downloads 84

Authors: Babak Forouraghi

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A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of the flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on the spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts, as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with an attention mechanism. In previous works on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work, with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on the presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: machine learning, classification and regression, gene circuit design, bidirectional transformers

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Authors: Krzysztof Skiba, Zbigniew Czyz, Ksenia Siadkowska, Piotr Borowiec

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The article presents selected concepts of technologies that use intelligent materials in aircraft in order to improve their performance. Most of the research focuses on solutions that improve the performance of fixed wing aircraft due to related to their previously dominant market share. Recently, the development of the rotorcraft has been intensive, so there are not only helicopters but also gyroplanes and unmanned aerial vehicles using rotors and vertical take-off and landing. There are many different technologies to change a shape of the aircraft or its elements. Piezoelectric, deformable actuator systems can be applied in the system of an active control of vibration dampening in the aircraft tail structure. Wires made of shape memory alloys (SMA) could be used instead of hydraulic cylinders in the rear part of the aircraft flap. The aircraft made of intelligent materials (piezoelectrics and SMA) is one of the NASA projects which provide the possibility of changing a wing shape coefficient by 200%, a wing surface by 50%, and wing deflections by 20 degrees. Active surfaces made of shape memory alloys could be used to control swirls in the flowing stream. An intelligent control system for helicopter blades is a method for the active adaptation of blades to flight conditions and the reduction of vibrations caused by the rotor. Shape memory alloys are capable of recovering their pre-programmed shapes. They are divided into three groups: nickel-titanium-based, copper-based, and ferromagnetic. Due to the strongest shape memory effect and the best vibration damping ability, a Ni-Ti alloy is the most commercially important. The subject of this work was to prepare a conceptual design of a rotor blade with SMA actuators. The scope of work included 3D design of the supporting rotor blade, 3D design of beams enabling to change the geometry by changing the angle of rotation and FEM (Finite Element Method) analysis. The FEM analysis was performed using NX 12 software in the Pre/Post module, which includes extended finite element modeling tools and visualizations of the obtained results. Calculations are presented for two versions of the blade girders. For FEM analysis, three types of materials were used for comparison purposes (ABS, aluminium alloy 7057, steel C45). The analysis of internal stresses and extreme displacements of crossbars edges was carried out. The internal stresses in all materials were close to the yield point in the solution of girder no. 1. For girder no. 2 solution, the value of stresses decreased by about 45%. As a result of the displacement analysis, it was found that the best solution was the ABS girder no. 1. The displacement of about 0.5 mm was obtained, which resulted in turning the crossbars (upper and lower) by an angle equal to 3.59 degrees. This is the largest deviation of all the tests. The smallest deviation was obtained for beam no. 2 made of steel. The displacement value of the second girder solution was approximately 30% lower than the first solution. Acknowledgement: This work has been financed by the Polish National Centre for Research and Development under the LIDER program, Grant Agreement No. LIDER/45/0177/L-9/17/NCBR/2018.

Keywords: aircraft, helicopters, shape memory alloy, SMA, smart material, unmanned aerial vehicle, UAV

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Authors: Raham El-Kahlout, Hadi Yassin, Asmaa Athani, Marwan Abou Madi, Gheyath Nasrallah

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Background: Since its first isolation in September 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has diffused across 27 countries infecting more than two thousand individuals with a high case fatality rate. MERS-CoV–specific antibodies are widely found in Dromedary camel along with viral shedding of similar viruses detected in human at same region, suggesting that MERS epidemiology may be central role by camel. Interestingly, MERS-CoV has also been also reported to be asymptomatic or to cause influenza-like mild illnesses. Therefore, in a country like Qatar (bordered Saudi Arabia), where camels are widely spread, serological surveys are important to explore the role of camels in MERS-CoV transmission. However, widespread strategic serological surveillances of MERS-CoV among populations, particularly in endemic country, are infrequent. In the absence of clear epidemiological view, cross-sectional MERS antibody surveillances in human populations are of global concern. Method: We performed a comparative serological screening of 4719 healthy blood donors, 135 baseline case contacts (high risk individual), and four MERS confirmed patients (by PCR) for the presence of anti-MERS IgG. Initially, samples were screened using Euroimmune anti- MERS-CoV IgG ELISA kit, the only commercial kit available in the market and recommended by the CDC as a screening kit. To confirm ELISA test results, farther serological testing was performed for all borderline and positive samples using two assays; the anti MERS-CoV IgG and IgM Euroimmune indirect immunofluorescent test (IIFT) and pseudoviral particle neutralizing assay (PPNA). Additionally, to test cross reactivity of anti-MERS-CoV antibody with other family members of coronavirus, borderline and positive samples were tested for the presence of the of IgG antibody of the following viruses; SARS, HCoV-229E, HKU1 using the Euroimmune IIFT for SARS and HCoV-229E and ELISA for HKU1. Results: In all of 4858 screened 15 samples [10 donors (0.21%, 10/4719), 1 case contact (0.77 %, 1/130), 3 patients (75%, 3/4)] anti-MERS IgG reactive/borderline samples were seen in ELISA. However, only 7 (0.14%) of them gave positive with in IIFT and only 3 (0.06%) was confirmed by the specific anti-MERS PPNA. One of the interesting findings was, a donor, who was selected in the control group as a negative anti-MERS IgG ELISA, yield reactive for anti-MERS IgM IIFT and was confirmed with the PPNA. Further, our preliminary results showed that there was a strong cross reactivity between anti- MERS-COV IgG with both HCoV-229E or anti-HKU1 IgG, yet, no cross reactivity of SARS were found. Conclusions: Our findings suggest that MERS-CoV is not heavily circulated among the population of Qatar and this is also indicated by low number of confirmed cases (only 18) since 2012. Additionally, the presence of antibody of other pathogenic human coronavirus may cause false positive results of both ELISA and IIFT, which stress the need for more evaluation studies for the available serological assays. Conclusion: this study provides an insight about the epidemiological view for MERS-CoV in Qatar population. It also provides a performance evaluation for the available serologic tests for MERS-CoV in a view of serologic status to other human coronaviruses.

Keywords: seroprevalence, MERS-CoV, healthy individuals, Qatar

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Authors: Juan A. Arzate, Funda C. Ertem, M. Nicolas Cruz-Bournazou, Peter Neubauer, Stefan Junne

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— One of the biggest challenges the world faces today is global warming that is caused by greenhouse gases (GHGs) coming from the combustion of fossil fuels for energy generation. In order to mitigate climate change, the European Union has committed to reducing GHG emissions to 80–95% below the level of the 1990s by the year 2050. Renewable technologies are vital to diminish energy-related GHG emissions. Since water and biomass are limited resources, the largest contributions to renewable energy (RE) systems will have to come from wind and solar power. Nevertheless, high proportions of fluctuating RE will present a number of challenges, especially regarding the need to balance the variable energy demand with the weather dependent fluctuation of energy supply. Therefore, biogas plants in this content would play an important role, since they are easily adaptable. Feedstock availability varies locally or seasonally; however there is a lack of knowledge in how biogas plants should be operated in a stable manner by local feedstock. This problem may be prevented through suitable control strategies. Such strategies require the development of convenient mathematical models, which fairly describe the main processes. Modelling allows us to predict the system behavior of biogas plants when different feedstocks are used with different loading rates. Life cycle assessment (LCA) is a technique for analyzing several sides from evolution of a product till its disposal in an environmental point of view. It is highly recommend to use as a decision making tool. In order to achieve suitable strategies, the combination of a flexible energy generation provided by biogas plants, a secure production process and the maximization of the environmental benefits can be obtained by the combination of process modelling and LCA approaches. For this reason, this study focuses on the biogas plant which flexibly generates required energy from the co-digestion of maize, grass and cattle manure, while emitting the lowest amount of GHG´s. To achieve this goal AMOCO model was combined with LCA. The program was structured in Matlab to simulate any biogas process based on the AMOCO model and combined with the equations necessary to obtain climate change, acidification and eutrophication potentials of the whole production system based on ReCiPe midpoint v.1.06 methodology. Developed simulation was optimized based on real data from operating biogas plants and existing literature research. The results prove that AMOCO model can successfully imitate the system behavior of biogas plants and the necessary time required for the process to adapt in order to generate demanded energy from available feedstock. Combination with LCA approach provided opportunity to keep the resulting emissions from operation at the lowest possible level. This would allow for a prediction of the process, when the feedstock utilization supports the establishment of closed material circles within a smart bio-production grid – under the constraint of minimal drawbacks for the environment and maximal sustainability.

Keywords: AMOCO model, GHG emissions, life cycle assessment, modelling

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Authors: Aditi Chitharanjan Parmar, Marco Gottardo, Giulia Adele Tuci, Francesco Valentino

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The generation of urban organic waste is a significant environmental problem due to the potential release of leachate and/or methane into the environment. This contributes to climate change, discharging a valuable resource that could be used in various ways. This research addresses this issue by proposing a two-step approach by linking biowaste management to aquaculture industry via single cell proteins (SCP) production. A mixture of food waste and municipal sewage sludge (FW-MSS) was firstly subjected to a mesophilic (37°C) anaerobic fermentation to produce a liquid stream rich in short-chain fatty acids (SCFAs), which are important building blocks for the following microbial biomass growth. In the frame of stable fermentation activity (after 1 week of operation), the average value of SCFAs was 21.3  0.4 g COD/L, with a CODSCFA/CODSOL ratio of 0.77 COD/COD. This indicated the successful strategy to accumulate SCFAs from the biowaste mixture by applying short hydraulic retention time (HRT; 4 days) and medium organic loading rate (OLR; 7 – 12 g VS/L d) in the lab-scale (V = 4 L) continuous stirred tank reactor (CSTR). The SCFA-rich effluent was then utilized as feedstock for the growth of a mixed microbial consortium able to store polyhydroxyalkanoates (PHA), a class of biopolymers completely biodegradable in nature and produced as intracellular carbon/energy source. Given the demonstrated properties of the intracellular PHA as antimicrobial and immunomodulatory effect on various fish species, the PHA-producing culture was intended to be utilized as SCP in aquaculture. The growth of PHA-storing biomass was obtained in a 2-L sequencing batch reactor (SBR), fully aerobic and set at 25°C; to stimulate a certain storage response (PHA production) in the cells, the feast-famine conditions were adopted, consisting in an alternation of cycles during which the biomass was exposed to an initial abundance of substrate (feast phase) followed by a starvation period (famine phase). To avoid the proliferation of other bacteria not able to store PHA, the SBR was maintained at low HRT (2 days). Along the stable growth of the mixed microbial consortium (the growth yield was estimated to be 0.47 COD/COD), the feast-famine strategy enhanced the PHA production capacity, leading to a final PHA content in the biomass equal to 16.5 wt%, which is suitable for the use as SCP. In fact, by incorporating the waste-derived PHA-rich biomass into fish feed at 20 wt%, the final feed could contain a PHA content around 3.0 wt%, within the recommended range (0.2–5.0 wt%) for promoting fish health. Proximate analysis of the PHA-rich biomass revealed a good crude proteins level (around 51 wt%) and the presence of all the essential amino acids (EAA), together accounting for 31% of the SCP total amino acid composition. This suggested that the waste-derived SCP was a source of good quality proteins with a good nutritional value. This approach offers a sustainable solution for urban waste management, potentially establishing a sustainable waste-to-value conversion route by connecting waste management to the growing aquaculture and fish feed production sectors.

Keywords: feed supplement, nutritional value, polyhydroxyalkanoates (PHA), single cell protein (SCP), urban organic waste.

Procedia PDF Downloads 42

Authors: F. Tang, S. Boskovich, A. Raheja, Z. Aliyazicioglu, S. Bhandari, N. Tsuchiya

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Calpoly Autonomous Transportation Experience (CATE) is a driverless vehicle that we are developing to provide safe, accessible, and efficient transportation of passengers throughout the Cal Poly Pomona campus for events such as orientation tours. Unlike the other self-driving vehicles that are usually developed to operate with other vehicles and reside only on the road networks, CATE will operate exclusively on walk-paths of the campus (potentially narrow passages) with pedestrians traveling from multiple locations. Safety becomes paramount as CATE operates within the same environment as pedestrians. As driverless vehicles assume greater roles in today’s transportation, this project will contribute to autonomous driving with pedestrian traffic in a highly dynamic environment. The CATE project requires significant interdisciplinary work. Researchers from mechanical engineering, electrical engineering and computer science are working together to attack the problem from different perspectives (hardware, software and system). In this abstract, we describe the software aspects of the project, with a focus on the requirements and the major components. CATE shall provide a GUI interface for the average user to interact with the car and access its available functionalities, such as selecting a destination from any origin on campus. We have developed an interface that provides an aerial view of the campus map, the current car location, routes, and the goal location. Users can interact with CATE through audio or manual inputs. CATE shall plan routes from the origin to the selected destination for the vehicle to travel. We will use an existing aerial map for the campus and convert it to a spatial graph configuration where the vertices represent the landmarks and edges represent paths that the car should follow with some designated behaviors (such as stay on the right side of the lane or follow an edge). Graph search algorithms such as A* will be implemented as the default path planning algorithm. D* Lite will be explored to efficiently recompute the path when there are any changes to the map. CATE shall avoid any static obstacles and walking pedestrians within some safe distance. Unlike traveling along traditional roadways, CATE’s route directly coexists with pedestrians. To ensure the safety of the pedestrians, we will use sensor fusion techniques that combine data from both lidar and stereo vision for obstacle avoidance while also allowing CATE to operate along its intended route. We will also build prediction models for pedestrian traffic patterns. CATE shall improve its location and work under a GPS-denied situation. CATE relies on its GPS to give its current location, which has a precision of a few meters. We have implemented an Unscented Kalman Filter (UKF) that allows the fusion of data from multiple sensors (such as GPS, IMU, odometry) in order to increase the confidence of localization. We also noticed that GPS signals can easily get degraded or blocked on campus due to high-rise buildings or trees. UKF can also help here to generate a better state estimate. In summary, CATE will provide on-campus transportation experience that coexists with dynamic pedestrian traffic. In future work, we will extend it to multi-vehicle scenarios.

Keywords: driverless vehicle, path planning, sensor fusion, state estimate

Procedia PDF Downloads 144

Authors: Yury S. Shpanskiy, Boris V. Kuteev

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Development of a fusion-fission hybrid facility based on superconducting conventional tokamak DEMO-FNS runs in Russia since 2013. The main design goal is to reach the technical feasibility and outline prospects of industrial hybrid technologies providing the production of neutrons, fuel nuclides, tritium, high-temperature heat, electricity and subcritical transmutation in Fusion-Fission Hybrid Systems. The facility should operate in a steady-state mode at the fusion power of 40 MW and fission reactions of 400 MW. Major tokamak parameters are the following: major radius R=3.2 m, minor radius a=1.0 m, elongation 2.1, triangularity 0.5. The design provides the neutron wall loading of ~0.2 MW/m², the lifetime neutron fluence of ~2 MWa/m², with the surface area of the active cores and tritium breeding blanket ~100 m². Core plasma modelling showed that the neutron yield ~10¹⁹ n/s is maximal if the tritium/deuterium density ratio is 1.5-2.3. The design of the electromagnetic system (EMS) defined its basic parameters, accounting for the coils strength and stability, and identified the most problematic nodes in the toroidal field coils and the central solenoid. The EMS generates toroidal, poloidal and correcting magnetic fields necessary for the plasma shaping and confinement inside the vacuum vessel. EMC consists of eighteen superconducting toroidal field coils, eight poloidal field coils, five sections of a central solenoid, correction coils, in-vessel coils for vertical plasma control. Supporting structures, the thermal shield, and the cryostat maintain its operation. EMS operates with the pulse duration of up to 5000 hours at the plasma current up to 5 MA. The vacuum vessel (VV) is an all-welded two-layer toroidal shell placed inside the EMS. The free space between the vessel shells is filled with water and boron steel plates, which form the neutron protection of the EMS. The VV-volume is 265 m³, its mass with manifolds is 1800 tons. The nuclear blanket of DEMO-FNS facility was designed to provide functions of minor actinides transmutation, tritium production and enrichment of spent nuclear fuel. The vertical overloading of the subcritical active cores with MA was chosen as prospective. Analysis of the device neutronics and the hybrid blanket thermal-hydraulic characteristics has been performed for the system with functions covering transmutation of minor actinides, production of tritium and enrichment of spent nuclear fuel. A study of FNS facilities role in the Russian closed nuclear fuel cycle was performed. It showed that during ~100 years of operation three FNS facilities with fission power of 3 GW controlled by fusion neutron source with power of 40 MW can burn 98 tons of minor actinides and 198 tons of Pu-239 can be produced for startup loading of 20 fast reactors. Instead of Pu-239, up to 25 kg of tritium per year may be produced for startup of fusion reactors using blocks with lithium orthosilicate instead of fissile breeder blankets.

Keywords: fusion-fission hybrid system, conventional tokamak, superconducting electromagnetic system, two-layer vacuum vessel, subcritical active cores, nuclear fuel cycle

Procedia PDF Downloads 147

Authors: Kyriaki Hatziagapiou, Konstantinos Bethanis, Olti Nikola, Elias Christoforides, Eleni Koniari, Eleni Kakouri, George Lambrou, Christina Kanaka-Gantenbein

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Glioblastoma multiforme (GBM) remains a serious health challenge, as current therapeutic modalities continue to yield unsatisfactory results, with the average survival rarely exceeding 1-2 years. Natural compounds still provide some of the most promising approaches for discovering new drugs. The non-psychotropic cannabidiol (CBD) deriving from Cannabis sativa L. provides such promise. CBD is endowed with anticancer, antioxidant, and genoprotective properties as established in vitro and in in vivo experiments. CBD’s selectivity towards cancer cells and its safe profile suggest its usage in cancer therapies. However, the bioavailability of oral CBD is low due to poor aqueous solubility, erratic gastrointestinal absorption, and significant first-pass metabolism, hampering its therapeutic potential and resulting in a variable pharmacokinetic profile. In this context, CBD can take great advantage of nanomedicine-based formulation strategies. Cyclodextrins (CDs) are cyclic oligosaccharides used in the pharmaceutical industry to incorporate apolar molecules inside their hydrophobic cavity, increasing their stability, water solubility, and bioavailability or decreasing their side effects. CBD-inclusion complexes with CDs could be a good strategy to improve its properties, like solubility and stability to harness its full therapeutic potential. The current research aims to study the potential cytotoxic effect of CBD and CBD-CDs complexes CBD-RMβCD (randomly methylated β-cyclodextrin) and CBD-HPβCD (hydroxypropyl-b-CD) on the A172 glioblastoma cell line. CBD is diluted in 10% DMSO, and CBD/CDs solutions are prepared by mixing solid CBD, solid CDs, and dH2O. For the biological assays, A172 cells are incubated at a range of concentrations of CBD, CBD-RMβCD and CBD-HPβCD, RMβCD, and HPβCD (0,03125-4 mg/ml) at 24, 48, and 72 hours. Analysis of cell viability after incubation with the compounds is performed with Alamar Blue viability assay. CBD’s dilution to DMSO 10% was inadequate, as crystals are observed; thus cytotoxicity experiments are not assessed. CBD’s solubility is enhanced in the presence of both CDs. CBD/CDs exert significant cytotoxicity in a dose and time-dependent manner (p < 0.005 for exposed cells to any concentration at 48, 72, and 96 hours versus cells not exposed); as their concentration and time of exposure increases, the reduction of resazurin to resofurin decreases, indicating a reduction in cell viability. The cytotoxic effect is more pronounced in cells exposed to CBD-HPβCD for all concentrations and time-points. RMβCD and HPβCD at the highest concentration of 4 mg/ml also exerted antitumor action per se since manifesting cell growth inhibition. The results of our study could afford the basis of research regarding the use of natural products and their inclusion complexes as anticancer agents and the shift to targeted therapy with higher efficacy and limited toxicity. Acknowledgments: The research is partly funded by ΙΚΥ (State Scholarships Foundation) – Post-doc Scholarships-Partnership Agreement 2014-2020.

Keywords: cannabidiol, cyclodextrins, glioblastoma, hydroxypropyl-b-Cyclodextrin, randomly-methylated-β-cyclodextrin

Procedia PDF Downloads 180

Authors: Maria Ledinskaya

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This paper examines the Morris Collection Conservation Project at the Sainsbury Centre for Visual Arts in the context of Agile, Lean, and Hybrid project management. It is part case study and part literature review. To date, relatively little has been written about non-traditional project management approaches in heritage conservation. This paper seeks to introduce Agile, Lean, and Hybrid project management concepts from business, software development, and manufacturing fields to museum conservation, by referencing their practical application on a recent museum-based conservation project. The Morris Collection Conservation Project was carried out in 2019-2021 in Norwich, UK, and concerned the remedial conservation of around 150 Abstract Constructivist artworks bequeathed to the Sainsbury Centre for Visual Arts by private collectors Michael and Joyce Morris. The first part introduces the chronological timeline and key elements of the project. It describes a medium-size conservation project of moderate complexity, which was planned and delivered in an environment with multiple known unknowns – unresearched collection, unknown condition and materials, unconfirmed budget. The project was also impacted by the unknown unknowns of the COVID-19 pandemic, such as indeterminate lockdowns, and the need to accommodate social distancing and remote communications. The author, a staff conservator at the Sainsbury Centre who acted as project manager on the Morris Collection Conservation Project, presents an incremental, iterative, and value-based approach to managing a conservation project in an uncertain environment. Subsequent sections examine the project from the point of view of Traditional, Agile, Lean, and Hybrid project management. The author argues that most academic writing on project management in conservation has focussed on a Traditional plan-driven approach – also known as Waterfall project management – which has significant drawbacks in today’s museum environment, due to its over-reliance on prediction-based planning and its low tolerance to change. In the last 20 years, alternative Agile, Lean and Hybrid approaches to project management have been widely adopted in software development, manufacturing, and other industries, although their recognition in the museum sector has been slow. Using examples from the Morris Collection Conservation Project, the author introduces key principles and tools of Agile, Lean, and Hybrid project management and presents a series of arguments on the effectiveness of these alternative methodologies in museum conservation, as well as the ethical and practical challenges to their implementation. These project management approaches are discussed in the context of consequentialist, relativist, and utilitarian developments in contemporary conservation ethics, particularly with respect to change management, bespoke ethics, shared decision-making, and value-based cost-benefit conservation strategy. The author concludes that the Morris Collection Conservation Project had multiple Agile and Lean features which were instrumental to the successful delivery of the project. These key features are identified as distributed decision making, a co-located cross-disciplinary team, servant leadership, focus on value-added work, flexible planning done in shorter sprint cycles, light documentation, and emphasis on reducing procedural, financial, and logistical waste. Overall, the author’s findings point largely in favour of a Hybrid model which combines traditional and alternative project processes and tools to suit the specific needs of the project.

Keywords: project management, conservation, waterfall, agile, lean, hybrid

Procedia PDF Downloads 99

Authors: Zakia Hbellaq

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The Mediterranean region is considered a hotbed for climate change. Morocco is a semi-arid Mediterranean country facing water shortages and poor water quality. Its limited water resources limit the activities of various economic sectors. Most of Morocco's territory is in arid and desert areas. The potential water resources are estimated at 22 billion m3, which is equivalent to about 700 m3/inhabitant/year, and Morocco is in a state of structural water stress. Strictly speaking, the Kingdom of Morocco is one of the “very riskiest” countries, according to the World Resources Institute (WRI), which oversees the calculation of water stress risk in 167 countries. The surprising results of the Institute (WRI) rank Morocco as one of the riskiest countries in terms of water scarcity, ranking 3.89 out of 5, thus occupying the 23rd place out of a total of 167 countries, which indicates that the demand for water exceeds the available resources. Agriculture with a score of 3.89 is most affected by water stress from irrigation and places a heavy burden on the water table. Irrigation is an unavoidable technical need and has undeniable economic and social benefits given the available resources and climatic conditions. Irrigation, and therefore the agricultural sector, currently uses 86% of its water resources, while industry uses 5.5%. Although its development has undeniable economic and social benefits, it also contributes to the overfishing of most groundwater resources and the surprising decline in levels and deterioration of water quality in some aquifers. In this context, REUSE is one of the proposed solutions to reduce the water footprint of the agricultural sector and alleviate the shortage of water resources. Indeed, wastewater reuse, also known as REUSE (reuse of treated wastewater), is a step forward not only for the circular economy but also for the future, especially in the context of climate change. In particular, water reuse provides an alternative to existing water supplies and can be used to improve water security, sustainability, and resilience. However, given the introduction of organic trace pollutants or, organic micro-pollutants, the absorption of emerging contaminants, and decreasing salinity, it is possible to tackle innovative capabilities to overcome these problems and ensure food and health safety. To this end, attention will be paid to the adoption of an integrated and attractive approach, based on the reinforcement and optimization of the treatments proposed for the elimination of the organic load with particular attention to the elimination of emerging pollutants, to achieve this goal. , membrane bioreactors (MBR) as stand-alone technologies are not able to meet the requirements of WHO guidelines. They will be combined with heterogeneous Fenton processes using persulfate or hydrogen peroxide oxidants. Similarly, adsorption and filtration are applied as tertiary treatment In addition, the evaluation of crop performance in terms of yield, productivity, quality, and safety, through the optimization of Trichoderma sp strains that will be used to increase crop resistance to abiotic stresses, as well as the use of modern omics tools such as transcriptomic analysis using RNA sequencing and methylation to identify adaptive traits and associated genetic diversity that is tolerant/resistant/resilient to biotic and abiotic stresses. Hence, ensuring this approach will undoubtedly alleviate water scarcity and, likewise, increase the negative and harmful impact of wastewater irrigation on the condition of crops and the health of their consumers.

Keywords: water scarcity, food security, irrigation, agricultural water footprint, reuse, emerging contaminants

Procedia PDF Downloads 160

Authors: Emilie Gout, Mathias Monnot, Olivier Boutin, Pierre Vanloot, Philippe Moulin

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Water is a precious resource. Treating industrial wastewater remains a considerable technical challenge of our century. The effluent considered for this study is landfill leachate treated by reverse osmosis (RO). Nowadays, in most developed countries, sanitary landfilling is the main method to deal with municipal solid waste. Rainwater percolates through solid waste, generating leachates mostly comprised of organic and inorganic matter. Whilst leachate ages, its composition varies, becoming more and more bio-refractory. RO is already used for landfill leachates as it generates good quality permeate. However, its mains drawback is the production of highly polluted concentrates that cannot be discharged in the environment or reused, which is an important industrial issue. It is against this background that the study of coupling RO with wet air oxidation (WAO) was set to intensify and optimize processes to meet current regulations for water discharge in the environment. WAO is widely studied for effluents containing bio-refractory compounds. Oxidation consists of a destruction reaction capable of mineralizing the recalcitrant organic fraction of pollution into carbon dioxide and water when complete. WAO process in subcritical conditions requires a high-energy consumption, but it can be autothermic in a certain range of chemical oxygen demand (COD) concentrations (10-100 g.L⁻¹). Appropriate COD concentrations are reached in landfill leachate RO concentrates. Therefore, the purpose of this work is to report the performances of mineralization during WAO on RO concentrates. The coupling of RO/WAO has shown promising results in previous works on both synthetic and real effluents in terms of organic carbon (TOC) reduction by WAO and retention by RO. Non-catalytic WAO with air as oxidizer was performed in a lab-scale stirred autoclave (1 L) on landfill leachates RO concentrates collected in different seasons in a sanitary landfill in southern France. The yield of WAO depends on operating parameters such as total pressure, temperature, and time. Compositions of the effluent are also important aspects for process intensification. An experimental design methodology was used to minimize the number of experiments whilst finding the operating conditions achieving the best pollution reduction. The simulation led to a set of 18 experiments, and the responses to highlight process efficiency are pH, conductivity, turbidity, COD, TOC, and inorganic carbon. A 70% oxygen excess was chosen for all the experiments. First experiments showed that COD and TOC abatements of at least 70% were obtained after 90 min at 300°C and 20 MPa, which attested the possibility to treat RO leachate concentrates with WAO. In order to meet French regulations and validate process intensification with industrial effluents, some continuous experiments in a bubble column are foreseen, and some further analyses will be performed, such as biological oxygen demand and study of gas composition. Meanwhile, other industrial effluents are treated to compare RO-WAO performances. These effluents, coming from pharmaceutical, petrochemical, and tertiary wastewater industries, present different specific pollutants that will provide a better comprehension of the hybrid process and prove the intensification and feasibility of the process at an industrial scale. Acknowledgments: This work has been supported by the French National Research Agency (ANR) for the Project TEMPO under the reference number ANR-19-CE04-0002-01.

Keywords: hybrid process, landfill leachates, process intensification, reverse osmosis, wet air oxidation

Procedia PDF Downloads 137

Authors: Gloria M. Ntuba-Jua, Afui M. Mih, Eneke E. T. Bechem

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Prunus africana (Hook. F.) Kalkman, commonly known as Pygeum or African cherry belongs to the Rosaceae family. It is a medium to large, evergreen tree with a spreading crown of 10 to 20 m. It is used by the traditional medical practitioners for the treatment of over 45ailments in Cameroon and sub-Sahara Africa. In modern medicine, it is used in the treatment of benign prostrate hyperplasia (BPH), prostate gland hypertrophy (enlarged prostate glands). This is possible because of its ability to produce some secondary metabolites which are believed to have bioactivity against these ailments. The ready international market for the sale of Prunus bark, uncontrolled exploitation, illegal harvesting using inappropriate techniques and poor timing of harvesting have contributed enormously to making the plant endangered. It is known to harbor a large number of endophytic fungi with the potential to produce similar secondary metabolites as the parent plant. Alternative sourcing of medicinal principles through endophytic fungi requires succinct knowledge of the endophytic fungi. This will serve as a conservation measure for Prunus africana by reducing dependence on Prunus bark for such metabolites. This work thus sought to compare the production of some major secondary metabolites produced by P. africana and some of its associated endophytic fungi. The leaves and stem bark of the plant from different provenances were soaked in methanol for 72 hrs to yield the methanolic crude extract. The phytochemical screening of the methanolic crude extracts using different standard procedures revealed the presence of tannins, flavonoids, terpenoids, saponins, phenolics and steroids. Pure cultures of some predominantly isolated endophyte species from the difference Prunus provenances such as Curvularia sp, and Morphospecies P001 were also grown in Potato Dextrose Broth (PDB) for 21 days and later extracted with Methylene dichloride (MDC) solvent after 24hrs to produce crude culture extracts. Qualitative assessment of crude culture extracts showed the presence of tannins, terpenoids, phenolics and steroids particularly β-Sitosterol, (a major bioactive metabolite) as did the plant tissues. Qualitative analysis by thin layer chromatography (TLC) was done to confirm and compare the production of β-Sitosterol (as marker compounds) in the crude extracts of the plant and endophyte. Samples were loaded on TLC silica gel aluminium barked plate (Kieselgel 60 F254, 0.2 mm, Merck) using acetone/hexane, (3.0:7.0) solvent system. They were visualized under an ultra violet lamp (UV254 and UV360). TLC revealed that leaves had a higher concentration of β-sitosterol in terms of band intensity than stem barks from the different provenances. The intensity of β-sitosterol bands in the culture extracts of endophytes was comparable to the plant extracts except for Curvularia sp (very minute) whose band was very faint. The ability of these fungi to make β-sitosterol was confirmed by TLC analysis with the compound having chromatographic properties (retention factor) similar to those of β-sitosterol standard. The ability of these major endophytes to produce secondary metabolites similar to the host has therefore been demonstrated. There is, therefore, the potential of developing the in vitro production system of Prunus secondary metabolites thereby enhancing its conservation.

Keywords: Caneroon, endophytic fungi, Prunus africana, secondary metabolite

Procedia PDF Downloads 230

Authors: Georgios A. Fragkiadakis, Antonia Psaroudaki, Theodora Mouratidou, Eirini Sfakianaki

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Research: Within the project "Actions for the optimal utilization of the potential of carob in the Region of Crete" which is financed-supervised by the Region, with collaboration of Crete University and Hellenic Mediterranean University, a SWOT (strengths, weaknesses, opportunities, threats) survey was carried out, to evaluate the prospects of carob in human nutrition, in Crete. Results and conclusions: 1). Strengths: There exists a local production of carob for human consumption, based on international reports, and local-product reports. The data on products in the market (over 100 brands of carob food), indicates a sufficiency of carob materials offered in Crete. The variety of carob food products retailed in Crete indicates a strong demand-production-consumption trend. There is a stable number (core) of businesses that invest significantly (Creta carob, Cretan mills, etc.). The great majority of the relevant food stores (bakery, confectionary etc.) do offer carob products. The presence of carob products produced in Crete is strong on the internet (over 20 main professionally designed websites). The promotion of the carob food-products is based on their variety and on a few historical elements connected with the Cretan diet. 2). Weaknesses: The international prices for carob seed affect the sector; the seed had an international price of €20 per kg in 2021-22 and fell to €8 in 2022, causing losses to carob traders. The local producers do not sort the carobs they deliver for processing, causing 30-40% losses of the product in the industry. The occasional high price triggers the collection of degraded raw material; large losses may emerge due to the action of insects. There are many carob trees whose fruits are not collected, e.g. in Apokoronas, Chania. The nutritional and commercial value of the wild carob fruits is very low. Carob trees-production is recorded by Greek statistical services as "other cultures" in combination with prickly pear i.e., creating difficulties in retrieving data. The percentage of carob used for human nutrition, in contrast to animal feeding, is not known. The exact imports of carob are not closely monitored. We have no data on the recycling of carob by-products in Crete. 3). Opportunities: The development of a culture of respect for carob trade may improve professional relations in the sector. Monitoring carob market and connecting production with retailing-industry needs may allow better market-stability. Raw material evaluation procedures may be implemented to maintain carob value-chain. The state agricultural services may be further involved in carob-health protection. The education of farmers on carob cultivation/management, can improve the quality of the product. The selection of local productive varieties, may improve the sustainability of the culture. Connecting the consumption of carob with health-food products, may create added value in the sector. The presence and extent of wild carob threes in Crete, represents, potentially, a target for grafting. 4). Threats: The annual fluctuation of carob yield challenges the programming of local food industry activities. Carob is a forest species also - there is danger of wrong classification of crops as forest areas, where land ownership is not clear.

Keywords: human nutrition, carob food, SWOT analysis, crete, greece

Procedia PDF Downloads 92

Authors: Artem Kim, Clara Savary, Christele Dubourg, Wilfrid Carre, Houda Hamdi-Roze, Valerie Dupé, Sylvie Odent, Marie De Tayrac, Veronique David

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Holoprosencephaly (HPE) is a rare congenital brain malformation resulting from the incomplete separation of the two cerebral hemispheres. It is characterized by a wide phenotypic spectrum and a high degree of locus heterogeneity. Genetic defects in 16 genes have already been implicated in HPE, but account for only 30% of cases, suggesting that a large part of genetic factors remains to be discovered. HPE has been recently redefined as a complex multigenic disorder, requiring the joint effect of multiple mutational events in genes belonging to one or several developmental pathways. The onset of HPE may result from accumulation of the effects of multiple rare variants in functionally-related genes, each conferring a moderate increase in the risk of HPE onset. In order to decipher the genetic basis of HPE, unconventional patterns of inheritance involving multiple genetic factors need to be considered. The primary objective of this study was to uncover possible disease causing combinations of multiple rare variants underlying HPE by performing trio-based Whole Exome Sequencing (WES) of familial cases where no molecular diagnosis could be established. 39 families were selected with no fully-penetrant causal mutation in known HPE gene, no chromosomic aberrations/copy number variants and without any implication of environmental factors. As the main challenge was to identify disease-related variants among a large number of nonpathogenic polymorphisms detected by WES classical scheme, a novel variant prioritization approach was established. It combined WES filtering with complementary gene-level approaches: transcriptome-driven (RNA-Seq data) and clinically-driven (public clinical data) strategies. Briefly, a filtering approach was performed to select variants compatible with disease segregation, population frequency and pathogenicity prediction to identify an exhaustive list of rare deleterious variants. The exome search space was then reduced by restricting the analysis to candidate genes identified by either transcriptome-driven strategy (genes sharing highly similar expression patterns with known HPE genes during cerebral development) or clinically-driven strategy (genes associated to phenotypes of interest overlapping with HPE). Deeper analyses of candidate variants were then performed on a family-by-family basis. These included the exploration of clinical information, expression studies, variant characteristics, recurrence of mutated genes and available biological knowledge. A novel bioinformatics pipeline was designed. Applied to the 39 families, this final integrated workflow identified an average of 11 candidate variants per family. Most of candidate variants were inherited from asymptomatic parents suggesting a multigenic inheritance pattern requiring the association of multiple mutational events. The manual analysis highlighted 5 new strong HPE candidate genes showing recurrences in distinct families. Functional validations of these genes are foreseen.

Keywords: complex genetic disorder, holoprosencephaly, multiple rare variants, whole exome sequencing

Procedia PDF Downloads 203

Authors: Adeline Meriaux, Claire Gaiani, Jennifer Burgain, Frantz Fournier, Lionel Muniglia, Jérémy Petit

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Spray-drying process is widely used for the production of dairy powders for food and pharmaceuticals industries. It involves the atomization of a liquid feed into fine droplets, which are subsequently dried through contact with a hot air flow. The resulting powders permit transportation cost reduction and shelf life increase but can also exhibit various interesting functionalities (flowability, solubility, protein modification or acid gelation), depending on operating conditions and milk composition. Indeed, particles porosity, surface composition, lactose crystallization, protein denaturation, protein association or crust formation may change. Links between spray-drying conditions and physicochemical and functional properties of powders were investigated by a design of experiment methodology and analyzed by principal component analysis. Quadratic models were developed, and multicriteria optimization was carried out by the use of genetic algorithm. At the time of abstract submission, verification spray-drying trials are ongoing. To perform experiments, milk from dairy farm was collected, skimmed, froze and spray-dried at different air pressure (between 1 and 3 bars) and outlet temperature (between 75 and 95 °C). Dry matter, minerals content and proteins content were determined by standard method. Solubility index, absorption index and hygroscopicity were determined by method found in literature. Particle size distribution were obtained by laser diffraction granulometry. Location of the powder color in the Cielab color space and water activity were characterized by a colorimeter and an aw-value meter, respectively. Flow properties were characterized with FT4 powder rheometer; in particular compressibility and shearing test were performed. Air pressure and outlet temperature are key factors that directly impact the drying kinetics and powder characteristics during spray-drying process. It was shown that the air pressure affects the particle size distribution by impacting the size of droplet exiting the nozzle. Moreover, small particles lead to more cohesive powder and less saturated color of powders. Higher outlet temperature results in lower moisture level particles which are less sticky and can explain a spray-drying yield increase and the higher cohesiveness; it also leads to particle with low water activity because of the intense evaporation rate. However, it induces a high hygroscopicity, thus, powders tend to get wet rapidly if they are not well stored. On the other hand, high temperature provokes a decrease of native serum proteins which is positively correlated to gelation properties (gel point and firmness). Partial denaturation of serum proteins can improve functional properties of powder. The control of air pressure and outlet temperature during the spray-drying process significantly affects the physicochemical and functional properties of powder. This study permitted to better understand the links between physicochemical and functional properties of powder, to identify correlations between air pressure and outlet temperature. Therefore, mathematical models have been developed and the use of genetic algorithm will allow the optimization of powder functionalities.

Keywords: dairy powders, spray-drying, powders functionalities, design of experiment

Procedia PDF Downloads 92

Authors: Desireina Delancy, Tannice Hall, Eric Garraway, Dwight Robinson

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Aphis gossypii, as a pest, directly damages its host plant by extracting phloem sap (sucking) and indirectly damages it by the transmission of viruses, ultimately affecting the yield of the host. Due to its polyphagous nature, this species affects a wide range of host plants, some of which may serve as a reservoir for colonisation of important crops. In Jamaica, there have been outbreaks of viral plant pathogens that were transmitted by Aphis gossypii. Three such examples are Citrus tristeza virus, the Watermelon mosaic virus, and Papaya ringspot virus. Aphis gossypii also heavily colonized economically significant host plants, including pepper, eggplant, watermelon, cucumber, and hibiscus. To facilitate integrated pest management, it is imperative to understand the biology of the aphid and its host preference. Preliminary work in Jamaica has indicated differences in biology and host preference, as well as host variety within the species. However, specific details of fecundity, colony growth, host preference, distribution, and insecticide resistance of Aphis gossypii were unknown to the best of our knowledge. The aim was to investigate the following in relation to Aphis gossypii: influence of the host plant on colonization, life span, fecundity, population size, and morphology; the impact of host transfer on fecundity and population size as a measure of host preference and host transfer success and susceptibility to four commonly used insecticides. Fecundity and colony size were documented daily from aphids acclimatized on Capsicum chinense Jacquin 1776, Cucumis sativus Linnaeus 1630, Gossypium hirsutum Linnaeus 1751 and Abelmoschus esculentus (L.) Moench 1794 for three generations. The same measures were used after third instar aphids were transferred among the hosts as a measure of suitability and success. Mortality, and fecundity of survivors, were determined after aphids were exposed to varying concentrations of Actara®, Diazinon™, Karate Zeon®, and Pegasus®. Host preference results indicated that, over a 24-day period, Aphis gossypii reached its largest colony size on G. hirsutum (x̄ 381.80), with January – February being the most fecund period. Host transfer experiments were all significantly different, with the most significant occurring between transfers from C. chinense to C. sativus (p < 0.05). Colony sizes were found to increase significantly every 5 days, which has implications for regimes implemented to monitor and evaluate plots. Insecticides ranked on lethality are Karate Zeon®> Actara®> Pegasus® > Diazinon™. The highest LC50 values were obtained for aphids on G. hirsutum and C. chinense was with Pegasus® and for those on C. sativus with Diazinon™. Survivors of insecticide treatments had colony sizes on average that were 98 % less than untreated aphids. Cotton was preferred both in the field and in the glasshouse. It is on cotton the aphids settled first, had the highest fecundity, and the lowest mortality. Cotton can serve as reservoir for (re)populating other cotton or different host species based on migration due to overcrowding, heavy showers, high wind, or ant attendance. Host transfer success between all three hosts is highly probable within an intercropping system. Survivors of insecticide treatments can successfully repopulate host plants.

Keywords: Aphis gossypii, host-plant preference, colonization sequence, host transfers, insecticide susceptibility

Procedia PDF Downloads 95

Authors: Adeline Meriaux, Claire Gaiani, Jennifer Burgain, Frantz Fournier, Lionel Muniglia, Jérémy Petit

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Spray-drying process is widely used for the production of dairy powders for food and pharmaceuticals industries. It involves the atomization of a liquid feed into fine droplets, which are subsequently dried through contact with a hot air flow. The resulting powders permit transportation cost reduction and shelf life increase but can also exhibit various interesting functionalities (flowability, solubility, protein modification or acid gelation), depending on operating conditions and milk composition. Indeed, particles porosity, surface composition, lactose crystallization, protein denaturation, protein association or crust formation may change. Links between spray-drying conditions and physicochemical and functional properties of powders were investigated by a design of experiment methodology and analyzed by principal component analysis. Quadratic models were developed, and multicriteria optimization was carried out by the use of genetic algorithm. At the time of abstract submission, verification spray-drying trials are ongoing. To perform experiments, milk from dairy farm was collected, skimmed, froze and spray-dried at different air pressure (between 1 and 3 bars) and outlet temperature (between 75 and 95 °C). Dry matter, minerals content and proteins content were determined by standard method. Solubility index, absorption index and hygroscopicity were determined by method found in literature. Particle size distribution were obtained by laser diffraction granulometry. Location of the powder color in the Cielab color space and water activity were characterized by a colorimeter and an aw-value meter, respectively. Flow properties were characterized with FT4 powder rheometer; in particular, compressibility and shearing test were performed. Air pressure and outlet temperature are key factors that directly impact the drying kinetics and powder characteristics during spray-drying process. It was shown that the air pressure affects the particle size distribution by impacting the size of droplet exiting the nozzle. Moreover, small particles lead to more cohesive powder and less saturated color of powders. Higher outlet temperature results in lower moisture level particles which are less sticky and can explain a spray-drying yield increase and the higher cohesiveness; it also leads to particle with low water activity because of the intense evaporation rate. However, it induces a high hygroscopicity, thus, powders tend to get wet rapidly if they are not well stored. On the other hand, high temperature provokes a decrease of native serum proteins, which is positively correlated to gelation properties (gel point and firmness). Partial denaturation of serum proteins can improve functional properties of powder. The control of air pressure and outlet temperature during the spray-drying process significantly affects the physicochemical and functional properties of powder. This study permitted to better understand the links between physicochemical and functional properties of powder to identify correlations between air pressure and outlet temperature. Therefore, mathematical models have been developed, and the use of genetic algorithm will allow the optimization of powder functionalities.

Keywords: dairy powders, spray-drying, powders functionalities, design of experiment

Procedia PDF Downloads 65

Authors: V. Saccà, A. Sarica, F. Novellino, S. Barone, T. Tallarico, E. Filippelli, A. Granata, P. Valentino, A. Quattrone

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The work aim was to evaluate how well Random Forest (RF) and Support Vector Machine (SVM) algorithms could support the early diagnosis of Multiple Sclerosis (MS) from resting-state functional connectivity data. In particular, we wanted to explore the ability in distinguishing between controls and patients of mean signals extracted from ICA components corresponding to 15 well-known networks. Eighteen patients with early-MS (mean-age 37.42±8.11, 9 females) were recruited according to McDonald and Polman, and matched for demographic variables with 19 healthy controls (mean-age 37.55±14.76, 10 females). MRI was acquired by a 3T scanner with 8-channel head coil: (a)whole-brain T1-weighted; (b)conventional T2-weighted; (c)resting-state functional MRI (rsFMRI), 200 volumes. Estimated total lesion load (ml) and number of lesions were calculated using LST-toolbox from the corrected T1 and FLAIR. All rsFMRIs were pre-processed using tools from the FMRIB's Software Library as follows: (1) discarding of the first 5 volumes to remove T1 equilibrium effects, (2) skull-stripping of images, (3) motion and slice-time correction, (4) denoising with high-pass temporal filter (128s), (5) spatial smoothing with a Gaussian kernel of FWHM 8mm. No statistical significant differences (t-test, p < 0.05) were found between the two groups in the mean Euclidian distance and the mean Euler angle. WM and CSF signal together with 6 motion parameters were regressed out from the time series. We applied an independent component analysis (ICA) with the GIFT-toolbox using the Infomax approach with number of components=21. Fifteen mean components were visually identified by two experts. The resulting z-score maps were thresholded and binarized to extract the mean signal of the 15 networks for each subject. Statistical and machine learning analysis were then conducted on this dataset composed of 37 rows (subjects) and 15 features (mean signal in the network) with R language. The dataset was randomly splitted into training (75%) and test sets and two different classifiers were trained: RF and RBF-SVM. We used the intrinsic feature selection of RF, based on the Gini index, and recursive feature elimination (rfe) for the SVM, to obtain a rank of the most predictive variables. Thus, we built two new classifiers only on the most important features and we evaluated the accuracies (with and without feature selection) on test-set. The classifiers, trained on all the features, showed very poor accuracies on training (RF:58.62%, SVM:65.52%) and test sets (RF:62.5%, SVM:50%). Interestingly, when feature selection by RF and rfe-SVM were performed, the most important variable was the sensori-motor network I in both cases. Indeed, with only this network, RF and SVM classifiers reached an accuracy of 87.5% on test-set. More interestingly, the only misclassified patient resulted to have the lowest value of lesion volume. We showed that, with two different classification algorithms and feature selection approaches, the best discriminant network between controls and early MS, was the sensori-motor I. Similar importance values were obtained for the sensori-motor II, cerebellum and working memory networks. These findings, in according to the early manifestation of motor/sensorial deficits in MS, could represent an encouraging step toward the translation to the clinical diagnosis and prognosis.

Keywords: feature selection, machine learning, multiple sclerosis, random forest, support vector machine

Procedia PDF Downloads 240

Authors: Khiem M. Nguyen, Ming C. Yang

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Chloroplast pigments are extremely important during photosynthesis since they play essential roles in light absorption and energy transfer. Therefore, understanding the efficiency of chlorophyll (Chl) biosynthesis could facilitate enhancement in photo-assimilates accumulation, and ultimately, in crop yield. The Chl-deficient mutants have been used extensively to study the Chl biosynthetic pathways and the biogenesis of the photosynthetic apparatus. Rice (Oryza sativa L.) is one of the most leading food crops, serving as staple food for many parts of the world. To author’s best knowledge, Chl b–lacking rice has been found; however the molecular mechanism of Chl biosynthesis still remains unclear compared to wild-type rice. In this study, the ultrastructure analysis, photosynthetic properties, and transcriptome profile of wild-type rice (Norin No.8, N8) and its Chl b-lacking mutant (Chlorina 1, C1) were examined. The finding concluded that total Chl content and Chl b content in the C1 leaves were strongly reduced compared to N8 leaves, suggesting that reduction in the total Chl content contributes to leaf color variation at the physiological level. Plastid ultrastructure of C1 possessed abnormal thylakoid membranes with loss of starch granule, large number of vesicles, and numerous plastoglobuli. The C1 rice also exhibited thinner stacked grana, which was caused by a reduction in the number of thylakoid membranes per granum. Thus, the different Chl a/b ratio of C1 may reflect the abnormal plastid development and function. Transcriptional analysis identified 23 differentially expressed genes (DEGs) and 671 transcription factors (TFs) that were involved in Chl metabolism, chloroplast development, cell division, and photosynthesis. The transcriptome profile and DEGs revealed that the gene encoding PsbR (PSII core protein) was down-regulated, therefore suggesting that the lower in light-harvesting complex proteins are responsible for the lower photosynthetic capacity in C1. In addition, expression level of cell division protein (FtsZ) genes were significantly reduced in C1, causing chloroplast division defect. A total of 19 DEGs were identified based on KEGG pathway assignment involving Chl biosynthesis pathway. Among these DEGs, the GluTR gene was down-regulated, whereas the UROD, CPOX, and MgCH genes were up-regulated. Observation through qPCR suggested that later stages of Chl biosynthesis were enhanced in C1, whereas the early stages were inhibited. Plastid structure analysis together with transcriptomic analysis suggested that the Chl a/b ratio was amplified both by the reduction in Chl contents accumulation, owning to abnormal chloroplast development, and by the enhanced conversion of Chl b to Chl a. Moreover, the results indicated the same Chl-cycle pattern in the wild-type and C1 rice, indicating another Chl b degradation pathway. Furthermore, the results demonstrated that normal grana stacking, along with the absence of Chl b and greatly reduced levels of Chl a in C1, provide evidence to support the conclusion that other factors along with LHCII proteins are involved in grana stacking. The findings of this study provide insight into the molecular mechanisms that underlie different Chl a/b ratios in rice.

Keywords: Chl-deficient mutant, grana stacked, photosynthesis, RNA-Seq, transcriptomic analysis

Procedia PDF Downloads 124

Authors: Alexander A. Stakheev, Larisa V. Samokhvalova, Sergey K. Zavriev

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Fusarium fungi are among the most devastating plant pathogens distributed all over the world. Significant reduction of grain yield and quality caused by Fusarium leads to multi-billion dollar annual losses to the world agricultural production. These organisms can also cause infections in immunocompromised persons and produce the wide range of mycotoxins, such as trichothecenes, fumonisins, and zearalenone, which are hazardous to human and animal health. Identification of Fusarium fungi based on the morphology of spores and spore-forming structures, colony color and appearance on specific culture media is often very complicated due to the high similarity of these features for closely related species. Modern Fusarium taxonomy increasingly uses data of crossing experiments (biological species concept) and genetic polymorphism analysis (phylogenetic species concept). A number of novel Fusarium sibling species has been established using DNA barcoding techniques. Species recognition is best made with the combined phylogeny of intron-rich protein coding genes and ribosomal DNA sequences. However, the internal transcribed spacer of (ITS), which is considered to be universal DNA barcode for Fungi, is not suitable for genus Fusarium, because of its insufficient variability between closely related species and the presence of non-orthologous copies in the genome. Nowadays, the translation elongation factor 1 alpha (TEF1α) gene is the “gold standard” of Fusarium taxonomy, but the search for novel informative markers is still needed. In this study, we used two novel DNA markers, frataxin (FXN) and heat shock protein 90 (HSP90) to discover phylogenetic relationships between Fusarium species. Multilocus phylogenetic analysis based on partial sequences of TEF1α, FXN, HSP90, as well as intergenic spacer of ribosomal DNA (IGS), beta-tubulin (β-TUB) and phosphate permease (PHO) genes has been conducted for 120 isolates of 19 Fusarium species from different climatic zones of Russia and neighboring countries using maximum likelihood (ML) and maximum parsimony (MP) algorithms. Our analyses revealed that FXN and HSP90 genes could be considered as informative phylogenetic markers, suitable for evolutionary and taxonomic studies of Fusarium genus. It has been shown that PHO gene possesses more variable (22 %) and parsimony informative (19 %) characters than other markers, including TEF1α (12 % and 9 %, correspondingly) when used for elucidating phylogenetic relationships between F. avenaceum and its closest relatives – F. tricinctum, F. acuminatum, F. torulosum. Application of novel DNA barcodes confirmed the fact that F. arthrosporioides do not represent a separate species but only a subspecies of F. avenaceum. Phylogeny based on partial PHO and FXN sequences revealed the presence of separate cluster of four F. avenaceum strains which were closer to F. torulosum than to major F. avenaceum clade. The strain F-846 from Moldova, morphologically identified as F. poae, formed a separate lineage in all the constructed dendrograms, and could potentially be considered as a separate species, but more information is needed to confirm this conclusion. Variable sites in PHO sequences were used for the first-time development of specific qPCR-based diagnostic assays for F. acuminatum and F. torulosum. This work was supported by Russian Foundation for Basic Research (grant № 15-29-02527).

Keywords: DNA barcode, fusarium, identification, phylogenetics, taxonomy

Procedia PDF Downloads 324

Authors: Olga V. Chervyakova, Elmira T. Tailakova, Vitaliy M. Strochkov, Kulyaisan T. Sultankulova, Nurlan T. Sandybayev, Lev G. Nemchinov, Rosemarie W. Hammond

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Sheep pox is a highly contagious infection that OIE regards to be one of the most dangerous animal diseases. It causes enormous economic losses because of death and slaughter of infected animals, lower productivity, cost of veterinary and sanitary as well as quarantine measures. To control spread of sheep pox infection the attenuated vaccines are widely used in the Republic of Kazakhstan and other Former Soviet Union countries. In spite of high efficiency of live vaccines, the possible presence of the residual virulence, potential genetic instability restricts their use in disease-free areas that leads to necessity to exploit new approaches in vaccine development involving recombinant DNA technology. Vaccines on the basis of recombinant proteins are the newest generation of prophylactic preparations. The main advantage of these vaccines is their low reactogenicity and this fact makes them widely used in medical and veterinary practice for vaccination of humans and farm animals. The objective of the study is to produce recombinant immunogenic proteins for development of the high-performance means for sheep pox prophylaxis. The SPV proteins were chosen for their homology with the known immunogenic vaccinia virus proteins. Assay of nucleotide and amino acid sequences of the target SPV protein genes. It has been shown that four proteins SPPV060 (ortholog L1), SPPV074 (ortholog H3), SPPV122 (ortholog A33) and SPPV141 (ortholog B5) possess transmembrane domains at N- or C-terminus while in amino acid sequences of SPPV095 (ortholog А 4) and SPPV117 (ortholog А 27) proteins these domains were absent. On the basis of these findings the primers were constructed. Target genes were amplified and subsequently cloned into the expression vector рЕТ26b(+) or рЕТ28b(+). Six constructions (pSPPV060ΔТМ, pSPPV074ΔТМ, pSPPV095, pSPPV117, pSPPV122ΔТМ and pSPPV141ΔТМ) were obtained for expression of the SPV genes under control of T7 promoter in Escherichia coli. To purify and detect recombinant proteins the amino acid sequences were modified by adding six histidine molecules at C-terminus. Induction of gene expression by IPTG was resulted in production of the proteins with molecular weights corresponding to the estimated values for SPPV060, SPPV074, SPPV095, SPPV117, SPPV122 and SPPV141, i.e. 22, 30, 20, 19, 17 and 22 kDa respectively. Optimal protocol of expression for each gene that ensures high yield of the recombinant protein was identified. Assay of cellular lysates by western blotting confirmed expression of the target proteins. Recombinant proteins bind specifically with antibodies to polyhistidine. Moreover all produced proteins are specifically recognized by the serum from experimentally SPV-infected sheep. The recombinant proteins SPPV060, SPPV074, SPPV117, SPPV122 and SPPV141 were also shown to induce formation of antibodies with virus-neutralizing activity. The results of the research will help to develop a new-generation high-performance means for specific sheep pox prophylaxis that is one of key moments in animal health protection. The research was conducted under the International project ISTC # K-1704 “Development of methods to construct recombinant prophylactic means for sheep pox with use of transgenic plants” and under the Grant Project RK MES G.2015/0115RK01983 "Recombinant vaccine for sheep pox prophylaxis".

Keywords: prophylactic preparation, recombinant protein, sheep pox virus, subunit vaccine

Procedia PDF Downloads 242

Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

Procedia PDF Downloads 181

Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa

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Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

Procedia PDF Downloads 188