Search results for: principal strains

Authors: Olumayowa M. Olowe, Michael D. Asemoloye Odunayo J. Olawuyi, Hilda Vasanthakaalam

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Poor management of maize ear rot caused by fungal infection in Nigeria affected the quantity and quality of maize. This study, therefore, aims at characterizing and controlling Fusarium strains using arbuscular mycorrhizal fungi. Maize ear showing rot symptoms were obtained from some selected farms located at Ilesa East and West using random sampling technique. Isolation of Fusarium pathogen from infected maize grain was done using direct pour plate method on potato dextrose agar (PDA) and was characterized based on morphological and molecular ITS-amplification methods. The reaction of PVASYN8F2, T2LCOMP1STR SYN-W-1, and T2LCOMP4 maize varieties, to the Fusarium ear rot pathogens and biocontrol efficacy of the mycorrhizal fungi were assessed on growth, yield, agronomic parameters and symptoms observed. The strains; olowILH1 and olowILH2 identified as Fusarium napiforme were the most dominant and virulent pathogens associated with the maize. They showed genetic similarity with documented ear rot pathogens on NCBI with accession numbers Fusarium proliferatum KT224027, KT224023, and Fusarium sp AY237110. They both exhibited varying inhibitory effects on the three maize varieties compare to control (uninfected plant) which had better growth characteristics. It was also observed that strain olowILH1 was more virulent than olowILH2. T2LCOMP4 was generally more susceptible to both fungal strains compared to the other two maize (T2LCOMP1STR SYN-W-1 and T2LCOMP4 ). In all, strain olowILH1 was more virulent than olowILH2, and Glomus clarum had higher inhibitory pathogenic effect against Fusarium strains compared to G. deserticola.

Keywords: arbuscular mycorrhizal fungi, disease management, Fusarium strains, identification

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Authors: Ismail Mahdi, Nidal Fahsi, Mohamed Hafidi, Abdelmounaim Allaoui, Latefa Biskri

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To meet the worldwide demand for food, smart management of arable lands is needed. This could be achieved through sustainable approaches such as the use of plant growth-promoting microorganisms including bacteria. Phosphate (P) solubilization is one of the major mechanisms of plant growth promotion by associated bacteria. In the present study, we isolated and screened 14 strains from the rhizosphere of Chenopodium quinoa wild grown in the experimental farm of UM6P and assessed their plant growth promoting properties. Next, they were identified by using 16S rRNA and Cpn60 genes sequencing as Bacillus, Pseudomonas and Enterobacter. These strains showed dispersed capacities to solubilize P (up to 346 mg L−1) following five days of incubation in NBRIP broth. We also assessed their abilities for indole acetic acid (IAA) production (up to 795,3 µg ml−1) and in vitro salt tolerance. Three Bacillus strains QA1, QA2, and S8 tolerated high salt stress induced by NaCl with a maximum tolerable concentration of 8%. Three performant isolates, QA1, S6 and QF11, were further selected for seed germination assay because of their pronounced abilities in terms of P solubilization, IAA production and salt tolerance. The early plant growth potential of tested strains showed that inoculated quinoa seeds displayed greater germination rate and higher seedlings growth under bacterial treatments. The positive effect on seed germination traits strongly suggests that the tested strains are growth promoting, halotolerant and P solubilizing bacteria which could be exploited as biofertilizers.

Keywords: phosphate solubilizing bacteria, IAA, Seed germination, salt tolerance, quinoa

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Authors: Rachida Ouysse

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This paper proposes a constrained principal components (CnPC) estimator for efficient estimation of large-dimensional factor models when errors are cross sectionally correlated and the number of cross-sections (N) may be larger than the number of observations (T). Although principal components (PC) method is consistent for any path of the panel dimensions, it is inefficient as the errors are treated to be homoskedastic and uncorrelated. The new CnPC exploits the assumption of bounded cross-sectional dependence, which defines Chamberlain and Rothschild’s (1983) approximate factor structure, as an explicit constraint and solves a constrained PC problem. The CnPC method is computationally equivalent to the PC method applied to a regularized form of the data covariance matrix. Unlike maximum likelihood type methods, the CnPC method does not require inverting a large covariance matrix and thus is valid for panels with N ≥ T. The paper derives a convergence rate and an asymptotic normality result for the CnPC estimators of the common factors. We provide feasible estimators and show in a simulation study that they are more accurate than the PC estimator, especially for panels with N larger than T, and the generalized PC type estimators, especially for panels with N almost as large as T.

Keywords: high dimensionality, unknown factors, principal components, cross-sectional correlation, shrinkage regression, regularization, pseudo-out-of-sample forecasting

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Authors: J. M. Kim, Y. W. Jung, E. Lee, Y. K. Kwack, , S. K. Sim*

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Cyanobacterial blooms in lakes, reservoirs, and rivers have been environmental and social issues due to its toxicity, odor, etc. Among the cyanotoxins, microcystins exist mostly within the cyanobacterial cells, and they are released from the cells. Therefore, an innovative technology is needed to detoxify the harvested microalgae for environment-friendly utilization of the harvested microalgae. This study develops detoxification method of microcystins in the harvested microalgae and recycling harvested microalgae with food waste using salt-tolerant mushroom strains and natural ecosystem decomposer. During this eco-friendly organic waste recycling process, diverse bacteria or various enzymes of the salt-tolerant mushroom strains decompose the microystins and cyclic peptides. Using PHLC/Mass analysis, it was verified that 99.8% of the microcystins of the harvested microalgae was detoxified in the harvested mushroom as well as in the recycled organic biomass. Further study is planned to verify the decomposition mechanisms of the microcystins by the bacteria or enzymes. In this study, the harvested microalgae is mixed with the food waste, and then the mixed toxic organic waste is used as mushroom compost by adjusting the water content of about 70% using cellulose such as sawdust cocopeats and cottonseeds. The mushroom compost is bottled, sterilized, and salt-tolerant mushroom spawn is inoculated. The mushroom is then cultured and growing in the temperature, humidity, and CO2 controlled environment. During the cultivation and growing process of the mushroom, microcystins are decomposed into non-toxic organic or inorganic compounds by diverse bacteria or various enzymes of the mushroom strains. Various enzymes of the mushroom strains decompose organics of the mixed organic waste and produce nutritious and antibiotic mushrooms. Cultured biomass compost after mushroom harvest can be used for organic fertilizer, functional bio-feed, and RE-100 biomass renewable energy source. In this eco-friendly organic waste recycling process, no toxic material, wastewater, nor sludge is generated; thus, sustainable with the circular economy.

Keywords: microalgae, microcystin, food waste, salt-tolerant mushroom strains, sustainability, circular economy

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Authors: Ridwaan N. Milase, Leonardo J. Van Zyl, Marla Trindade

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American foulbrood (AFB) is the world’s most devastating honeybee disease that has drastically reduced the population of Apis mellifera capensis since 2009. The outbreak has jeopardized the South African bee keeping industry as well as the agricultural sector dependent on honeybees for honey production and pollination, leading to significant economic losses. AFB is caused by Paenibacillus larvae, a spore-forming, Gram positive facultative anaerobic and flagellated bacterium. The use of antibiotics within beehives has selected for resistant strains of P. larvae, while the current practice of burning spore contaminated beehives and equipment contributes to the economic losses in the honeybee-keeping industry. Therefore, phage therapy is proposed as a promising alternative to combat P. larvae strains affecting A. mellifera capensis. The genomes of two P. larvae strains isolated from infected combs in the Western Cape have been sequenced and annotated using bioinformatics tools. Genome analyses has revealed that these P. larvae strains are lysogens to more than 6 different prophages and possess different type of clustered regularly interspaced short palindromic repeat (CRISPRs) regions per strain. Active prophages from one of the two P. larvae strains were detected and identified using PCR. Electron microscopy was used to determine the family of the identified active prophages. Lytic bacteriophages that specifically target the two P. larvae strains were purified from sewage wastewater, beehive materials, and soil samples to investigate their potential development as anti-P. larvae agents. Another alternative treatment being investigated is the development of a prophage endolysin cocktail. Endolysin genes of the prophages have been targeted, cloned and expressed in Escherichia coli. The heterologously expressed endolysins have been purified and are currently being assessed for their lytic activity against P. larvae strains and other commensal microorganisms that compose the honeybee larvae microbiota. The study has shown that phage therapy and endolysins have a great potential as alternative control methods for AFB disease affecting A. mellifera capensis.

Keywords: American foulbrood, bacteriophage, honeybee, Paenibacillus larvae

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Authors: Mini P. Singh, Jagat Ram, Archit Kumar, Tripti Rungta, Jasmine Khurana, Amit Gupta, R. K. Ratho

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Introduction: Human adenovirus is the most common agent involved in viral conjunctivitis. The clinical manifestations vary with different serotypes. The identification of the circulating strains followed by phylogenetic analysis can be helpful in understanding the origin and transmission of the disease. The present study aimed to carry out molecular epidemiology of the adenovirus types in the patients with conjunctivitis presenting to the eye centre of a tertiary care hospital in North India. Materials and Methods: The conjunctival swabs were collected from 23 suspected adenoviral conjunctivitis patients between April-August, 2014 and transported in viral transport media. The samples were subjected to nested PCR targeting hexon gene of human adenovirus. The band size of 956bp was eluted and 8 representative positive samples were subjected to sequencing. The sequences were analyzed by using CLUSTALX2.1 and MEGA 5.1 software. Results: The male: female ratio was found to be 3.6:1. The mean age of presenting patients was 43.95 years (+17.2). Approximately 52.1% (12/23) of patients presented with bilateral involvement while 47.8% (11/23) with unilateral involvement of the eye. Human adenovirus DNA could be detected in 65.2% (15/23) of the patients. The phylogenetic analysis revealed presence of serotype 8 in 7 patients and serotype 4 in one patient. The serotype 8 sequences showed 99-100% identity with Tunisian, Indian and Japanese strains. The adenovirus serotype 4 strains had 100% identity with strains from Tunisia, China and USA. Conclusion: Human adenovirus was found be an important etiological agent for conjunctivitis in our set up. The phylogenetic analysis showed that the predominant circulating strains in our epidemic keratoconjunctivitis were serotypes 8 and 4.

Keywords: conjunctivitis, human adenovirus, molecular epidemiology, phylogenetics

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Authors: A. Brunel, A. Kernevez, F. Leclere, J. Trenteseaux

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Today, wine quality is only evaluated by wine experts with their own different personal tastes, even if they may agree on some common features. So producers do not have any unbiased way to independently assess the quality of their products. A tool is here proposed to evaluate wine quality by an objective ranking based upon the variables entering wine elaboration, and analysed through principal component analysis (PCA) method. Actual climatic data are compared by measuring the relative distance between each considered wine, out of which the general ranking is performed.

Keywords: wine, grape, weather conditions, rating, climate, principal component analysis, metric analysis

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Authors: Dennis Okora Amima Ondieki

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Fertility transition has been identified to be affected by numerous factors. This research aimed to investigate the most real factors affecting fertility transition in Kenya. These factors were firstly extracted from the literature convened into demographic features, social, and economic features, social-cultural features, reproductive features and modernization features. All these factors had 23 factors identified for this study. The data for this study was from the Kenya Demographic and Health Surveys (KDHS) conducted in 1999-2003 and 2003-2008/9. The data was continuous, and it involved the mean birth order for the ten periods. Principal component analysis (PCA) was utilized using 23 factors. Principal component analysis conveyed religion, region, education and marital status as the real factors. PC scores were calculated for every point. The identified principal components were utilized as forecasters in the multiple regression model, with the fertility level as the response variable. The four components were found to be affecting fertility transition differently. It was found that fertility is affected positively by factors of region and marital and negatively by factors of religion and education. These four factors can be considered in the planning policy in Kenya and Africa at large.

Keywords: fertility transition, principal component analysis, Kenya demographic health survey, birth order

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Authors: Nora Laref, Bettache Guessas

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Preservation of foods mainly depends on delaying or inhibiting the growth of spoilage microorganisms, and antifungal activity of lactic acid bacteria is one of the technological properties researched. The antifungal activity was screened with overlay method of six strains of lactic acid bacteria (Lactobacillus plantarum LB54, LB52, LB51, LB20, LB24 Lactobacillus farciminis LB53) isolated from silage, camel milk and carrot against Aspergillus sp. Lactobacillus plantarum and farciminis inhibit spore germination and mycelia growth of Aspergillus sp., the production of antifungal compounds by these strains was detectable after 4h of incubation at 30°C and show total inhibition after 24h in liquid media, but in solid media showed a good inhibition after 96h of incubation, these compounds cause malformations in the thalle, conidiophore and conidia. These strains could be used as agents of biopreservation since have the ability to retard Aspergillus sp., growth in apricot juice with and without sugar conserved in refrigerator but not in bread.

Keywords: lactobacillus, antifungal substances, aspergillus, biopreservation

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Authors: T. Büyüksırıt, H. Kuleaşan

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Natural antimicrobials are used to preserve foods that can be found in plants, animals, and microorganisms. Antimicrobial substances are natural or artificial agents that produced by microorganisms or obtained semi/total chemical synthesis are used at low concentrations to inhibit the growth of other microorganisms. Food borne pathogens and spoilage microorganisms are inactivated by the use of antagonistic microorganisms and their metabolites. Yeasts can produce toxic proteins or glycoproteins (toxins) that cause inhibition of sensitive bacteria and yeast species. Antimicrobial substance producing phenotypes belonging different yeast genus were isolated from different sources. Toxins secreted by many yeast strains inhibiting the growth of other yeast strains. These strains show antimicrobial activity, inhibiting the growth of mold and bacteria. The effect of antimicrobial agents produced by yeasts can be extremely fast, and therefore may be used in various treatment procedures. Rapid inhibition of microorganisms is possibly caused by microbial cell membrane lipopolysaccharide binding and in activation (neutralization) effect. Antimicrobial agents inhibit the target cells via different mechanisms of action.

Keywords: antimicrobial agents, yeast, toxic protein, glycoprotein

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Authors: Goksen Arik, Mihriban Korukluoglu

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Lactic acid bacteria (LAB) has been used commonly in the food industry. They can be used as natural preservatives because acidifying carried out in the medium can protect the last product against microbial spoilage. Besides, other metabolites produced by LAB during fermentation period have also an antimicrobial effect on pathogen and spoilage microorganisms in the food industry. LAB are responsible for the desirable and distinctive aroma and flavour which are observed in fermented food products such as pickle, kefir, yogurt, and cheese. Various LAB strains are able to produce B-group vitamins such as folate (B11), riboflavin (B2) and cobalamin (B12). Especially wild-type strains of LAB can produce B-group vitamins in high concentrations. These cultures may be used in food industry as a starter culture and also the microbial strains can be used in encapsulation technology for new and functional food product development. This review is based on the current applications of B-group vitamin producing LAB. Furthermore, the new technologies and innovative researches about B vitamin production in LAB have been demonstrated and discussed for determining their usage availability in various area in the food industry.

Keywords: B vitamin, food industry, lactic acid bacteria, starter culture, technology

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Authors: Mohamed Trigui, Fatma Masmoudi, Imen Zouari

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Massive utilizations of chemical fertilizer and chemical pesticides in agriculture sector to improve the farming productivity have created increasing environmental damages. Then, agriculture must become sustainable, focusing on production systems that respect the environment and help to reduce climate change. Isolation and microbial identification of new bacterial strains from naturally saline habitats and compost extracts could be a prominent way in pest management and crop production under saline conditions. In this study, potential mechanisms involved in plant growth promotion and suppressive activity against fungal diseases of a compost extract produced from poultry manure/olive husk compost and halotolerant and halophilic bacterial strains under saline stress were investigated. On the basis of the antimicrobial tests, different strains isolated from Sfax solar saltern (Tunisia) and from compost extracts were selected and tested for their plant growth promoting traits, such as siderophores production, nitrogen fixation, phosphate solubilization and the production of extracellular hydrolytic enzymes (protease and lipase) under in-vitro conditions. Among 450 isolated bacterial strains, 16 isolates showed potent antifungal activity against the tested plant pathogenic fungi. Their identification based on 16S rRNA gene sequence revealed they belonged to different species. Some of these strains were also characterized for their plant growth promoting capacities. Obtained results showed the ability of four strains belonging to Bacillus genesis to ameliorate germination rate and root elongation compared to the untreated positive controls. Combinatorial capacity of halotolerant bacteria with antimicrobial activity and plant growth promoting traits could be promising sources of interesting bioactive substances under saline stress.

Keywords: abiotic stress, biofertilizer, biotic stress, compost extract, halobacteria, plant growth promoting (PGP), soil fertility

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Authors: A. M. Isakhanyan, F. N. Tkhruni, N. N. Yakimovich, Z. I. Kuvaeva, T. V. Khachatryan

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Introduction: At present, the simbiotics based on different genera and species of lactic acid bacteria (LAB) and yeasts are used. One of the basic properties of probiotics is presence of antimicrobial activity and therefore selection of LAB and yeast strains for their co-cultivation with the aim of increasing of the activity is topical. Since probiotic yeast and bacteria have different mechanisms of action, natural synergies between species, higher viability and increasing of antimicrobial activity might be expected from mixing both types of probiotics. Endemic strains of LAB Enterococcus faecium БТK-64, Lactobaccilus plantarum БТK-66, Pediococcus pentosus БТK-28, Lactobacillus rhamnosus БТK-109 and Kluyveromyces lactis БТX-412, Saccharomycopsis sp. БТX- 151 strains of yeast, with probiotic properties and hight antimicrobial activity, were selected. Strains are deposited in "Microbial Depository Center" (MDC) SPC "Armbiotechnology". Methods: LAB and yeast strains were isolated from different dairy products from rural households of Armenia. The genotyping by 16S rRNA sequencing for LAB and 26S RNA sequencing for yeast were used. Combined cultivation of LAB and yeast strains was carried out in the nutrient media on the basis of milk whey, in anaerobic conditions (without shaker, in a thermostat at 37oC, 48 hours). The complex preparations were obtained by purification of cell free culture broth (CFC) broth by the combination of ion-exchange chromatography and gel filtration methods. The spot-on-lawn method was applied for determination of antimicrobial activity and expressed in arbitrary units (AU/ml). Results. The obtained data showed that at the combined growth of bacteria and yeasts, the cultivation conditions (medium composition, time of growth, genera of LAB and yeasts) affected the display of antimicrobial activity. Purification of CFC broth allowed obtaining partially purified antimicrobial complex preparation which contains metabiotics from both bacteria and yeast. The complex preparation inhibited the growth of pathogenic and conditionally pathogenic bacteria, isolated from various internal organs from diseased animals and poultry with greater efficiency than the preparations derived individually alone from yeast and LAB strains. Discussion. Thus, our data shown perspectives of creation of a new class of antimicrobial preparations on the basis of combined cultivation of endemic strains of LAB and yeast. Obtained results suggest the prospect of use of the partially purified complex preparations instead antibiotics in the agriculture and for food safety. Acknowledgments: This work was supported by the RA MES State Committee of Science and Belarus National Foundation for Basic Research in the frames of the joint Armenian - Belarusian joint research project 13РБ-064.

Keywords: co-cultivation, antimicrobial activity, biosafety, metabiotics, lactic acid bacteria, yeast

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Authors: Memoona Ramzan, Bushra Tabassum, Anwar Khan, Muhammad Tariq, Mudassar Fareed Awan, Idrees Ahmad Nasir, Zahida Qamar, Naila Shahid, Tayyab Husnain

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Biological control is a novel approach being used in crop protection nowadays. Bacteria like Bacillus and Pseudomonas are reported for this purpose and few of their products are commercially available too. Rhizosphere and phyllosphere of healthy cotton plants were used as a source to isolate bacteria capable of exhibiting properties worthy for selection as biocontrol agent. For this purpose all isolated strains were screened for the activities like phosphate solubilization, Indole acetic acid (IAA) production and biocontrol against fungi. Two strains S1HL3 and S1HL4 showed phosphate solubilization and IAA production simultaneously while two other JS2HR4 and JS3HR2 were good inhibitors of fungal pathogens. Through biochemical and molecular characterization these bacteria were identified as P. aeruginosa, Burkholderia and Bacillus respectively. In green house trials of these isolates against Cotton leaf curl virus (CLCuV), seven treatments including individual bacterial isolate and consortia were included. Treated plants were healthy as compared to control plants in which upto 74% CLCuV symptomatic plants exist. Maximum inhibition of CLCuV was observed in T7 treated plants where viral load was only 0.4% as compared to control where viral load was upto 74%. This treatment consortium included Bacillus and Pseudomonas isolates; S1HL3, S1HL4, JS2HR4 and JS3HR2. Principal Component Biplot depicted highly significant correlation between percentage viral load and the disease incidence.

Keywords: cotton leaf curl virus, biological control, bacillus, pseudomonas

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Authors: C. Watson, T. Glare, M. O'Callaghan, M. Hurst

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The endemic New Zealand grass grub (Costelytra giveni, Coleoptera: Scarabaeidae) is an economically significant grassland pest in New Zealand. Due to their impacts on production within the agricultural sector, one of New Zealand's primary industries, several methods are being used to either control or prevent the establishment of new grass grub populations in the pasture. One such method involves the use of a biopesticide based on the bacterium Serratia entomophila. This species is one of the causative agents of amber disease, a chronic disease of the larvae which results in death via septicaemia after approximately 2 to 3 months. The ability of S. entomophila to cause amber disease is dependant upon the presence of the amber disease associated plasmid (pADAP), which encodes for the key virulence determinants required for the establishment and maintenance of the disease. Following the collapse of grass grub populations within the soil, resulting from either natural population build-up or application of the bacteria, non-pathogenic plasmid-free Serratia strains begin to predominate within the soil. Whilst the interactions between S. entomophila and grass grub larvae are well studied, less information is known on the interactions between plasmid-bearing and plasmid-free strains, particularly the potential impact of these interactions upon the efficacy of an applied biopesticide. Using a range of constructed strains with antibiotic tags, in vitro (broth culture) and in vivo (soil and larvae) experiments were conducted using inoculants comprised of differing ratios of isogenic pathogenic and non-pathogenic Serratia strains, enabling the relative growth of pADAP+ and pADAP- strains under competition conditions to be assessed. In nutrient-rich, the non-pathogenic pADAP- strain outgrew the pathogenic pADAP+ strain by day 3 when inoculated in equal quantities, and by day 5 when applied as the minority inoculant, however, there was an overall gradual decline in the number of viable bacteria for both strains over a 7-day period. Similar results were obtained in additional experiments using the same strains and continuous broth cultures re-inoculated at 24-hour intervals, although in these cultures, the viable cell count did not diminish over the 7-day period. When the same ratios were assessed in soil microcosms with limited available nutrients, the strains remained relatively stable over a 2-month period. Additionally, in vivo grass grub co-infections assays using the same ratios of tagged Serratia strains revealed similar results to those observed in the soil, but there was also evidence of horizontal transfer of pADAP from the pathogenic to the non-pathogenic strain within the larval gut after a period of 4 days. Whilst the influence of competition is more apparent in broth cultures than within the soil or larvae, further testing is required to determine whether this competition between pathogenic and non-pathogenic Serratia strains has any influence on efficacy and disease progression, and how this may impact on the ability of S. entomophila to cause amber disease within grass grub larvae when applied as a biopesticide.

Keywords: biological control, entomopathogen, microbial ecology, New Zealand

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Authors: Ejazulhaq Rahimi

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The development of techniques evaluating deterioration on concrete structures is vital for structural health monitoring (SHM). One of the main reasons for reinforced concrete structure's deterioration is the corroding of embedded rebars. It is a natural process that begins when the rebar starts to rust. It occurs when the protective layer on the rebar is destroyed. The rebar in concrete is usually protected against corrosion by the high pH of the surrounding cement paste. However, there are chemicals that can destroy the protective layer, making it susceptible to corrosion. It is very destructive for the lifespan and durability of the concrete structure. Corrosion products which are 3 to 6 times voluminous than the rebar stress its surrounding concrete and lead to fracture as cracks even peeling off the cover concrete over the rebar. As is clear that concrete shows limit elastic behavior in its stress strain property, so corrosion product stresses can be detected as strains from the concrete surface. It means that surface strains have a relation with the situation and amount of corrosion products and related concrete fractures inside reinforced concrete. In this paper, a comparative study of surface strains due to corrosion products detected by strain gauges and acoustic emission (AE) testing under periodic accelerated corrosion in the salty environment with 3% NaCl is reported. From the results, three different stages of strains were clearly observed based on the type and rate of strains in each corrosion situation and related fracture types. AE parameters which mostly are related to fracture and their shapes, describe the same phases. It is confirmed that there is a great agreement to the result of each other and describes three phases as generation and expansion of corrosion products and initiation and propagation of corrosion-induced cracks, and surface cracks. In addition, the strain on the concrete surface was rapidly increased before the cracks arrived at the surface of the concrete.

Keywords: acoustic emission, monitoring, rebar corrosion, reinforced concrete, strain

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Authors: F. Z. Aliyat, M. El Guilli, L. Nassiri, J. Ibijbijen

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Climate change is becoming a crucial factor that can significantly impact all ecosystems. It has a negative impact on the environment in many parts of the planet. Agriculture is the main sector affected by climate change. Particularly, the salinity of agricultural soils is among the problems caused by climate change. The use of phosphate solubilizing bacteria (PSB) as a biofertilizer requires previous research on their tolerance to abiotic stress, specifically saline stress tolerance, before the formation of biofertilizers. In this context, the main goal of this research was to assess the salinity tolerance of four strains: Serratia rubidaea strain JCM1240, Enterobacter bugandensis strain 247BMC, Pantoea agglomerans strain ATCC 27155, Pseudomonas brassicacearum subsp. Neoaurantiaca strain CIP109457, which was isolated from solid phosphate sludge. Additionally, their capacity to solubilize potassium and zinc, as well as their effect on Wheat (Triticum Durum 'Karim') germination. The four PSB strains were tested for their ability to solubilize phosphate in NBRIP medium with tricalcium phosphate (TCP) as the sole source of phosphorus under salt stress. Five concentrations of NaCl were used (0%, 0.5%, 1%, 2.5%, 5%). Their phosphate solubilizing activity was estimated by the vanadate-molybdate method. The potassium and zinc solubilization has been tested qualitatively and separately on solid media with mica and zinc oxide as the only sources of potassium and zinc, respectively. The result showed that the solubilization decreases with the increase in the concentration of NaCl; all the strains solubilize the TCP even with 5% NaCl, with a significant difference among the four strains. The Serratia rubidaea strain was the most tolerant strain. In addition, the four strains solubilize the potassium and the zinc. The Serratia rubidaea strain was the most efficient. Therefore, biofertilization with PSB salt-tolerant strains could be a climate-change-preparedness strategy for agriculture in salt soil.

Keywords: bioavailability of mineral nutrients, phosphate solid sludge; phosphate solubilization, potassium solubilization, salt stress, zinc solubilization.

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Authors: Sujay Kotwale, Ramasubba Reddy M.

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Electrocardiogram (ECG) is a non-invasive technique used to study and analyze various heart diseases. Cardiac arrhythmia is a serious heart disease which leads to death of the patients, when left untreated. An early-time detection of cardiac arrhythmia would help the doctors to do proper treatment of the heart. In the past, various algorithms and machine learning (ML) models were used to early-time detection of cardiac arrhythmia, but few of them have achieved better results. In order to improve the performance, this paper implements principal component analysis (PCA) along with XGBoost model. The PCA was implemented to the raw ECG signals which suppress redundancy information and extracted significant features. The obtained significant ECG features were fed into XGBoost model and the performance of the model was evaluated. In order to valid the proposed technique, raw ECG signals obtained from standard MIT-BIH database were employed for the analysis. The result shows that the performance of proposed method is superior to the several state-of-the-arts techniques.

Keywords: cardiac arrhythmia, electrocardiogram, principal component analysis, XGBoost

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Authors: Tao Peng, Jing Zhao, Yanqing Xu, Jing Cai

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Due to missing/ambiguous boundaries between the prostate and neighboring structures, the presence of shadow artifacts, as well as the large variability in prostate shapes, ultrasound prostate segmentation is challenging. To handle these issues, this paper develops a hybrid method for ultrasound prostate segmentation by combining an optimized closed principal curve-based method and the evolutionary neural network; the former can fit curves with great curvature and generate a contour composed of line segments connected by sorted vertices, and the latter is used to express an appropriate map function (represented by parameters of evolutionary neural network) for generating the smooth prostate contour to match the ground truth contour. Both qualitative and quantitative experimental results showed that our proposed method obtains accurate and robust performances.

Keywords: ultrasound prostate segmentation, optimized closed polygonal segment method, evolutionary neural network, smooth mathematical model, principal curve

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Authors: Clara Tramuta, Floris Irene, Daniela Manila Bianchi, Monica Pitti, Giulia Federica Cazzaniga, Lucia Decastelli

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This work presents the results obtained by the Regional Reference Centre for Salmonella Typing (CeRTiS) in a retrospective study aimed to investigate, through Pulsed-field Gel Electrophoresis (PFGE) analysis, the genetic relatedness of emerging Salmonella serotypes of human origin circulating in North-West of Italy. Furthermore, the goal of this work was to create a Regional database to facilitate foodborne outbreak investigation and to monitor them at an earlier stage. A total of 112 strains, isolated from 2016 to 2018 in hospital laboratories, were included in this study. The isolates were previously identified as Salmonella according to standard microbiological techniques and serotyping was performed according to ISO 6579-3 and the Kaufmann-White scheme using O and H antisera (Statens Serum Institut®). All strains were characterized by PFGE: analysis was conducted according to a standardized PulseNet protocol. The restriction enzyme XbaI was used to generate several distinguishable genomic fragments on the agarose gel. PFGE was performed on a CHEF Mapper system, separating large fragments and generating comparable genetic patterns. The agarose gel was then stained with GelRed® and photographed under ultraviolet transillumination. The PFGE patterns obtained from the 112 strains were compared using Bionumerics version 7.6 software with the Dice coefficient with 2% band tolerance and 2% optimization. For each serotype, the data obtained with the PFGE were compared according to the geographical origin and the year in which they were isolated. Salmonella strains were identified as follow: S. Derby n. 34; S. Infantis n. 38; S. Napoli n. 40. All the isolates had appreciable restricted digestion patterns ranging from approximately 40 to 1100 kb. In general, a fairly heterogeneous distribution of pulsotypes has emerged in the different provinces. Cluster analysis indicated high genetic similarity (≥ 83%) among strains of S. Derby (n. 30; 88%), S. Infantis (n. 36; 95%) and S. Napoli (n. 38; 95%) circulating in north-western Italy. The study underlines the genomic similarities shared by the emerging Salmonella strains in Northwest Italy and allowed to create a database to detect outbreaks in an early stage. Therefore, the results confirmed that PFGE is a powerful and discriminatory tool to investigate the genetic relationships among strains in order to monitoring and control Salmonellosis outbreak spread. Pulsed-field gel electrophoresis (PFGE) still represents one of the most suitable approaches to characterize strains, in particular for the laboratories for which NGS techniques are not available.

Keywords: emerging Salmonella serotypes, genetic characterization, human strains, PFGE

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Authors: Alaa H. J. Al-Rkaby, A. Chegenizadeh, H. R. Nikraz

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Anisotropy is one of the major aspects that affect soil behavior, and extensive efforts have investigated its effect on the mechanical properties of soil. However, very little attention has been given to the combined effect of anisotropy and fine contents. Therefore, in this paper, the anisotropic strength of sand containing different fine content (F) of 5%, 10%, 15%, and 20%, was investigated using hollow cylinder tests under different principal stress directions of α = 0° and α = 90°. For a given principal stress direction (α), it was found that increasing fine content resulted in decreasing deviator stress (q). Moreover, results revealed that all fine contents showed anisotropic strength where there is a clear difference between the strength under 0° and the strength under 90°. This anisotropy was greatest under F = 5% while it decreased with increasing fine contents, particularly at F = 10%. Mixtures with low fine content show low contractive behavior and tended to show more dilation. Moreover, all sand-clay mixtures exhibited less dilation and more compression at α = 90° compared with that at α = 0°.

Keywords: anisotropy, principal stress direction, fine content, hollow cylinder sample

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Authors: Ergun Guntekin

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Elastic constants of Fir wood (Abies cilicica) have been investigated by means of ultrasound and compression tests. Three modulus of elasticity in principal directions (EL, ER, ET), six Poisson’s ratios (ʋLR, ʋLT, ʋRT, ʋTR, ʋRL, ʋTL) and three shear modules (GLR, GRT, GLT) were determined. 20 x 20 x 60 mm samples were conditioned at 65 % relative humidity and 20ºC before testing. Three longitudinal and six shear wave velocities propagating along the principal axes of anisotropy, and additionally, three quasi-shear wave velocities at 45° angle with respect to the principal axes of anisotropy were measured. 2.27 MHz longitudinal and 1 MHz shear sensors were used for obtaining sound velocities. Stress-strain curves of the samples in compression tests were obtained using bi-axial extensometer in order to calculate elastic constants. Test results indicated that most of the elastic constants determined in the study are within the acceptable range. Although elastic constants determined from ultrasound are usually higher than those determined from compression tests, the values of EL and GLR determined from compression tests were higher in the study. The results of this study can be used in the numerical modeling of elements or systems under load using Fir wood.

Keywords: compression tests, elastic constants, fir wood, ultrasound

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Authors: Mohamed Sadek Bachene, Soraya Temim, Hassina Ainbaziz, Asma Bachene

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The present study was conducted to assess the safety and the efficacy of a vaccine containing the Algerian precocious strains of Eimeria magna and Eimeria media used separately or together against rabbit coccidiosis. The samples consisted of 56 young rabbits reared in specific pathogen-free conditions. Following the challenge inoculation, statistically significant decreases in oocyst excretion were noticed in the vaccinated rabbits with the precocious strain of Eimeria magna, Eimeria media, and both species leading toa good immune response acquired by the vaccination associated with a good growth rate. Moreover, there was a statistically significant increase in oocyst output following the challenge in all challenged groups. Unlike the vaccinated groups, the challenged groups showed poor weight gains. More than 50% of the young rabbits from all the challenged groups presented diarrhea. Consequently, these precocious strains constitute good candidates for mono or polyvalent anticoccidial vaccines in the future.

Keywords: precocious strain, rabbits, vaccination, wild strain

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Authors: Fatih Özogul, Sezen Özçeli̇k, Yesim Özogul

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Lactic, acetic, succinic, propionic, formic and butyric acid production by lactic acid bacteria (LAB) were monitored in M17 broth (the control) and some fish (squid, shrimp, octopus, and eel) infusion broth by using HPLC method. There were significant differences in terms of lactic, acetic, succinic, propionic, formic and butyric acid production (p < 0.005) among bacterial strains. Acetic acid production was the lowest by LAB while succinic acid followed by propionic acid was synthesized at the highest levels. Lactic acid production ranged from 0 to 938 mg/L by all LAB strains in different infusion broth. The highest acetic acid production was found by Lb. acidophilus and Lb. delbrueckii subsp. lactic in octopus and shrimp infusion broth, with values of 872 and 674 mg/L, respectively while formic acid formation ranged from 1747 mg/L by Lb. acidophilus in octopus infusion broth to 69 mg/L by Lb. delbrueckii subsp. lactis in shrimp infusion broth. Propionic acid and butyric acid productions by St. thermophilus were 9852 and 3999 mg/L in shrimp infusion broth while Leu. mes. subsp. cremoris synthesized 312 and 9 mg/L of those organic acid in European squid infusion broth, respectively. Apparently, LAB strains had a great capability to generate succinic acid followed by propionic and butyric acid. In addition, other organic acid production differed significantly depending on bacterial strains and growth medium.

Keywords: Lactic acid bacteria , organic acid, HPLC analysis, growth medium

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Authors: Zunnu Raen Akhtar, U. Irshad, M. Majid

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Due to the widespread cultivation of transgenic cotton, intense selection pressure resulted in resistant allele in pink bollworm, Pectinophora gossypiella (Gelechiidae: Lepidoptera). A resistant strain of pink bollworm against transgenic cotton has become a challenge to Integrated Resistance Management (IRM) in the World. Laboratory and field studies were conducted to determine the resistant strains of pink bollworm by performing bioassay, extracting the DNA, conducting PCR of both laboratory as well as field collected pink bollworms to observe the developed resistance. In all of the studies, two Bt varieties FH-142 and FH-118 expressing Cry1Ac compared to non-Bt (Control) were tested against pink bollworm. In the laboratory, bioassay results showed that there was no significant mortality difference between Bt and non-Bt varieties. Similar mortality percentage was observed in transgenic and non-transgenic (control) variety. Insects which were survived after bioassay, as well as those collected from the Bt cotton fields, were selected for further molecular studies. DNA extraction followed by PCR was conducted to check the resistant strains in pink bollworm. In field studies, we also observed the population dynamics of pink boll worms on Bt as compared to non-Bt varieties. Laboratory and field studies confirmed that resistant strains occurs in Pakistani Bt cotton fields. Different strategies should be adopted to combat that serious prevailing resistance issues.

Keywords: transgenic cotton, resistance, pectinophora gossypiella, , integrated resistance management (IRM), polymerase chain reaction (PCR)

Procedia PDF Downloads 209

Authors: G. R. Hashemi Tabar, G. R. Razmi, F. Mirshekar

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Echinococcus granulosus have ten strains from G1 to G9. Each strain is related to special intermediated host. The morphology, epidemiology, treatment and control in these strains are different. There are many morphological and molecular methods to differentiate of Echinococcus strains. However, using both methods were provided better information about identification of each strain. The aim of study was to identify Echinococcus granulosus strain of hydrated cysts in slaughtered sheep using morphological and molecular methods in Mashhad area. In the present study, the infected liver and lung with hydatid cysts were collected and transferred to laboratory. The hydatid cyst liquid was extracted and morphological characters of rostellar hook protosclocies were measured using micrometer ocular. The total length of large blade length of large hooks, total length of small and blade length of small hooks, and number of hooks per protoscolex were 23± 0.3μm, 11.7±0.5 μm, 19.3±1.1 μm,8±1.1 and 33.7±0.7 μm, respectively. In molecular section of the study, DNA each samples was extracted with MBST Kit and development of PCR using special primers (EgF, EgR) which amplify fragment of ITS1 gen. The PCR product was digested with Bsh1236I enzyme. Based on pattern of PCR-RLFP results (four band forming), G1, G2 and G3 strain of Echinococcus granulosus were obtained. Differentiation of three strains was done using sequencing analysis and G1 strain was diagnosed. The agreement between the molecular results with morphometric characters of rosetellar hook was confirmed the presence of G1 strain of Echinococcus in the slaughtered sheep of Mashhad area.

Keywords: Echinococcus granulosus, Hydatid cyst, PCR, sheep

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Authors: Edvard P. G. Bruun

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One of the best ways of improving our understanding of reinforced concrete is through large-scale experimental testing. The gathered information is critical in making inferences about structural mechanics and deriving the mathematical models that are the basis for finite element analysis programs and design codes. An effective way of measuring the strains across a region of a specimen is by using a system of surface mounted Linear Variable Differential Transformers (LVDTs). While a single LVDT can only measure the linear strain in one direction, by combining several measurements at known angles a Mohr’s circle of strain can be derived for the whole region under investigation. This paper presents a method that can be used by researchers, which improves the accuracy and removes experimental bias in the calculation of the Mohr’s circle, using four rather than three independent strain measurements. Obtaining high quality strain data is essential, since knowing the angular deviation (shear strain) and the angle of principal strain in the region are important properties in characterizing the governing structural mechanics. For example, the Modified Compression Field Theory (MCFT) developed at the University of Toronto, is a rotating crack model that requires knowing the direction of the principal stress and strain, and then calculates the average secant stiffness in this direction. But since LVDTs can only measure average strains across a plane (i.e., between discrete points), localized cracking and spalling that typically occur in reinforced concrete, can lead to unrealistic results. To build in redundancy and improve the quality of the data gathered, the typical experimental setup for a large-scale shell specimen has four independent directions (X, Y, H, and V) that are instrumented. The question now becomes, which three should be used? The most common approach is to simply discard one of the measurements. The problem is that this can produce drastically different answers, depending on the three strain values that are chosen. To overcome this experimental bias, and to avoid simply discarding valuable data, a more rigorous approach would be to somehow make use of all four measurements. This paper presents the derivation of a method to draw what is effectively a Mohr’s circle of 'best-fit', which optimizes the circle by using all four independent strain values. The four-strain optimized Mohr’s circle approach has been utilized to process data from recent large-scale shell tests at the University of Toronto (Ruggiero, Proestos, and Bruun), where analysis of the test data has shown that the traditional three-strain method can lead to widely different results. This paper presents the derivation of the method and shows its application in the context of two reinforced concrete shells tested in pure torsion. In general, the constitutive models and relationships that characterize reinforced concrete are only as good as the experimental data that is gathered – ensuring that a rigorous and unbiased approach exists for calculating the Mohr’s circle of strain during an experiment, is of utmost importance to the structural research community.

Keywords: reinforced concrete, shell tests, Mohr’s circle, experimental research

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Authors: Syahira Ibrahim, Herlina Abdul Rahim

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The amylose content is an essential element in determining the texture and taste of rice grains. This paper evaluates the use of VIS-SWNIRS in estimating the amylose content for seven varieties of rice grains available in the Malaysian market. Each type consists of 30 samples and all the samples are scanned using the spectroscopy to obtain a range of values between 680-1000nm. The Savitzky-Golay (SG) smoothing filter is applied to each sample’s data before the Principal Component Regression (PCR) technique is used to examine the data and produce a single value for each sample. This value is then compared with reference values obtained from the standard iodine colorimetric test in terms of its coefficient of determination, R2. Results show that this technique produced low R2 values of less than 0.50. In order to improve the result, the range should include a wavelength range of 1100-2500nm and the number of samples processed should also be increased.

Keywords: amylose content, diffuse reflectance, Malaysia rice grain, principal component regression (PCR), Visible and Shortwave near-infrared spectroscopy (VIS-SWNIRS)

Procedia PDF Downloads 357

Authors: Dheepshika Kodieswaran

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The persisting problem in the world that continuously impose our planet at risk is the increasing amounts of recalcitrant. One such issue is the disposal of the Petroleum Refinery Sludge (PRS) which constitutes hydrocarbons that are hazardous to terrestrial and aquatic life. The comparatively safe approach to handling these wastes is by microbial degradation, while the other chemical and physical methods are either expensive and/or produce secondary pollutants. The bacterial and algal systems have different pathways for the degradation of hydrocarbons, and their growth rates vary. This study shows how different bacterial and microalgal strains degrade the polyaromatic hydrocarbon PAHs individually and their symbiotic influence on degradation as well. In this system, the metabolites and gaseous exchange help each other in growth. This method using also aids in the accumulation of lipids in microalgal cells and from which bio-oils can also be extracted. The bacterial strains used in this experiment are reported to be indigenous strains isolated from PRS. The target PAH studied were anthracene and pyrene for a period of 28 days. The PAH degradation kinetics best fitted the Gompertz model, and the order of the kinetics, rate constants, and half-life was determined.

Keywords: petroleum refinery sludge, co-culturing, polycyclic hydrocarbons, microalgal-bacterial consortia

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Authors: Murada Alholy, Mengshi Lin, Omar Alhaj, Mahmoud Abugoush

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Alicyclobacillus is a causative agent of spoilage in pasteurized and heat-treated apple juice products. Differentiating between this genus and the closely related Bacillus is crucially important. In this study, Fourier transform infrared spectroscopy (FT-IR) was used to identify and discriminate between four Alicyclobacillus strains and four Bacillus isolates inoculated individually into apple juice. Loading plots over the range of 1350 and 1700 cm-1 reflected the most distinctive biochemical features of Bacillus and Alicyclobacillus. Multivariate statistical methods (e.g. principal component analysis (PCA) and soft independent modeling of class analogy (SIMCA)) were used to analyze the spectral data. Distinctive separation of spectral samples was observed. This study demonstrates that FT-IR spectroscopy in combination with multivariate analysis could serve as a rapid and effective tool for fruit juice industry to differentiate between Bacillus and Alicyclobacillus and to distinguish between species belonging to these two genera.

Keywords: alicyclobacillus, bacillus, FT-IR, spectroscopy, PCA

Procedia PDF Downloads 455