Search results for: massively parallel sequencing

Authors: Seungwoo Kim, Yeongcheol Cho

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In this paper, a holonomic mobile robot is designed in omnidirectional wheels and an adaptive fuzzy controller is presented for its precise trajectories. A kind of adaptive controller based on fuzzy multi-layered algorithm is used to solve the big parametric uncertainty of motor-controlled dynamic system of 3-wheels omnidirectional mobile robot. The system parameters such as a tracking force are so time-varying due to the kinematic structure of omnidirectional wheels. The fuzzy adaptive control method is able to solve the problems of classical adaptive controller and conventional fuzzy adaptive controllers. The basic idea of new adaptive control scheme is that an adaptive controller can be constructed with parallel combination of robust controllers. This new adaptive controller uses a fuzzy multi-layered architecture which has several independent fuzzy controllers in parallel, each with different robust stability area. Out of several independent fuzzy controllers, the most suited one is selected by a system identifier which observes variations in the controlled system parameter. This paper proposes a design procedure which can be carried out mathematically and systematically from the model of a controlled system. Finally, the good performance of a holonomic mobile robot is confirmed through live tests of the tracking control task.

Keywords: fuzzy adaptive control, fuzzy multi-layered controller, holonomic mobile robot, omnidirectional wheels, robustness and stability.

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Authors: Chengwei Wang, Shuqing Xu, Philipp M. Schlüter

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The genus Ophrys is remarkable for its mimicry, flower-lip closely resembling pollinator females in a species-specific manner. Therefore, floral traits associated with pollinator attraction, especially scent, are suitable models for investigating the molecular basis of adaption, speciation, and evolution. Within the two Ophrys species groups: O. sphegodes (S) and O. fusca (F), pollinator shifts among the same insect species have taken place. Preliminary data suggest that they involve a comparable hydrocarbon profile in their scent, which is mainly composed of alkanes and alkenes. Genes encoding stearoyl-acyl carrier protein desaturases (SAD) involved in alkene biosynthesis have been identified in the S group. This study aims to investigate the control and parallel evolution of ecologically significant alkene production in Ophrys. Owing to the central role those SAD genes play in determining positioning of the alkene double-bonds, a detailed understanding of their functional mechanism and of regulatory aspects is of utmost importance. We have identified 5 transcription factors potentially related to SAD expression in O. sphegodes which belong to the MYB, GTE, WRKY, and MADS families. Ultimately, our results will contribute to understanding genes important in the regulatory control of floral scent synthesis.

Keywords: floral traits, transcription factors, biosynthesis, parallel evolution

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Authors: Ritula Thakur, Babankumar S. Bansod, Puneet Mehta, S. Chatterji

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Moisture plays an important role in storage, harvesting and processing of food grains and related agricultural products. It is an important characteristic of most agricultural products for maintenance of quality. Accurate knowledge of the moisture content can be of significant value in maintaining quality and preventing contamination of cereal grains. The present work reports the design and development of microcontroller based low cost non-destructive moisture meter, which uses complex impedance measurement method for moisture measurement of wheat using parallel plate capacitor arrangement. Moisture can conveniently be sensed by measuring the complex impedance using a small parallel-plate capacitor sensor filled with the kernels in-between the two plates of sensor, exciting the sensor at 30 KHz and 100 KHz frequencies. The effects of density and temperature variations were compensated by providing suitable compensations in the developed algorithm. The results were compared with standard dry oven technique and the developed method was found to be highly accurate with less than 1% error. The developed moisture meter is low cost, highly accurate, non-destructible method for determining the moisture of grains utilizing the fast computing capabilities of microcontroller.

Keywords: complex impedance, moisture content, electrical properties, safety of food

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Authors: Fei Sun, Meilan Xu, Jianghui Zhu, Maria Stefanie Dwiyanti, Cheolwoo Park, Fanjiang Kong, Baohui Liu, Tetsuya Yamada, Jun Abe

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Reduced or lack of sensitivity to long daylengths is a key character for soybean, a short-day crop, to adapt to higher latitudinal environments. However, the photoperiod-insensitivity often results in a reduction of the duration of vegetative growth and final yield. To overcome this limitation, a photoperiod insensitive line (RIL16) was developed in this study that delayed flowering from the recombinant inbred population derived from a cross between a photoperiod-insensitive cultivar AGS292 and a late-flowering Thai cultivar K3. Expression analyses under SD and LD conditions revealed that the expression levels of FLOWERING LOCUS T (FT) orthologues, FT2a and FT5a, were lowered in RIL16 relative to AGS292, although the expression of E1, a soybean-specific suppressor for FTs, was inhibited in both conditions. A soybean orthologue of TARGET OF EAT1 (TOE1), another suppressor of FT, showed an upregulated expression in RIL16, which appeared to reflect a lower expression of miR172a. Our data suggest that the delayed flowering of RIL16 most likely is controlled by genes involved in an age-dependent pathway in flowering. The QTL analysis based on 1,125 SNPs obtained from Restriction Site Associated DNA Sequencing revealed two major QTLs for flowering dates in Chromosome 16 and two minor QTLs in Chromosome 4, all of which accounted for 55% and 48% of the whole variations observed in natural day length and artificially-induced long day length conditions, respectively. The intervals of the major QTLs harbored FT2a and FT5a, respectively, on the basis of annotated genes in the Williams 82 reference genome. Sequencing analysis further revealed a nonsynonymous mutation in FT2a and an SNP in the 3′ UTR region of FT5a. A further study may elucidate a detailed mechanism underlying the QTL for late flowering. The alleles from K3 at the two QTLs can be used singly or in combination to retain an appropriate duration of vegetative growth to maximize the final yield of photoperiod-insensitive soybeans.

Keywords: FT genes, miR72a, photoperiod-insensitive, soybean flowering

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Authors: Waleed M. Al-Othman, Hamid Bayati, Abdullah Al-Shahrani, Haitham Al-Jabr

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Pearlite bands commonly form parallel to the surface of the hot rolled steel and have significant influence on the properties of the steel. This study investigated the correlation between segregation pattern of Mn, Si, C and formation of the pearlite bands in hot rolled Gr 60 steel plate. Microstructural study indicated formation of a distinguished thick band at centerline of the plate with number of parallel bands through thickness of the steel plate. The thickness, frequency, and continuity of the bands are reduced from mid-thickness toward external surface of the steel plate. Analysis showed a noticeable increase of C, Si and Mn levels within the bands. Such alloying segregation takes place during metal solidification. EDS analysis verified presence of particles rich in Ti, Nb, Mn, C, N, within the bands. Texture analysis by Electron Backscatter Detector (EBSD) indicated the grains size/misorientation can noticeably change within the bands. Effect of banding on through-thickness properties of the steel was examined by carrying out microhardness, toughness and tensile tests. Results suggest the Mn and C contents are changed in sinusoidal pattern through thickness of the hot rolled plate and pearlite bands are formed at the peaks of this sinusoidal segregation pattern. Changes in grain size/misorientation, formation of highly alloyed particles, and pearlite within these bands, facilitate crack formation along boundaries of these bands.

Keywords: pearlite band, alloying segregation, hot rolling, Ti, Nb, N, C

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Authors: Nizar Ibnus

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The term 'pribumi' or indigenous people was originally coined in the colonisation era to differentiate between Dutch colonials and native Indonesian people. The term was also used to trigger nationalism among Indonesian people to liberate their country from any kind of colonialism which had seized their freedom for ages. However, after the war was over and the colonials had fled from the country, the usage began to be altered. It changed from nationalist propaganda term to somewhat racist term. Immigrants and half-blooded people were massively victimized. Then, in 1998 the government forbade the use of this term for public use. Apparently, this racial issue happens again. On 16th October 2017, Anies Baswedan as the new government of DKI Jakarta province mentioned this term in his inauguration speech. This indeed raises controversy among Indonesian people. Using critical discourse analysis, this paper examines how Indonesian media portray the figure of Anies Baswedan regarding the issue. The findings reveal that Indonesian media depict Anies Baswedan differently. Some view him guilty as he mentioned the controversial and forbidden term in public. While, the other media consider him as innocent as he used the term in different contexts. This various media point of view and framing is presumably emerged from their different ideologies.

Keywords: critical discourse analysis, media framing, racism, pribumi

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Authors: Sakeh N. Mohd, Bahari M. N. Abdul, Abdullah S. N. Akmar

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Oil palm production generates high export earnings to many countries especially in Southeast Asian region. Infection by necrotrophic fungus, Ganoderma boninense on oil palm results in basal stem rot which compromises oil palm production leading to significant economic loss. There are no reliable disease treatments nor promising resistant oil palm variety has been cultivated to eradicate the disease up to date. Thus, understanding molecular mechanisms underlying early interactions of oil palm with Ganoderma boninense may be vital to promote preventive or control measure of the disease. In the present study, four months old oil palm seedlings were infected via artificial inoculation of Ganoderma boninense on rubber wood blocks. Roots of six biological replicates of treated and untreated oil palm seedlings were harvested at 0, 3, 7 and 11 days post inoculation. Next-generation sequencing was performed to generate high-throughput RNA-Seq data and identify differentially expressed genes (DEGs) during early oil palm-Ganoderma boninense interaction. Based on de novo transcriptome assembly, a total of 427,122,605 paired-end clean reads were assembled into 30,654 unigenes. DEGs analysis revealed upregulation of 173 transcription factors on Ganoderma boninense-treated oil palm seedlings. Sixty-one transcription factors were categorized as DEGs according to stringent cut-off values of genes with log2 ratio [Number of treated oil palm seedlings/ Number of untreated oil palm seedlings] ≥ |1.0| (corresponding to 2-fold or more upregulation) and P-value ≤ 0.01. Transcription factors in response to biotic stress will be screened out from abiotic stress using reverse transcriptase polymerase chain reaction. Transcription factors unique to biotic stress will be verified using real-time polymerase chain reaction. The findings will help researchers to pinpoint defense response mechanism specific against Ganoderma boninense.

Keywords: Ganoderma boninense, necrotrophic, next-generation sequencing, transcription factors

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Authors: María de los Ángeles Crespo López, Carmen García García

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The highly competitive nature of today's globalised marketplace requires that brands and stores develop effective commercial strategies to ensure their economic survival. Maintaining the loyalty of existing customers constitutes one key strategy that yields the best results. Although the relationship between consumers' self-congruity and their manifestations of loyalty towards a store has been investigated, the role of store personality in this relationship remains unclear. In this study, multiple parallel mediation analysis was used to examine the effect of Store Personality on the relationship between Self-Congruity of consumers and their Manifestations of Loyalty. For this purpose, 457 Spanish consumers of the Fnac store completed three self-report questionnaires assessing Store Personality, Self-Congruity, and Store Loyalty. The data were analyzed using the SPSS macro PROCESS. The results revealed that three dimensions of Store Personality, namely Exciting, Close and Competent Store, positively and significantly mediated the relationship between Self-Congruity and Manifestations of Loyalty. The indirect effect of Competent Store was the greatest. This means that a consumer with higher levels of Self-Congruity with the store will exhibit more Manifestations of Loyalty when the store is perceived as Exciting, Close or Competent. These findings suggest that more attention should be paid to the perceived personality of stores for the development of effective marketing strategies to maintain or increase consumers' manifestations of loyalty towards stores.

Keywords: multiple parallel mediation, PROCESS, self-congruence, store loyalty, store personality

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Authors: Sara Salehi, Ka Yu Cheng, Anna Heitz, Maneesha Ginige

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This study investigated the efficiency of granular sludge for phosphorous (P) recovery from wastewater. A laboratory scale sequencing batch reactor (SBR) was operated under alternating aerobic/anaerobic conditions to enrich a P accumulating granular biomass. This study showed that an overall 45-fold increase in P concentration could be achieved by reducing the volume of the P capturing liquor by 5-fold in the anaerobic P release phase. Moreover, different fractions of the granular biomass have different individual contributions towards generating a concentrated stream of P.

Keywords: granular sludge, PAOs, P recovery, SBR

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Authors: Ian Campbell, Gillian Mitchell, Paul James, Na Li, Ella Thompson

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The genetic cause of the majority of multiple-case breast cancer families remains unresolved. Next generation sequencing has emerged as an efficient strategy for identifying predisposing mutations in individuals with inherited cancer. We are conducting whole exome sequence analysis of germ line DNA from multiple affected relatives from breast cancer families, with the aim of identifying rare protein truncating and non-synonymous variants that are likely to include novel cancer predisposing mutations. Data from more than 200 exomes show that on average each individual carries 30-50 protein truncating mutations and 300-400 rare non-synonymous variants. Heterogeneity among our exome data strongly suggest that numerous moderate penetrance genes remain to be discovered, with each gene individually accounting for only a small fraction of families (~0.5%). This scenario marks validation of candidate breast cancer predisposing genes in large case-control studies as the rate-limiting step in resolving the missing heritability of breast cancer. The aim of this study is to screen genes that are recurrently mutated among our exome data in a larger cohort of cases and controls to assess the prevalence of inactivating mutations that may be associated with breast cancer risk. We are using the Agilent HaloPlex Target Enrichment System to screen the coding regions of 168 genes in 1,000 BRCA1/2 mutation-negative familial breast cancer cases and 1,000 cancer-naive controls. To date, our interim analysis has identified 21 genes which carry an excess of truncating mutations in multiple breast cancer families versus controls. Established breast cancer susceptibility gene PALB2 is the most frequently mutated gene (13/998 cases versus 0/1009 controls), but other interesting candidates include NPSR1, GSN, POLD2, and TOX3. These and other genes are being validated in a second cohort of 1,000 cases and controls. Our experience demonstrates that beyond PALB2, the prevalence of mutations in the remaining breast cancer predisposition genes is likely to be very low making definitive validation exceptionally challenging.

Keywords: predisposition, familial, exome sequencing, breast cancer

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: Ronal Muresano, Andrea Pagano

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Nowadays, the mathematical/statistical applications are developed with more complexity and accuracy. However, these precisions and complexities have brought as result that applications need more computational power in order to be executed faster. In this sense, the multicore environments are playing an important role to improve and to optimize the execution time of these applications. These environments allow us the inclusion of more parallelism inside the node. However, to take advantage of this parallelism is not an easy task, because we have to deal with some problems such as: cores communications, data locality, memory sizes (cache and RAM), synchronizations, data dependencies on the model, etc. These issues are becoming more important when we wish to improve the application’s performance and scalability. Hence, this paper describes an optimization method developed for Systemic Model of Banking Originated Losses (SYMBOL) tool developed by the European Commission, which is based on analyzing the application's weakness in order to exploit the advantages of the multicore. All these improvements are done in an automatic and transparent manner with the aim of improving the performance metrics of our tool. Finally, experimental evaluations show the effectiveness of our new optimized version, in which we have achieved a considerable improvement on the execution time. The time has been reduced around 96% for the best case tested, between the original serial version and the automatic parallel version.

Keywords: algorithm optimization, bank failures, OpenMP, parallel techniques, statistical tool

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Authors: Laurentiu Moruz, Jens Kitzhofer, Mircea Dinulescu

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The paper aims to extend the knowledge about jet behavior and jet interaction between five plane unventilated jets with large aspect ratio (AR). The distance between the single plane jets is two times the channel height. The experimental investigation applies 2D Particle Image Velocimetry (PIV) and static pressure measurements. Our study focuses on the influence of two different outlet nozzle geometries (triangular shape with 2 x 7.5° and blunt geometry) with respect to variation of Reynolds number from 5500 - 12000. It is shown that the outlet geometry has a major influence on the jet formation in terms of uniformity of velocity profiles downstream of the sudden expansion. Furthermore, we describe characteristic regions like converging region, merging region and combined region. The triangular outlet geometry generates most uniform velocity distributions in comparison to a blunt outlet nozzle geometry. The blunt outlet geometry shows an unstable behavior where the jets tend to attach to one side of the walls (ceiling) generating a large recirculation region on the opposite side. Static pressure measurements confirm the observation and indicate that the recirculation region is connected to larger pressure drop.

Keywords: 2D particle image velocimetry, parallel jet interaction, pressure drop, sudden expansion

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Authors: Ece A. Irmak, Amdulla O. Mekhrabov, M. Vedat Akdeniz

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There is a growing interest in the modeling and simulation of magnetic nanoalloys by various computational methods. Magnetic crystalline/amorphous nanoparticles (NP) are interesting materials from both the applied and fundamental points of view, as their properties differ from those of bulk materials and are essential for advanced applications such as high-performance permanent magnets, high-density magnetic recording media, drug carriers, sensors in biomedical technology, etc. As an important magnetic material, Fe-Ni based nanoalloys have promising applications in the chemical industry (catalysis, battery), aerospace and stealth industry (radar absorbing material, jet engine alloys), magnetic biomedical applications (drug delivery, magnetic resonance imaging, biosensor) and computer hardware industry (data storage). The physical and chemical properties of the nanoalloys depend not only on the particle or crystallite size but also on composition and atomic ordering. Therefore, computer modeling is an essential tool to predict structural, electronic, magnetic and optical behavior at atomistic levels and consequently reduce the time for designing and development of new materials with novel/enhanced properties. Although first-principles quantum mechanical methods provide the most accurate results, they require huge computational effort to solve the Schrodinger equation for only a few tens of atoms. On the other hand, molecular dynamics method with appropriate empirical or semi-empirical inter-atomic potentials can give accurate results for the static and dynamic properties of larger systems in a short span of time. In this study, structural evolutions, magnetic and electronic properties of Fe-Ni based nanoalloys have been studied by using molecular dynamics (MD) method in Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and Density Functional Theory (DFT) in the Vienna Ab initio Simulation Package (VASP). The effects of particle size (in 2-10 nm particle size range) and temperature (300-1500 K) on stability and structural evolutions of amorphous and crystalline Fe-Ni bulk/nanoalloys have been investigated by combining molecular dynamic (MD) simulation method with Embedded Atom Model (EAM). EAM is applicable for the Fe-Ni based bimetallic systems because it considers both the pairwise interatomic interaction potentials and electron densities. Structural evolution of Fe-Ni bulk and nanoparticles (NPs) have been studied by calculation of radial distribution functions (RDF), interatomic distances, coordination number, core-to-surface concentration profiles as well as Voronoi analysis and surface energy dependences on temperature and particle size. Moreover, spin-polarized DFT calculations were performed by using a plane-wave basis set with generalized gradient approximation (GGA) exchange and correlation effects in the VASP-MedeA package to predict magnetic and electronic properties of the Fe-Ni based alloys in bulk and nanostructured phases. The result of theoretical modeling and simulations for the structural evolutions, magnetic and electronic properties of Fe-Ni based nanostructured alloys were compared with experimental and other theoretical results published in the literature.

Keywords: density functional theory, embedded atom model, Fe-Ni systems, molecular dynamics, nanoalloys

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Authors: Suchithra V., Shreedhanya, Kavya Menon, Vidya Niranjan

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Skin metagenomics has a wide range of applications with direct relevance to the health of the organism. It gives us insight to the diverse community of microorganisms (the microbiome) harbored on the skin. In the recent years, it has become increasingly apparent that the interaction between skin microbiome and the human body plays a prominent role in immune system development, cancer development, disease pathology, and many other biological implications. Next Generation Sequencing has led to faster and better understanding of environmental organisms and their mutual interactions. This project is studying the human skin microbiome of different individuals having varied skin conditions. Bacterial 16S rRNA data of skin microbiome is downloaded from SRA toolkit provided by NCBI to perform metagenomics analysis. Twelve samples are selected with two controls, and 3 different categories, i.e., sex (male/female), skin type (moist/intermittently moist/sebaceous) and occlusion (occluded/intermittently occluded/exposed). Quality of the data is increased using Cutadapt, and its analysis is done using FastQC. USearch, a tool used to analyze an NGS data, provides a suitable platform to obtain taxonomy classification and abundance of bacteria from the metagenome data. The statistical tool used for analyzing the USearch result is METAGENassist. The results revealed that the top three abundant organisms found were: Prevotella, Corynebacterium, and Anaerococcus. Prevotella is known to be an infectious bacterium found on wound, tooth cavity, etc. Corynebacterium and Anaerococcus are opportunist bacteria responsible for skin odor. This result infers that Prevotella thrives easily in sebaceous skin conditions. Therefore it is better to undergo intermittently occluded treatment such as applying ointments, creams, etc. to treat wound for sebaceous skin type. Exposing the wound should be avoided as it leads to an increase in Prevotella abundance. Moist skin type individuals can opt for occluded or intermittently occluded treatment as they have shown to decrease the abundance of bacteria during treatment.

Keywords: bacterial 16S rRNA , next generation sequencing, skin metagenomics, skin microbiome, taxonomy

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Authors: Tarang Varmora, Krupa Shah, Karan Patel

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Environmental pollution and shortage of conventional fuel are the main concerns in the transportation sector. Most of the vehicles use an internal combustion engine (ICE), powered by gasoline fuels. This results into emission of toxic gases. Hybrid electric vehicle (HEV) powered by electric machine and ICE is capable of reducing emission of toxic gases and fuel consumption. However to build HEV, it is required to accommodate motor and batteries in the vehicle along with engine and fuel tank. Thus, overall weight of the vehicle increases. To improve the fuel economy and acceleration, the weight of the HEV can be minimized. In this paper, the design methodology to reduce the weight of the hybrid racing car is proposed. To this end, the chassis design is optimized. Further, attempt is made to obtain the maximum strength with minimum material weight. The best configuration out of the three main configurations such as series, parallel and the dual-mode (series-parallel) is chosen. Moreover, the most suitable type of motor, battery, braking system, steering system and suspension system are identified. The racing car is designed and analyzed in the simulating software. The safety of the vehicle is assured by performing static and dynamic analysis on the chassis frame. From the results, it is observed that, the weight of the racing car is reduced by 11 % without compromising on safety and cost. It is believed that the proposed design and specifications can be implemented practically for manufacturing hybrid racing car.

Keywords: design optimization, hybrid racing car, simulation, vehicle, weight reduction

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Authors: Ibrahim Tiryakioglu, Mehmet Ali Ugur, Caglar Ozkaymak

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The development of GNSS technology has led to increasingly widespread and successful applications of GNSS surveys for monitoring crustal movements. However, multi-period GPS survey solutions have not been applied in monitoring vertical surface deformation. This study uses long-term GNSS time series that are required to determine vertical deformations. In recent years, the surface deformations that are parallel and semi-parallel to Bolvadin fault have occurred in Western Anatolia. These surface deformations have continued to occur in Bolvadin settlement area that is located mostly on alluvium ground. Due to these surface deformations, a number of cracks in the buildings located in the residential areas and breaks in underground water and sewage systems have been observed. In order to determine the amount of vertical surface deformations, two continuous GNSS stations have been established in the region. The stations have been operating since 2015 and 2017, respectively. In this study, GNSS observations from the mentioned two GNSS stations were processed with GAMIT/GLOBK (GNSS Analysis Massachusetts Institute of Technology/GLOBal Kalman) program package to create a coordinate time series. With the time series analyses, the GNSS stations’ behavior models (linear, periodical, etc.), the causes of these behaviors, and mathematical models were determined. The study results from the time series analysis of these two 2 GNSS stations shows approximately 50-80 mm/yr vertical movement.

Keywords: Bolvadin fault, GAMIT, GNSS time series, surface deformations

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Authors: Rihab Hamdi, Amel Hadri Hamida, Ouafae Bennis, Sakina Zerouali

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This paper features a performance analysis and robustness assessment of a digitally controlled DC-DC three-cell buck converter associated in parallel, operating in continuous conduction mode (CCM), facing feeding parameters variation and loads disturbance. The control strategy relies on the continuous-time with an averaged modeling technique for high-frequency switching converter. The methodology is to modulate the complete design procedure, in regard to the existence of an instantaneous current operating point for designing the digital closed-loop, to the same continuous-time domain. Moreover, the adopted approach is to include a digital voltage control (DVC) technique, taking an account for digital control delays and sampling effects, which aims at improving efficiency and dynamic response and preventing generally undesired phenomena. The results obtained under load change, input change, and reference change clearly demonstrates an excellent dynamic response of the proposed technique, also as provide stability in any operating conditions, the effectiveness is fast with a smooth tracking of the specified output voltage. Simulations studies in MATLAB/Simulink environment are performed to verify the concept.

Keywords: continuous conduction mode, digital control, parallel multi-cells converter, performance analysis, power electronics

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Authors: M. Gogniashvili, I. Maisaia, A. Kotorashvili, N. Kotaria, T. Beridze

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Three types of plasmon (A, B and G) is typical for genus Triticum. In polyploid species - Triticum turgidum L. and Triticum aestivum L. plasmon B is detected. In the forthcoming paper, complete nucleotide sequence of chloroplast DNA of 11 representatives of Georgian wheat polyploid species, carrying plasmon B was determined. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. All contigs were aligned to the reference chloroplast genome sequence using BLASTN. For detection of SNPs and Indels and phylogeny tree construction computer programs Mafft and Blast were used. Using Triticum aestivum L. subsp. macha (Dekapr. & Menabde) Mackey var. paleocolchicum Dekapr. et Menabde as a reference, 5 SNPs can be identified in chloroplast DNA of Georgian endemic polyploid wheat. The number of noncoding substitutions is 2, coding substitutions - 3. In comparison with reference DNA two - 38 bp and 56 bp inversions were observed in paleocolchicum subspecies. There were six 1 bp indels detected in Georgian polyploid wheats, all of them at microsatellite stretches. The phylogeny tree shows that subspecies macha, carthlicum and paleocolchicum occupy different positions. According to the simplified scheme based on SNP and indel data, the ancestral, female parent of the all studied polyploid wheat is unknown X predecesor, from which four lines were formed. 1 SNP and two inversions (38 bp and 56 bp) caused the formation of subsp. paleocolchicum. Three other lines are macha, durum and carthlicum lines. Macha line is further divided into two sublines (M_1 and M_4). Carthlicum line includes subsp.carthlicum and T.aestivum - C_1 - C_2 - A_1. One of the central question of wheat domestication is which people(s) participated in wheat domestication? It is proposed that the predecessors of Georgian peoples (Proto-Kartvelians) must be placed, on the evidence of archaic lexical and toponymic data, in the mountainous regions of the western and central part of the Little Caucasus (the Transcaucasian foothills) at least 4,000 years ago. One of the possibility to explain the ‘wheat puzzle’ is that Kartvelian speakers brought domesticated wheat species and subspecis from Fertile Crescent further north to South Caucasus.

Keywords: chloroplast DNA, sequencing, SNP, triticum

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Youngjae Jin, Daeshik Kim

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This paper describes a cycle accurate simulation results of weight values learned by an auto-encoder behavior model in terms of pre-route simulation. Given the results we visualized the first layer representations with natural images. Many common deep learning threads have focused on learning high-level abstraction of unlabeled raw data by unsupervised feature learning. However, in the process of handling such a huge amount of data, the learning method’s computation complexity and time limited advanced research. These limitations came from the fact these algorithms were computed by using only single core CPUs. For this reason, parallel-based hardware, FPGAs, was seen as a possible solution to overcome these limitations. We adopted and simulated the ready-made auto-encoder to design a behavior model in Verilog HDL before designing hardware. With the auto-encoder behavior model pre-route simulation, we obtained the cycle accurate results of the parameter of each hidden layer by using MODELSIM. The cycle accurate results are very important factor in designing a parallel-based digital hardware. Finally this paper shows an appropriate operation of behavior model based pre-route simulation. Moreover, we visualized learning latent representations of the first hidden layer with Kyoto natural image dataset.

Keywords: auto-encoder, behavior model simulation, digital hardware design, pre-route simulation, Unsupervised feature learning

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Authors: Corey F. Fitzgerald

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This study provides a comprehensive examination of the biomechanical sequencing inherent in pitching motions, coupled with an advanced methodology for interpreting gathered data to inform programming strategies. The analysis is conducted utilizing state-of-the-art biomechanical laboratory equipment capable of detecting subtle changes and deviations, facilitating highly informed decision-making processes. Through this presentation, the intricate dynamics of pitching sequences are meticulously discussed to highlight the complex movement patterns accessible and actionable for performance enhancement purposes in the weight room.

Keywords: sport science, applied biomechanics, strength and conditioning, applied research

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Authors: Mirvat Shamseddine, Issam Lakkis

Abstract:

We present an efficient, three-dimensional parallel multi-scale Direct Simulation Monte Carlo (DSMC) algorithm for the simulation of unsteady rarefied gas flows in micro/nanosystems. The algorithm employs a novel spatiotemporal adaptivity scheme. The scheme performs a fully dynamic multi-level grid adaption based on the gradients of flow macro-parameters and an automatic temporal adaptation. The computational domain consists of a hierarchical octree-based Cartesian grid representation of the flow domain and a triangular mesh for the solid object surfaces. The hybrid mesh, combined with the spatiotemporal adaptivity scheme, allows for increased flexibility and efficient data management, rendering the framework suitable for efficient particle-tracing and dynamic grid refinement and coarsening. The parallel algorithm is optimized to run DSMC simulations of strongly unsteady, non-equilibrium flows over multiple cores. The presented method is validated by comparing with benchmark studies and then employed to improve the design of micro-scale hotwire thermal sensors in rarefied gas flows.

Keywords: DSMC, oct-tree hierarchical grid, ray tracing, spatial-temporal adaptivity scheme, unsteady rarefied gas flows

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Authors: Osamede Asowata, Christo Pienaar, Johan Bekker

Abstract:

Photovoltaic (PV) modules may become a trend for future PV systems because of their greater flexibility in distributed system expansion, easier installation due to their nature, and higher system-level energy harnessing capabilities under shaded or PV manufacturing mismatch conditions. This is as compared to the single or multi-string inverters. Novel residential scale PV arrays are commonly connected to the grid by a single DC–AC inverter connected to a series, parallel or series-parallel string of PV panels, or many small DC–AC inverters which connect one or two panels directly to the AC grid. With an increasing worldwide interest in sustainable energy production and use, there is renewed focus on the power electronic converter interface for DC energy sources. Three specific examples of such DC energy sources that will have a role in distributed generation and sustainable energy systems are the photovoltaic (PV) panel, the fuel cell stack, and batteries of various chemistries. A high-efficiency inverter using Metal Oxide Semiconductor Field-Effect Transistors (MOSFETs) for all active switches is presented for a non-isolated photovoltaic and AC-module applications. The proposed configuration features a high efficiency over a wide load range, low ground leakage current and low-output AC-current distortion with no need for split capacitors. The detailed power stage operating principles, pulse width modulation scheme, multilevel bootstrap power supply, and integrated gate drivers for the proposed inverter is described. Experimental results of a hardware prototype, show that not only are MOSFET efficient in the system, it also shows that the ground leakage current issues are alleviated in the proposed inverter and also a 98 % maximum associated driver circuit is achieved. This, in turn, provides the need for a possible photovoltaic panel switching technique. This will help to reduce the effect of cloud movements as well as improve the overall efficiency of the system.

Keywords: grid connected photovoltaic (PV), Matlab efficiency simulation, maximum power point tracking (MPPT), module integrated converters (MICs), multilevel converter, series connected converter

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Authors: Jia-Yu Wu, Chih-Han Chang, Shu-Fen Chuang, Rong-Yang Lai

Abstract:

Objective: This study was to examine the stress distribution of tooth with different class V restorations under different loading situations and geometry by 3D finite element (FE) analysis. `Methods: A series of FE models of mandibular premolars containing class V cavities were constructed using micro-CT. The class V cavities were assigned as the combinations of different cavity depths x occlusal -gingival heights: 1x2, 1x4, 2x2, and 2x4 mm. Three alveolar bone loss conditions were examined: 0, 1, and 2 mm. 200 N force was exerted on the buccal cusp tip under various directions (vertical, V; obliquely 30° angled, O; oblique and parallel the individual occlusal cavity wall, P). A 3-D FE analysis was performed and the von-Mises stress was used to summarize the data of stress distribution and maximum stress. Results: The maximal stress did not vary in different alveolar bone heights. For each geometry, the maximal stress was found at bilateral corners of the cavity. The peak stress of restorations was significantly higher under load P compared to those under loads V and O while the latter two were similar. 2x2mm cavity exhibited significantly increased (2.88 fold) stress under load P compared to that under load V, followed by 1x2mm (2.11 fold), 2x4mm (1.98 fold) and 1x4mm (1.1fold). Conclusion: Load direction causes the greatest impact on the results of stress, while the effect of alveolar bone loss is minor. Load direction parallel to the cavity wall may enhance the stress concentration especially in deep and narrow class cavities.

Keywords: class v restoration, finite element analysis, loading situation, stress

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Authors: Danish Laidin, Peter Gostomski, Aaron Marshall, Carlo Carere

Abstract:

Groundwater contamination of nitrate (NO3-) is becoming more prevalent in regions of intensive and extensive agricultural activities. Household nitrate removal involves using ion exchange membranes and reverse osmosis (RO) systems, whereas industrial nitrate removal may use organic carbon substrates (e.g. methanol) for heterotrophic microbial denitrification. However, these approaches both require high capital investment and operating costs. In this study, denitrification was demonstrated using bio-electrochemical systems (BESs) inoculated from sediments and microbial enrichment cultures. The BES reactors were operated continuously as microbial electrolytic cells (MECs) with a poised potential of -0.7V and -1.1V vs Ag/AgCl. Three parallel MECs were inoculated using hydrogen-driven denitrifying enrichments, stream sediments, and biofilm harvested from a denitrifying biotrickling filter, respectively. These reactors were continuously operated for over a year as various operating conditions were investigated to determine the optimal conditions for electroactive denitrification. The mass loading rate of nitrate was varied between 10 – 70 mg NO3-/d, and the maximum observed nitrate removal rate was 22 mg NO3- /(cm2∙d) with a current of 2.1 mA. For volumetric load experiments, the dilution rate of 1 mM NO3- feed was varied between 0.01 – 0.1 hr-1 to achieve a nitrate loading rate similar to the mass loading rate experiments. Under these conditions, the maximum rate of denitrification observed was 15.8 mg NO3- /(cm2∙d) with a current of 1.7mA. Hydrogen (H2) was supplied intermittently to investigate the hydrogenotrophic potential of the denitrifying biofilm electrodes. H2 supplementation at 0.1 mL/min resulted in an increase of nitrate removal from 0.3 mg NO3- /(cm2∙d) to 3.4 mg NO3- /(cm2∙d) in the hydrogenotrophically subcultured reactor but had no impact on the reactors which exhibited direct electron transfer properties. Results from this study depict the denitrification performance of the immobilized biofilm electrodes, either by direct electron transfer or hydrogen-driven denitrification, and the contribution of the planktonic cells present in the growth medium. Other results will include the microbial community analysis via 16s rDNA amplicon sequencing, varying the effect of poising cathodic potential from 0.7V to 1.3V vs Ag/AgCl, investigating the potential of using in-situ electrochemically produced hydrogen for autotrophic denitrification and adjusting the conductivity of the feed solution to mimic groundwater conditions. These findings highlight the overall performance of sediment inoculated MECs in removing nitrate and will be used for the future development of sustainable solutions for the treatment of nitrate polluted groundwater.

Keywords: bio-electrochemical systems, groundwater, electroactive denitrification, microbial electrolytic cell

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Authors: Vinayak Bassi, Rajpreet Singh

Abstract:

Over the years, with the emergence of sophisticated computers and algorithms, finance has been quantified using computational prowess. Asset valuation has been one of the key components of quantitative finance. In fact, it has become one of the embryonic steps in determining risk related to a portfolio, the main goal of quantitative finance. This study comprises a drawing comparison between valuation output generated by two stochastic dynamic models, namely Black-Scholes and Dupire’s bi-dimensionality model. Both of these models are formulated for computing the valuation function for a portfolio of European options using Monte Carlo simulation methods. Although Monte Carlo algorithms have a slower convergence rate than calculus-based simulation techniques (like FDM), they work quite effectively over high-dimensional dynamic models. A fidelity gap is analyzed between the static (historical) and stochastic inputs for a sample portfolio of underlying assets. In order to enhance the performance efficiency of the model, the study emphasized the use of variable reduction methods and customizing random number generators to implement parallelization. An attempt has been made to further implement the Dupire’s model on a GPU to achieve higher computational performance. Furthermore, ideas have been discussed around the performance enhancement and bottleneck identification related to the implementation of options-pricing models on GPUs.

Keywords: monte carlo, stochastic models, computational finance, parallel programming, scientific computing

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Authors: Esther Burkitt

Abstract:

Background: Evidence is mounting that mixed emotions can be experienced simultaneously in different ways across the lifespan. Four types of patterns of simultaneously mixed emotions (sequential, prevalent, highly parallel, and inverse types) have been identified in middle childhood and adolescence. Moreover, the recognition of these experiences tends to develop firstly when children consider peers rather than the self. This evidence from children and adolescents is based on examining the presence of experiences specified in adulthood. The present study, therefore, applied an exhaustive coding scheme to investigate whether children experience types of previously unidentified simultaneous mixed emotional experiences. Methodology: One hundred and twenty children (60 girls) aged 7 years 1 month - 9 years 2 months (X=8 years 1 month; SD = 10 months) were recruited from mainstream schools across the UK. Two age groups were formed (youngest, n = 61, 7 years 1 month- 8 years 1 months: oldest, n = 59, 8 years 2 months – 9 years 2 months) and allocated to one of two conditions hearing vignettes describing happy and sad mixed emotion events in age and gender-matched protagonist or themselves. Results: Loglinear analyses identified new types of flexuous, vertical, and other experiences along with established sequential, prevalent, highly parallel, and inverse types of experience. Older children recognised more complex experiences other than the self-condition. Conclusion: Several additional types of simultaneously mixed emotions are recognised in middle childhood. The theoretical relevance of simultaneous mixed emotion processing in childhood is considered, and the potential utility of the findings in emotion assessments is discussed.

Keywords: emotion, childhood, self, other

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Authors: Nidhi Chadha, A. K. Tiwari, Marilyn D. Milton, Anil K. Mishra

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Translocator protein (18 kDa) TSPO is highly expressed during microglia activation in neuroinflammation. Although a number of PET ligands have been developed for the visualization of activated microglia, one of the advantageous approaches is to develop potential optical imaging (OI) probe. Our study involves computational screening, synthesis and evaluation of TSPO ligand through various imaging modalities namely PET/SPECT/Optical. The initial computational screening involves pharmacophore modeling from the library designing having oxo-benzooxazol-3-yl-N-phenyl-acetamide groups and synthesis for visualization of efficacy of these compounds as multimodal imaging probes. Structure modeling of monomer, Ala147Thr mutated, parallel and anti-parallel TSPO dimers was performed and docking analysis was performed for distinct binding sites. Computational analysis showed pattern of variable binding profile of known diagnostic ligands and NBMP via interactions with conserved residues along with TSPO’s natural polymorphism of Ala147→Thr, which showed alteration in the binding affinity due to considerable changes in tertiary structure. Preliminary in vitro binding studies shows binding affinity in the range of 1-5 nm and selectivity was also certified by blocking studies. In summary, this skeleton was found to be potential probe for TSPO imaging due to ease in synthesis, appropriate lipophilicity and reach to specific region of brain.

Keywords: TSPO, molecular modeling, imaging, docking

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Authors: Shameel Pervez, Saad Aziz Durrani, Ibatsam Khokhar

Abstract:

Pectinase is an enzyme that breaks down pectin, a compound responsible for structural integrity of the plant. Pectin is difficult to break down mechanically and the cost is very high, that is why many industries including food industries use pectinase enzyme produced by microbes for pectin breakdown. Apple (Malus domestica) is an important fruit in terms of market value. Every year, millions of apples are wasted due to post-harvest rot caused by fungi. Fungi are natural decomposers of our ecosystem and are infamous for post-harvest rot of apple fruit but at the same time they are prized for their high production of valuable extracellular enzymes such as pectinase. In this study, fungi belonging to different genus were isolated from rotten apples. Rotten samples of apple were picked from different markets of Lahore. After surface sterilization, the rotten parts were cut into small pieces and placed onto MEA media plates for three days. Afterwards, distinct colonies were picked and purified by sub-culturing. The isolates were identified to genus level through the study of basic colony morphology and microscopic features. The isolates were then subjected to screening for pectinase activity on MS media to compare pectinase production and were then subsequently tested for pathogenic activity through wound suspension method to evaluate the pathogenic activity of isolates in comparison with their pectinolytic activity. A total of twelve fungal strains were isolates from rotten apples. They were belonging to genus Penicillium, Alternaria, Paecilomyces and Rhizopus. Upon screening for pectinolytic activity, isolates Pen 1, Pen 4, and Rz showed high pectinolytic activity and were further subjected to DNA isolation and partial sequencing for species identification. The results of partial sequencing were combined with in-depth study of morphological features revealing Pen 1 as Penicillium janthinellum, Pen 4 as Penicillium griseofulvum, and Rz as Rhizopus microsporus. Pathogenic activity of all twelve isolates was evaluated. Penicillium spp. were highly pathogenic and destructive and same was the case with Paecilomyces sp. and Rhizopus sp. However, Alternaria spp. were found to be more consistent in their pathogenic activity, on all types of apples.

Keywords: apple, pectinase, fungal pathogens, penicillium, rhizopus

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