Search results for: phylogenetic trees

Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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Authors: Monika Szymańska-Czerwińsk, Kinga Zaręba-Marchewka, Krzysztof Niemczuk

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Chlamydiaceae are Gram-negative bacteria distributed worldwide in animals and humans. One of them is Chlamydia gallinacea recently discovered. Available data show that C. gallinacea is dominant chlamydial agent found in poultry in European and Asian countries. The aim of the studies was screening of poultry flocks in order to evaluate frequency of C. gallinacea shedding and genetic diversity. Sampling was conducted in different regions of Poland in 2019-2020. Overall, 1466 cloacal/oral swabs were collected in duplicate from 146 apparently healthy poultry flocks including chickens, turkeys, ducks, geese and quails. Dry swabs were used for DNA extraction. DNA extracts were screened using a Chlamydiaceae 23S rRNA real-time PCR assay. To identify Chlamydia species, specific real-time PCR assays were performed. Furthermore, selected samples were used for sequencing based on ompA gene fragments and variable domains (VD1-2, VD3-4). In total, 10.3% of the tested flocks were Chlamydiaceae-positive (15/146 farms). The presence of Chlamydiaceae was confirmed mainly in chickens (13/92 farms) but also in turkey (1/19 farms) and goose (1/26 farms) flocks. Eleven flocks were identified as C. gallinacea-positive while four flocks remained unclassified. Phylogenetic analysis revealed at least 16 genetic variants of C. gallinacea. Research showed that Chlamydiaceae occur in a poultry flock in Poland. The strains of C. gallinacea as dominant species show genetic variability.

Keywords: C. gallinacea, emerging agent, poultry, real-time PCR

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Authors: Adewole Tomiwa Adetunji, Francis Bayo Lewu, Richard Mundembe

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Plants require nitrogen (N) to support desired production levels. There is a need for better understanding of N transport mechanism in order to improve N assimilation by plant root. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which N is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was amplified, sequenced and characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design 976 base pairs AMT1-specific primers which include forward primer 5’- GCCATCGCCGCCGCCGG-3’ and reverse primer 5’-GGGTCAGATCCATACCCGC-3’. These primers were used to amplify the Solanum tuberosum AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family due to the clade and high similarity it shared with other plant AMT1 genes. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1, and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th-10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: Ayuko Itsuki, Sachiyo Aburatani

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Soil enzyme activities in Kasuga-yama Hill Primeval Forest (Nara, Japan) were examined to determine levels of mineralization and metabolism. Samples were selected from the soil surrounding laurel-leaved (B_B-1) and Carpinus japonica (B_B-2 and P_w) trees for analysis. Cellulase, β-xylosidase, and protease activities were higher in B_B-1 samples those in B_B-2 samples. These activity levels corresponded to the distribution of cellulose and hemicellulose in the soil horizons. Cellulase, β-xylosidase, and chymotrypsin activities were higher in soil from the P_w forest than in that from the B_B-2 forest. The relationships between the soil enzymes calculated by Spearman’s rank correlation indicate that the interactions between enzymes in B_B-2 samples were more complex than those in P_w samples.

Keywords: comparative analysis, enzyme activities, forest soil, Spearman's rank correlation

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Authors: Lucy W. Mburu, Richard Karanja, Simon N. Mwendia

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Over recent years, learners have experienced a constant need to access on demand knowledge that is fully aligned with the paradigm of cloud computing. As motivated by the global sustainable development goal to ensure inclusive and equitable learning opportunities, this research has developed a framework hinged on the knowledge-as-a-service architecture that utilizes knowledge from ambient learning systems. Through statistical analysis and decision tree modeling, the study discovers influential variables for ambient learning among university students. The main aim is to generate a platform for disseminating and exploiting the available knowledge to aid the learning process and, thus, to improve educational support on the ambient learning system. The research further explores how collaborative effort can be used to form a knowledge network that allows access to heterogeneous sources of knowledge, which benefits knowledge consumers, such as the developers of ambient learning systems.

Keywords: actionable knowledge, ambient learning, cloud computing, decision trees, knowledge as a service

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Authors: D. Dorota

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This paper presents a method to generate and schedule task in the architecture of embedded systems based on the simulated annealing. This method takes into account the attribute of divisibility of tasks. A proposal represents the process in the form of trees. Despite the fact that the architecture of Network-on-Chip (NoC) is an interesting alternative to a bus architecture based on multi-processors systems, it requires a lot of work that ensures the optimization of communication. This paper proposes an effective approach to generate dedicated NoC topology solving communication problems. Network NoC is generated taking into account the energy consumption and resource issues. Ultimately generated is minimal, dedicated NoC topology. The proposed solution is assumed to be a simple router design and the minimum number of lines.

Keywords: Network-on-Chip, NoC-based embedded systems, scheduling task in embedded systems, simulated annealing

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Authors: Sam Ng, Lewis Leighton, Sam Atkinson, Carson Yan, Landan Hu, Leslie Cheung, Brian Yap, Kent Lung, Ketat Sarakune

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This paper introduces a method for verifying cryptocurrency reserves that balances the need for both transparency and data confidentiality. Our methodology employs cryptographic techniques, including Merkle Trees, Bulletproof, and zkSnark, to verify that total assets equal or exceed total liabilities, represented by customer funds. Importantly, this verification is achieved without disclosing sensitive information such as the total asset value, customer count, or cold wallet addresses. We delve into the construction and implementation of this methodology. While the system is robust and scalable, we also identify areas for potential enhancements to improve its efficiency and versatility. As the digital asset landscape continues to evolve, our approach provides a solid foundation for ensuring continued trust and security in digital asset platforms.

Keywords: cryptocurrency, crypto-currency, proof-of-reserve, por, zero-knowledge, ZKP

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Authors: Ali A. Aldosari

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Change detection of Earth surface features is extremely important for better understanding of our environment in order to promote better decision making. Al-Jawf is remarkable for its abundant agricultural water where there is fertile agricultural land due largely to underground water. As result, this region has large areas of cultivation of dates, olives and fruits trees as well as other agricultural products such as Alfa Alfa and wheat. However this agricultural area was declined due to the reduction of government supports in the last decade. This reduction was not officially recorded or measured in this region at large scale or governorate level. Remote sensing data are primary sources extensively used for change detection in agriculture applications. This study is applied the technology of GIS and used the Normalized Difference Vegetation Index (NDVI) which can be used to measure and analyze the spatial and temporal changes in the agriculture areas in the Aljouf region.

Keywords: spatial analysis, geographical information system, change detection

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Authors: Abeer A. Q. Ahmed, Tracey McKay

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Biomass can provide a sustainable source for the production of high valued chemicals. Under the uncertain availability of fossil resources biomass could be the only available source for chemicals in future. Cellulose and hemicellulose can be hydrolyzed into their building blocks (hexsoses and pentoses) which can be converted later to the desired high valued chemicals. A cellulase- and xylanase- producing bacterial strain identified as Paenibacillus illinoisensis CX11 by 16S rRNA gene sequencing and phylogenetic analysis was found to have the ability to saccharify different lignocellulosic materials. Cellulase and xylanase activities were evaluated by 3,5-dinitro-salicylic acid (DNS) method using CMC and xylan as substrates. Results showed that P. illinoisensis CX11 have cellulase (2.63± 0.09 mg/ml) and xylanase (3.25 ± 0.2 mg/ml) activities. The ability of P. illinoisensis CX11 to saccharify lignocellulosic materials was tested using wheat straw (WS), wheat bran (WB), saw dust (SD), and corn stover (CS). DNS method was used to determine the amount of reducing sugars that were released from lignocellulosic materials. P. illinoisensis CX11 showed to have the ability to saccharify lignocellulosic materials and producing total reducing sugars as 2.34 ± 0.12, 2.51 ± 0.37, 1.86 ± 0.16, and 3.29 ± 0.20 mg/l from WS, WB, SD, and CS respectively. According to the author's knowledge, current findings are the first to report P. illinoisensis CX11 as a cellulase and xylanase producing species and that it has the ability to saccharify different lignocellulosic materials. This study presents P. illinoisensis CX11 that can be good source for cellulase and xylanase enzymes which could be introduced into lignocellulose bioconversion processes to produce high valued chemicals.

Keywords: cellulase, high valued chemicals, lignocellulosic materials, Paenibacillus illinoisensis CX11, Xylanase

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Authors: Md. Ratin

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This paper aims to show how Dhaka city is getting destroyed and the creator and guide of the city – the architects destroying the city in more designed and creative way. The liability of architects should be first and foremost to make the would, country, city a better living environment. As without it where the architects will do their design? To make a better living environment architects should conserve the tress, river and other related ingredient related to the environment. This paper attempts to show how cutting down trees and filling rivers causing more problem than having a great architecture in those places. For increasing people in a city like Dhaka, we need more shelter. But for providing those architects building more living spaces. But as a liability of an architect, one should give something back to the environment too. With time the city’s greenery and water body are getting vanished like magic. And for this, the architects should be blamed for giving us a disastrous future. The analysis is based on literature survey and survey by questionnaire, interviews of users.

Keywords: architect, environment, liability, river

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Authors: Ablo Paul Igor Hounzandji, Benoit Lafleur, Annie DesRochers

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Introduction: Populus tremuloides [Michx] regenerates rapidly and abundantly by root suckering after harvest, creating stands with interconnected stems. Pre-commercial thinning can be used to concentrate growth on fewer stems to reach merchantability faster than un-thinned stands. However, conventional thinning methods are typically designed to reach even spacing between residual stems (1,100 stem ha⁻¹, evenly distributed), which can lead to treated stands consisting of weaker/smaller stems compared to the original stands. Considering the nature of P. tremuloides's regeneration, with large underground biomass of interconnected roots, aiming to keep the most vigorous and largest stems, regardless of their spatial distribution, inverted diameter-limit thinning could be more beneficial to post-thinning stand productivity because it would reduce the imbalance between roots and leaf area caused by thinning. Aims: This study aimed to compare stand and stem productivity of P. tremuloides stands thinned with a conventional thinning treatment (CT; 1,100 stem ha⁻¹, evenly distributed), two levels of inverted diameter-limit thinning (DL1 and DL2, keeping the largest 1100 or 2200 stems ha⁻¹, respectively, regardless of their spatial distribution) and a control unthinned treatment. Because DL treatments can create substantial or frequent gaps in the thinned stands, we also aimed to evaluate the potential of this treatment to recreate mixed conifer-broadleaf stands by fill-planting Picea glauca seedlings. Methods: Three replicate 21 year-old sucker-regenerated aspen stands were thinned in 2010 according to four treatments: CT, DL1, DL2, and un-thinned control. Picea glauca seedlings were underplanted in gaps created by the DL1 and DL2 treatments. Stand productivity per hectare, stem quality (diameter and height, volume stem⁻¹) and survival and height growth of fill-planted P. glauca seedlings were measured 8 year post-treatments. Results: Productivity, volume, diameter, and height were better in the treated stands (CT, DL1, and DL2) than in the un-thinned control. Productivity of CT and DL1 stands was similar 4.8 m³ ha⁻¹ year⁻¹. At the tree level, diameter and height of the trees in the DL1 treatment were 5% greater than those in the CT treatment. The average volume of trees in the DL1 treatment was 11% higher than the CT treatment. Survival after 8 years of fill planted P. glauca seedlings was 2% greater in the DL1 than in the DL2 treatment. DL1 treatment also produced taller seedlings (+20 cm). Discussion: Results showed that DL treatments were effective in producing post-thinned stands with larger stems without affecting stand productivity. In addition, we showed that these treatments were suitable to introduce slower growing conifer seedlings such as Picea glauca in order to re-create or maintain mixed stands despite the aggressive nature of P. tremuloides sucker regeneration.

Keywords: Aspen, inverted diameter-limit, mixed forest, populus tremuloides, silviculture, thinning

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Authors: Soroush Mokallaei

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Since ancient times, urbanization engineers have always thought of creating green spaces along with urbanization. Athens and Rome have attempted to construct public gardens around streets and palaces. Since then developing green space has become a part of urban civilization. In medieval ages, all Western cities had palaces and houses with internal gardens. In different sources green belt is defined as a green band of trees and bushes around the cities which has multiple functions. It is said that green belts are not only around the mountains, cities, and rivers but also around houses, subways, and highways. Constructing green belt around cities has different advantages such as: protecting cities against pollution, purifying air, screening dust, being a place for recreation, buffer zone of city internal lands, confronting the phenomenon of heat island, increasing agricultural products, helping to prevent illegal city development, confronting deforestation, preventing flood and increasing subterranean water resources.

Keywords: environment, garden cities, green belt, metropolises

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Authors: Boyun Lee

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This study aims to discuss whether anthropomorphism some scientists tend to use in cross-species comparison can be justified epistemologically, especially in the primate mind-reading debate. Concretely, this study critically analyzes Elliott Sober’s argument about mind-reading hypothesis (MRH), an anthropomorphic hypothesis which states that nonhuman primates (e.g., chimpanzee) are mind-readers like humans. Although many scientists consider anthropomorphism as an error and choosing anthropomorphic hypothesis like MRH without any definite evidence invalid, Sober advocates that anthropomorphism is supported by cladistic parsimony that suggests choosing the simplest hypothesis postulating the minimum number of evolutionary changes, which can be justified epistemologically in the mind-reading debate. However, his argument has several problems. First, Reichenbach’s theorem which Sober uses in process of showing that MRH has the higher likelihood than its competing hypothesis, behavior-reading hypothesis (BRH), does not fit in the context of inferring the evolutionary relationship. Second, the phylogenetic tree Sober supports is one of the possible scenarios of MRH, and even without this problem, it is difficult to prove that the possibility nonhuman primate species and human share mind-reading ability is higher than the possibility of the other case, considering how evolution occurs. Consequently, it seems hard to justify anthropomorphism of MRH under Sober’s argument. Some scientists and philosophers say that anthropomorphism sometimes helps observe interesting phenomena or make hypotheses in comparative biology. Nonetheless, we cannot determine that it provides answers about why and how the interesting phenomena appear or which of the hypotheses is better, at least the mind-reading debate, under the current state.

Keywords: anthropomorphism, cladistic parsimony, comparative biology, mind-reading debate

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Authors: Qiao Mao

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Starting from the theoretical viewpoints of relational aesthetics, this study explores the relationship between the university art gallery and the communities, taking Art Scattering Program in the Name of Trees of the Art Gallery of National Taiwan Normal University (NTNU) as a case. The researcher uses observational and interview methods to obtain research materials to explore how university art galleries interact with communities through public art exhibitions and strengthen the relatively weak relationships with community residents. The researcher also observes how community residents can change their opinions about the university gallery by participating in public art exhibitions. The results show that the university art gallery can effectively establish the interaction with the community residents and repair the relationship with them through such programs as "collection-sharing," "teacher-student co-creation," "artist stationing," and "education promotion activities," playing an active role in promoting interpersonal communication, sustaining the natural environment development and improving community public space.

Keywords: university art gallery, public art, relational aesthetics, communities, interaction

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Authors: Marasovic Branka, Aljinovic Zdravka, Poklepovic Tea

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Numerical methods like binomial and trinomial trees and finite difference methods can be used to price a wide range of options contracts for which there are no known analytical solutions. American options are the most famous of that kind of options. Besides numerical methods, American options can be valued with the approximation formulas, like Bjerksund-Stensland formulas from 1993 and 2002. When the value of American option is approximated by Bjerksund-Stensland formulas, the computer time spent to carry out that calculation is very short. The computer time spent using numerical methods can vary from less than one second to several minutes or even hours. However to be able to conduct a comparative analysis of numerical methods and Bjerksund-Stensland formulas, we will limit computer calculation time of numerical method to less than one second. Therefore, we ask the question: Which method will be most accurate at nearly the same computer calculation time?

Keywords: Bjerksund and Stensland approximations, computational analysis, finance, options pricing, numerical methods

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Authors: Estelle Arbellay, Lori D. Daniels, Shawn D. Mansfield, Alice S. Chang

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Mountain pine beetle (MPB) outbreaks are currently devastating lodgepole pine forests in western North America, which are also widely disturbed by frequent wildfires. Both MPB and fire can leave scars on lodgepole pine trees, thereby diminishing their commercial value and possibly compromising their utilization in solid wood products. In order to fully exploit the affected resource, it is crucial to understand how wounding from these two disturbance agents impact wood properties. Moreover, previous research on lodgepole pine has focused solely on sound wood and stained wood resulting from the MPB-transmitted blue fungi. By means of a quantitative multi-proxy approach, we tested the hypotheses that (i) wounding (of either MPB or fire origin) caused significant changes in wood properties of lodgepole pine and that (ii) MPB-induced wound effects could differ from those induced by fire in type and magnitude. Pith-to-bark strips were extracted from 30 MPB scars and 30 fire scars. Strips were cut immediately adjacent to the wound margin and encompassed 12 rings from normal wood formed prior to wounding and 12 rings from wound wood formed after wounding. Wood properties evaluated within this 24-year window included ring width, relative wood density, cellulose crystallinity, fibre dimensions, and carbon and nitrogen concentrations. Methods used to measure these proxies at a (sub-)annual resolution included X-ray densitometry, X-ray diffraction, fibre quality analysis, and elemental analysis. Results showed a substantial growth release in wound wood compared to normal wood, as both earlywood and latewood width increased over a decade following wounding. Wound wood was also shown to have a significantly different latewood density than normal wood 4 years after wounding. Latewood density decreased in MPB scars while the opposite was true in fire scars. By contrast, earlywood density was presented only minor variations following wounding. Cellulose crystallinity decreased in wound wood compared to normal wood, being especially diminished in MPB scars the first year after wounding. Fibre dimensions also decreased following wounding. However, carbon and nitrogen concentrations did not substantially differ between wound wood and normal wood. Nevertheless, insect-feeding and fire-heating wounding were shown to significantly alter most wood properties of lodgepole pine, as demonstrated by the existence of several morphological anomalies in wound wood. MPB and fire generally elicited similar anomalies, with the major exception of latewood density. In addition to providing quantitative criteria for differentiating between biotic (MPB) and abiotic (fire) disturbances, this study provides the wood industry with fundamental information on the physiological response of lodgepole pine to wounding in order to evaluate the utilization of scarred trees in solid wood products.

Keywords: elemental analysis, fibre quality analysis, lodgepole pine, wood properties, wounding, X-ray densitometry, X-ray diffraction

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Authors: Filiz Ersoz, Taner Ersoz, Erkin Guler

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This paper addresses the issues and technique for textile industry using data mining techniques. Data mining has been applied to the stitching of garments products that were obtained from a textile company. Data mining techniques were applied to the data obtained from the CHAID algorithm, CART algorithm, Regression Analysis and, Artificial Neural Networks. Classification technique based analyses were used while data mining and decision model about the production per person and variables affecting about production were found by this method. In the study, the results show that as the daily working time increases, the production per person also decreases. In addition, the relationship between total daily working and production per person shows a negative result and the production per person show the highest and negative relationship.

Keywords: data mining, textile production, decision trees, classification

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Authors: Tales H. J. Moreira, Thiago M. R. Dias, Gray F. Moita

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The adviser-advised relationship, in addition to the evident propagation of knowledge, can provide an increase in the scientific production of the advisors. Specifically, in post-graduate programs, in which the advised submit diverse papers in different means of publication, these end up boosting the production of their advisor, since in general the advisors appear as co-authors, responsible for instructing and assisting in the development of the work. Therefore, to visualize the orientation process and the scientific production resulting from this relation is another important way of analyzing the scientific collaboration in the different areas of knowledge. In this work, are used the data of orientations and postgraduate supervisions from the Lattes curricula, from the main advisors who work in the Engineering area, to obtain an overview of the process of orientation of this group, and even, to produce Academic genealogical trees, where it is possible to verify how knowledge has spread in the diverse areas of engineering.

Keywords: academic genealogy, advice, engineering, lattes platform

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Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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Authors: Shailaja Grover, Purvi Tiwari, Vigneshwaran S. R., U. Dinesh Kumar

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In India, grapes are one of the most important horticulture crops. Grapes are most vulnerable to downy mildew, which is one of the most devasting diseases. In the absence of a precise weather-based advisory system, farmers spray pesticides on their crops extensively. There are two main challenges associated with using these pesticides. Firstly, most of these sprays were panic sprays, which could have been avoided. Second, farmers use more expensive "Preventive and Eradicate" chemicals than "Systemic, Curative and Anti-sporulate" chemicals. When these chemicals are used indiscriminately, they can enter the fruit and cause health problems such as cancer. This paper utilizes decision trees and predictive modeling techniques to provide grape farmers with customized advice on grape disease management. This model is expected to reduce the overall use of chemicals by approximately 50% and the cost by around 70%. Most of the grapes produced will have relatively low residue levels of pesticides, i.e., below the permissible level.

Keywords: analytics in agriculture, downy mildew, weather based advisory, decision tree, predictive modelling

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Authors: M. P. Rajeeshkumar, K. V. Aneesh Kumar, J. L. Otero-Ferrer, A. Lombarte, M. Hashim, N. Saravanane, V. N.Sanjeevan, V. M. Tuset

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The anglerfishes are widely distributed from shallow to deep-water habitats and are highly diverse in morphology, behaviour, and niche occupancy patterns. To understand this interspecific variability and degree of niche overlap, we performed a functional analysis of five species inhabiting Indian waters where diversity of deep-sea anglerfishes is very high. The sensory capacities (otolith shape and eye size) were also studied to improve the understanding of coexistence of species. The analyses of fish body and otolith shape clustered species in two morphotypes related to phylogenetic lineages: i) Malthopsis lutea, Lophiodes lugubri and Halieutea coccinea were characterized by a dorso-ventrally flattened body with high swimming ability and relative small otoliths, and ii) Chaunax spp. were distinguished by their higher body depth, lower swimming efficiency, and relative big otoliths. The sensory organs did not show a pattern linked to depth distribution of species. However, the larger eye size in M. lutea suggested a nocturnal feeding activity, whereas Chaunax spp. had a large mouth and deeper body in response to different ecological niches. Therefore, the present study supports the hypothesis of spatial and temporal segregation of anglerfishes in the Indian waters, which can be explained from a functional approach and understanding from sensory capabilities.

Keywords: functional traits, otoliths, niche overlap, fishes, Indian waters

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Authors: Hatice Esra Akgül, Celaleddin Öztürk

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Lichen biodiversity in forests is controlled by environmental conditions. Epiphytic lichens have some degree of substrate specificity. Diversity and distribution of epiphytic lichens are affected by humidity, light, altitude, temperature, bark pH of the trees.This study describes the epiphytic lichen communities with comparing their preferred tree species. 34 epiphytic lichen taxa are reported on Pinus sp. L., Quercus sp. L., Fagus sp. L., Carpinus sp. L., Abies sp. Mill., Fraxinus sp. Tourn. ex L. from different altitudes around the Şeker Canyon (Karabük, Turkey). 11 of these taxa are growing on Quercus sp., 10 of them are growing on Fagus sp., 7 of them are growing on Pinus sp., 4 of them are on Carpinus sp., 2 of them are on Abies sp. and one of them is on Fraxinus sp. Evernia prunastri (L.) Ach. is growing on both of Fagus sp. and Quercus sp. Lecanora pulicaris (Pers.) Ach. is growing on both of Abies sp. and Quercus sp.

Keywords: biodiversity, epiphytic lichen, forest, Turkey

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Authors: Richard Nyanzi, Maupi E. Letsoalo, Jacobus N. Eloff, Piet J. Jooste

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Candida albicans naturally occurs in the gastrointestinal tract (GIT) of more than 50% of humans. Overgrowth of the fungus causes several forms of candidiasis including oral thrush. Overgrowth tends to occur in immunocompromised humans such as diabetic, cancer and HIV patients. Antifungal treatment is available, but not without shortcomings. In this study, inhibitory activity of five probiotic Lactobacillus strains was demonstrated against the growth of seven clinical strains of Candida albicans by co-culturing of the organisms in a maize gruel (MG) medium. Phenotypic tests, molecular techniques and phylogenetic analysis have enabled precise identification of the organisms used in the study. The quantitative pour plate technique was used to enumerate colonies of the yeasts and the lactobacilli and the Kruskal-Wallis test and ANOVA tests were employed to compare the distributions of the colonies of the organisms. The cereal medium, containing added carbon sources, was inoculated with a Candida and a Lactobacillus strain in combination and incubated at 37 °C for 168 h. Aliquots were regularly taken and subjected to pH determination and colony enumeration. Certain Lactobacillus strains proved to be inhibitory and also lethal to some Candida albicans strains. A low pH due to Lactobacillus acid production resulted in significant low Candida colony counts. Higher Lactobacillus colony counts did not necessarily result in lower Candida counts suggesting that inhibitory factors besides low pH and competitive growth by lactobacilli contributed to the reduction in Candida counts. Such anti-Candida efficacy however needs to be confirmed by in vivo studies.

Keywords: candida albicans, oral thrush, candidiasis, lactobacillus, probiotics

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Authors: Shef Amir Arasy

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In 2023, the world's population will be 7.8 billion, which has increased significantly in the last 20 years. Every country in the world is experiencing the impacts of climate change directly and indirectly. However, the community still needs to build massive infrastructure and buildings. The massive CO2 emissions which lead to climate change come from cement usage in construction activity. Bamboo is one of the most sustainable materials for reducing carbon emissions and releasing more than 30% oxygen compared to the mass of trees. Besides, bamboo harvest time is faster than other sustainable materials, around 3-4 years. Furthermore, Bamboo has a high tensile strength, which can provide ductility effectively to prevent damage to buildings during an earthquake. By the finite element method, this research analyzes bamboo configuration and connection for tall building structures under different earthquake frequencies and fire. The aim of this research is to provide proper design and connection of bamboo buildings that can be more reliable than concrete structures.

Keywords: bamboo, concrete, ductility, earthquake.

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Authors: Rezaei Hachesu Peyman, Oliyaee Azadeh, Salahzadeh Zahra, Alizadeh Somayyeh, Safaei Naser

Abstract:

Coronary Artery Disease (CAD) is one major cause of disability in adults and one main cause of death in developed. In this study, data mining techniques including Decision Trees, Artificial neural networks (ANNs), and Support Vector Machine (SVM) analyze CAD data. Data of 4948 patients who had suffered from heart diseases were included in the analysis. CAD is the target variable, and 24 inputs or predictor variables are used for the classification. The performance of these techniques is compared in terms of sensitivity, specificity, and accuracy. The most significant factor influencing CAD is chest pain. Elderly males (age > 53) have a high probability to be diagnosed with CAD. SVM algorithm is the most useful way for evaluation and prediction of CAD patients as compared to non-CAD ones. Application of data mining techniques in analyzing coronary artery diseases is a good method for investigating the existing relationships between variables.

Keywords: classification, coronary artery disease, data-mining, knowledge discovery, extract

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Authors: Shubhashree Mahalik, Dhanesh Kumar, Jatin Kumar Pradhan

Abstract:

Odisha is one of the coastal states situated on the eastern part of India with 480 km long coastline. The coastal Odisha is referred to as "Gift of Six Rivers". Balasore, a major coastal district of Odisha is bounded by Bay of Bengal in the East having 26 km long seashore. It is lined with several estuaries rich in biodiversity.Several studies have been carried out on the macro flora and fauna of this area but very few documented information are available regarding microbial biodiversity. In the present study, an attempt has been made to isolate and identify bacteria found along the estuaries of Balasore.Many marine microorganisms are sources of natural products which makes them potential industrial organisms. So the ability of the isolated bacteria to secrete one such industrially significant product, PHB (Polyhydroxybutyrate) has been elucidated. Several rounds of sampling, pure culture, morphological, biochemical and phylogenetic screening led to the identification of two PHB producing strains. Isolate 5 was identified to be Brevibacillus sp. and has maximum similarity to Brevibacillus parabrevis (KX83268). The isolate was named as Brevibacillus sp.KEI-5. Isolate 8 was identified asLysinibacillus sp. having closest similarity withLysinibacillus boroni-tolerance (KP314269) and named as Lysinibacillus sp. KEI-8.Media, temperature, carbon, nitrogen and salinity requirement were optimized for both isolates. Submerged fermentation of both isolates in Terrific Broth media supplemented with optimized carbon and nitrogen source at 37°C led to significant accumulation of PHB as detected by colorimetric method.

Keywords: Bacillus, estuary, marine, Odisha, polyhydroxy butyrate

Procedia PDF Downloads 331

Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

Abstract:

Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

Procedia PDF Downloads 64

Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck, Jason Stanley, Leroy Whilby

Abstract:

Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major threat to fruit and vegetable industries in the United States. The establishment of pest fruit fly in the agricultural industries and produce severe ecological and economic impacts on agricultural diversification and trade. Detection and identification of these agricultural pests in a timely manner will facilitate the possibility of eradication from newly invaded areas. Identification of larval stages to species level is difficult, but is required to determine pest loads and their pathways into the United States. The aim of this study is the New World genus, Anastrepha which includes pests of major economic importance. Mitochondrial cytochrome c oxidase I (COI) gene sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level. During phylogenetics analysis numerous nuclear mitochondrial pseudogenes (numts) were discovered in different specimens. The numts are nonfunctional copies of the mtDNA present in the nucleus and are easily coamplified with the mitochondrial COI gene copy by using conserved universal primers. This is problematic for DNA Barcoding, which attempts to characterize all living organisms by using the COI gene. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed.

Keywords: tephritid, Anastrepha fraterculus, COI, numts

Procedia PDF Downloads 212

Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

Abstract:

The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

Procedia PDF Downloads 153

Authors: Cristina Vatamanu, Doina Cosovan, Dragos Gavrilut, Henri Luchian

Abstract:

In the past few years, the amount of malicious software increased exponentially and, therefore, machine learning algorithms became instrumental in identifying clean and malware files through semi-automated classification. When working with very large datasets, the major challenge is to reach both a very high malware detection rate and a very low false positive rate. Another challenge is to minimize the time needed for the machine learning algorithm to do so. This paper presents a comparative study between different machine learning techniques such as linear classifiers, ensembles, decision trees or various hybrids thereof. The training dataset consists of approximately 2 million clean files and 200.000 infected files, which is a realistic quantitative mixture. The paper investigates the above mentioned methods with respect to both their performance (detection rate and false positive rate) and their practicability.

Keywords: ensembles, false positives, feature selection, one side class algorithm

Procedia PDF Downloads 270