Search results for: sequence diagram

Authors: Mohammad Salem Abdullah Al-Hwaiti

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The stratiform copper mineralization of the Burj-Dolomite shale (BDS) formations of deposits shows that the copper mineralization within the BDS occurs as hydrated copper chlorides and carbonates (mainly paratacamite and malachite, respectively), while copper silicates (mainly chrysocolla and planchette) are the major ore minerals in the BDS. Thus, on the basis of the petrographic and field occurrence, three main stages operated during the development of the copper ore in the sandy and shaly lithofacies. During the first stage, amorphous chrysocolla replaced clays, feldspars, and quartz. This stage was followed by the transition from an amorphous phase to a better-crystallized phase, i.e., the formation of planchette and veins from chrysocolla. The third stage was the formation of chrysocolla along fracture planes. Other secondary minerals are pseudomalachite, dioptase, neoticite together with authigenic fluorapatite. Paratacamite and malachite, which are common in the dolomitic lithofacies, are relatively rare in the sandy and silty lithofacies. The Rare Earth Elements (REEs) patterns for the BDS showed three stages in the evolution of the Precambrian–Cambrian copper mineralization system, involving the following: (A) Epigenetic mobilization of Cu-bearing solution with formation Cu-carbonate in dolomite and limestone mineralization and Cu-silicate mineralization in sandstone; (B) Transgression of Cambrian Sea and SSC deposition of Cu-sulphides during dolomite diagenesis in the BDS Formation; continued diagenesis and oxidation leads to the formation of Cu(II) minerals; (C) Erosion and supergene enrichment of Cu in basement rocks. Detrital copper-bearing sediments accumulate in the lower Cambrian clastic sequence.

Keywords: dolomite shale, copper mineralization, REE, Jordan

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Authors: Shuo Mu, Guangzhi Jiang, Jinsa Chen

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The analysis of Indel for RNA sequencing of clinical samples is easily affected by sequencing experiment errors and software selection. In order to improve the efficiency and accuracy of analysis, we developed an automatic reporting system for Indel recognition and annotation based on image snapshot of transcriptome reads alignment. This system includes sequence local-assembly and realignment, target point snapshot, and image-based recognition processes. We integrated high-confidence Indel dataset from several known databases as a training set to improve the accuracy of image processing and added a bioinformatical processing module to annotate and filter Indel artifacts. Subsequently, the system will automatically generate data, including data quality levels and images results report. Sanger sequencing verification of the reference Indel mutation of cell line NA12878 showed that the process can achieve 83% sensitivity and 96% specificity. Analysis of the collected clinical samples showed that the interpretation accuracy of the process was equivalent to that of manual inspection, and the processing efficiency showed a significant improvement. This work shows the feasibility of accurate Indel analysis of clinical next-generation sequencing (NGS) transcriptome. This result may be useful for RNA study for clinical samples with microsatellite instability in immunotherapy in the future.

Keywords: automatic reporting, indel, next-generation sequencing, NGS, transcriptome

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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: Feng Ji Mervin Goh, Edmund Chee Jian Pua, Stuart Alexander Cook

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Dilated cardiomyopathy (DCM) is a common cause of heart failure. Genetic mutations account for 50% of DCM cases with TTN mutations being the most common, accounting for up to 25% of DCM cases. However, the genetic architecture underlying Asian DCM patients is unknown. We evaluated 68 patients (female= 17) with DCM who underwent follow-up at the National Heart Centre, Singapore from 2013 through 2014. Clinical data were obtained and analyzed retrospectively. Genomic DNA was subjected to next-generation targeted sequencing. Nextera Rapid Capture Enrichment was used to capture the exons of a panel of 169 cardiac genes. DNA libraries were sequenced as paired-end 150-bp reads on Illumina MiSeq. Raw sequence reads were processed and analysed using standard bioinformatics techniques. The average age of onset of DCM was 46.1±10.21 years old. The average left ventricular ejection fraction (LVEF), left ventricular diastolic internal diameter (LVIDd), left ventricular systolic internal diameter (LVIDs) were 26.1±11.2%, 6.20±0.83cm, and 5.23±0.92cm respectively. The frequencies of mutations in major DCM-associated genes were as follows TTN (5.88% vs published frequency of 20%), LMNA (4.41% vs 6%), MYH7 (5.88% vs 4%), MYH6 (5.88% vs 4%), and SCN5a (4.41% vs 3%). The average callability at 10 times coverage of each major gene were: TTN (99.7%), LMNA (87.1%), MYH7 (94.8%), MYH6 (95.5%), and SCN5a (94.3%). In conclusion, TTN mutations are not common in Singaporean DCM patients. The frequencies of other major DCM-associated genes are comparable to frequencies published in the current literature.

Keywords: heart failure, dilated cardiomyopathy, genetics, next-generation sequencing

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Authors: Asma Karim

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Fish taxonomy plays a fundamental role in the study of biodiversity. However, traditional methods of fish taxonomy rely on morphological features, which can lead to confusion due to great similarities between closely related species. To overcome this limitation, modern taxonomy employs DNA barcoding as a species identification method. This involves using a short standardized mitochondrial DNA region as a barcode, specifically a 658 base pair fragment near the 5′ ends of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, to exploit the diversity in this region for identification of species. To test the effectiveness and reliability of DNA barcoding, 25 fish specimens from nine different fish species found in various rivers of Pakistan were identified morphologically using a dichotomous key at the start of the study. Comprising nine freshwater fish species, including Mystus cavasius, Mystus bleekeri, Osteobrama cotio, Labeo rohita, Labeo culbasu, Labeo gonius, Cyprinus carpio, Catla catla and Cirrhinus mrigala from different rivers of Pakistan were used in the present study. DNA was extracted from one of the pectoral fins and a partial sequence of CO1 gene was amplified using the conventional PCR method. Analysis of the barcodes confirmed that genetically identified fishes were the same as those identified morphologically at the beginning of the study. The sequences were also analyzed for biodiversity and phylogenetic studies. Based on the results of the study, it can be concluded that DNA barcoding is an effective and reliable method for studying biodiversity and conducting phylogenetic analysis of different fish species in Pakistan.

Keywords: DNA barcoding, fresh water fishes, taxonomy, biodiversity, Pakistan

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Sina Keyhanian, Abbas Ahmadi, Behrooz Karimi

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We present a multi-objective binary programming model which considers surgical cases are scheduling among operating rooms and the configuration of surgical instruments in limited capacity hospital trays, simultaneously. Many mathematical models have been developed previously in the literature addressing different challenges in health-care logistics such as assigning operating rooms, leveling beds, etc. But what happens inside the operating rooms along with the inventory management of required instruments for various operations, and also their integration with surgical scheduling have been poorly discussed. Our model considers the minimization of movements between trays during a surgery which recalls the famous cell formation problem in group technology. This assumption can also provide a major potential contribution to robotic surgeries. The tray configuration problem which consumes surgical instruments requirement plan (SIRP) and sequence of surgical procedures based on required instruments (SIRO) is nested inside the bin packing problem. This modeling approach helps us understand that most of the same-output solutions will not be necessarily identical when it comes to the rearrangement of surgeries among rooms. A numerical example has been dealt with via a proposed nested simulated annealing (SA) optimization approach which provides insights about how various configurations inside a solution can alter the optimal condition.

Keywords: health-care logistics, hospital tray configuration, off-line bin packing, simulated annealing optimization, surgical case scheduling

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Zeeshan Khan, Faisal Nouroz, Shumaila Noureen

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European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: rabbit, LTR retrotransposons, genome, chromosome

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Authors: Esther Chiramal, Kelvin Soh Boon Kai

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Explainable AI is a strong strategy implemented to understand complex black-box model predictions in a human-interpretable language. It provides the evidence required to execute the use of trustworthy and reliable AI systems. On the other hand, however, it also opens the door to locating possible vulnerabilities in an AI model. Traditional adversarial text attack uses word substitution, data augmentation techniques, and gradient-based attacks on powerful pre-trained Bidirectional Encoder Representations from Transformers (BERT) variants to generate adversarial sentences. These attacks are generally white-box in nature and not practical as they can be easily detected by humans e.g., Changing the word from “Poor” to “Rich”. We proposed a simple yet effective Grey-box cum Black-box approach that does not require the knowledge of the model while using a set of surrogate Transformer/BERT models to perform the attack using Explainable AI techniques. As Transformers are the current state-of-the-art models for almost all Natural Language Processing (NLP) tasks, an attack generated from BERT1 is transferable to BERT2. This transferability is made possible due to the attention mechanism in the transformer that allows the model to capture long-range dependencies in a sequence. Using the power of BERT generalisation via attention, we attempt to exploit how transformers learn by attacking a few surrogate transformer variants which are all based on a different architecture. We demonstrate that this approach is highly effective to generate semantically good sentences by changing as little as one word that is not detectable by humans while still fooling other BERT models.

Keywords: BERT, explainable AI, Grey-box text attack, transformer

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Authors: Eileen K. Africa, Karel J. van Deventer

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Neuro-typical children develop the motor skills necessary to play, do schoolwork and interact with others. However, this is not observed in children who have learning or behavioural problems. Children with Autism Spectrum Disorder (ASD) are often referred to as clumsy because their body parts do not work well together in a sequence. Physical Activity (PA) has shown to be beneficial to the general population, therefore, providing children with ASD opportunities to take part in PA programmes, could prove to be beneficial in many ways and should be investigated. The purpose of this study was to design a specialised group intervention programme, to attempt to improve gross motor skills of selected children diagnosed with ASD between the ages of eight and 13 years. A government school for ASD learners was recruited to take part in this study, and a sample of convenience (N=7) was selected. Children in the experimental group (n=4) participated in a 12-week group intervention programme twice per week, while the control group continued with their normal daily routine. The Movement Assessment Battery for Children-Second Edition (MABC-2), was administered pre- and post-test to determine the children’s gross motor proficiency and to determine if the group intervention programme had an effect on the gross motor skills of the experimental group. Statistically significant improvements were observed in total motor skill proficiency (p < 0.05), of the experimental group. These results demonstrate the importance of gross motor skills interventions for children diagnosed with ASD. Future research should include more participants to ensure that the results can be generalised.

Keywords: autism spectrum disorder, children, gross motor skills, group intervention programme

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Authors: Naoum Abderrahmane, Boumehed Meriem, Alshaqaqi Belal

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Background subtraction algorithm is a larger used technique for detecting moving objects in video surveillance to extract the foreground objects from a reference background image. There are many challenges to test a good background subtraction algorithm, like changes in illumination, dynamic background such as swinging leaves, rain, snow, and the changes in the background, for example, moving and stopping of vehicles. In this paper, we propose an efficient and accurate background subtraction method for moving object detection in video surveillance. The main idea is to use a developed fast-independent component analysis (ICA) algorithm to separate background, noise, and foreground masks from an image sequence in practical environments. The fast-ICA algorithm is adapted and adjusted with a matrix calculation and searching for an optimum non-quadratic function to be faster and more robust. Moreover, in order to estimate the de-mixing matrix and the denoising de-mixing matrix parameters, we propose to convert all images to YCrCb color space, where the luma component Y (brightness of the color) gives suitable results. The proposed technique has been verified on the publicly available datasets CD net 2012 and CD net 2014, and experimental results show that our algorithm can detect competently and accurately moving objects in challenging conditions compared to other methods in the literature in terms of quantitative and qualitative evaluations with real-time frame rate.

Keywords: background subtraction, moving object detection, fast-ICA, de-mixing matrix

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Authors: Mojgan Rabiey, Shyamali Roy, Billy Quilty, Ryan Creeth, George Sundin, Robert W. Jackson

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Bacterial canker is a major disease of Prunus species such as cherry (Prunus avium). It is caused by Pseudomonas syringae species including P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2). Concerns over the environmental impact of, and developing resistance to, copper controls call for alternative approaches to disease management. One method of control could be achieved using naturally occurring bacteriophage (phage) infective to the bacterial pathogens. Phages were isolated from soil, leaf, and bark of cherry trees in five locations in the South East of England. The phages were assessed for their host range against strains of Pss, Psm1, and Psm2. The phages exhibited a differential ability to infect and lyse different Pss and Psm isolates as well as some other P. syringae pathovars. However, the phages were unable to infect beneficial bacteria such as Pseudomonas fluorescens. A subset of 18 of these phages were further characterised genetically (Random Amplification of Polymorphic DNA-PCR fingerprinting and sequencing) and using electron microscopy. The phages are tentatively identified as belonging to the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae, with genetic material being dsDNA. Future research will fully sequence the phage genomes. The efficacy of the phage, both individually and in cocktails, to reduce disease progression in vivo will be investigated to understand the potential for practical use of these phages as biocontrol agents.

Keywords: bacteriophage, pseudomonas, bacterial cancker, biological control

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Authors: Muhammad SAFDAR, Mehmet Ozaslan, Musarrat Abbas Khan

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Babesiosis is a haemoparasitic disease due to the multiplication of protozoan’s parasite, Babesia ovis in the red blood cells of the host, and contributes numerous economical losses, including sheep and goat ruminants. The early identification and successful treatment of Babesia Ovis spp. belong to the key steps of control and health management of livestock resources. The objective of this study was to construct a polymerase chain reaction (PCR) based method for the detection of Babesia spp. in small ruminants and to determine the risk factors involved in the spreading of babesiosis infections. A total of 100 blood samples were collected from 50 sheep and 50 goats along with different areas of Muzaffargarh, Pakistan, from randomly selected herds. Data on the characteristics of sheep and goats were collected through questionnaires. Of 100 blood samples examined, 18 were positive for Babesia ovis upon microscopic studies, whereas 11 were positive for the presence of Babesia spp. by PCR assay. For the recognition of parasitic DNA, a set of 500bp oligonucleotide was designed by PCR amplification with sequence 18S rRNA gene for B. ovis. The prevalence of babesiosis in small ruminant’s sheep and goat detected by PCR was significantly higher in female animals (28%) than male herds (08%). PCR analysis of the reference samples showed that the detection limit of the PCR assay was 0.01%. Taken together, all data indicated that this PCR assay was a simple, fast, specific detection method for Babesia ovis species in small ruminants compared to other available methods.

Keywords: Babesia ovis, PCR amplification, 18S rRNA, sheep and goat

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Authors: Amrit Ladhani

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The cyclic universe theory is a model of cosmic evolution according to which the universe undergoes endless cycles of expansion and cooling, each beginning with a “big bang” and ending in a “big crunch”. In this paper, we propose a unique property of Space-time. This particular and marvelous nature of space shows us that space can stretch, expand, and shrink. This property of space is caused by the size of the universe change over time: growing or shrinking. The observed accelerated expansion, which relates to the stretching of Shrunk space for the new theory, is derived. This theory is based on three underlying notions: First, the Big Bang is not the beginning of Space-time, but rather, at the very beginning fraction of a second, there was an infinite force of infinite Shrunk space in the cosmic singularity that force gave rise to the big bang and caused the rapidly growing of space, and all other forms of energy are transformed into new matter and radiation and a new period of expansion and cooling begins. Second, there was a previous phase leading up to it, with multiple cycles of contraction and expansion that repeat indefinitely. Third, the two principal long-range forces are the gravitational force and the repulsive force generated by shrink space. They are the two most fundamental quantities in the universe that govern cosmic evolution. They may provide the clockwork mechanism that operates our eternal cyclic universe. The universe will not continue to expand forever; no need, however, for dark energy and dark matter. This new model of Space-time and its unique properties enables us to describe a sequence of events from the Big Bang to the Big Crunch.

Keywords: dark matter, dark energy, cosmology, big bang and big crunch

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Authors: Savjot Kaur, Mridula Mahajan, AJS Bhanwer, Santokh Singh, Kawaljit Matharoo

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Background: Disorders of lipid metabolism and genetic predisposition are CAD risk factors. ApoA1 is the apolipoprotein component of anti-atherogenic high density lipoprotein (HDL) particles. The protective action of HDL and ApoA1 is attributed to their central role in reverse cholesterol transport (RCT). Aim: This study was aimed at identifying sequence variations in ApoA1 (-75G>A) and its association with serum ApoA1 levels. Methods: A total of 300 CAD patients and 300 Normal individuals (controls) were analyzed. PCR-RFLP method was used to determine the DNA polymorphism in the ApoA1 gene, PCR products digested with restriction enzyme MspI, followed by Agarose Gel Electrophoresis. Serum apolipoprotein A1 concentration was estimated with immunoturbidimetric method. Results: Deviation from Hardy- Weinberg Equilibrium (HWE) was observed for this gene variant. The A- allele frequency was higher among Coronary Artery disease patients (53.8) compared to controls (45.5), p= 0.004, O.R= 1.38(1.11-1.75). Under recessive model analysis (AA vs. GG+GA) AA genotype of ApoA1 G>A substitution conferred ~1 fold increased risk towards CAD susceptibility (p= 0.002, OR= 1.72(1.2-2.43). With serum ApoA1 levels < 107 A allele frequency was higher among CAD cases (50) as compared to controls (43.4) [p=0.23, OR= 1.2(0.84-2)] and there was zero % occurrence of A allele frequency in individuals with ApoA1 levels > 177. Conclusion: Serum ApoA1 levels were associated with ApoA1 promoter region variation and influence CAD risk. The individuals with the APOA1 -75 A allele confer excess hazard of developing CAD as a result of its effect on low serum concentrations of ApoA1.

Keywords: apolipoprotein A1 (G>A) gene polymorphism, coronary artery disease (CAD), reverse cholesterol transport (RCT)

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Authors: Jyh-Cherng Chen, Yi-Jie Lin

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This study tries to reuse the fly ash of municipal solid waste incinerator (MSWI) for the synthesis of zeolites. The fly ashes were treated with NaOH alkali fusion at different temperatures for 40 mins and then synthesized the zeolites with hydrothermal method at 105oC for different operation times. The effects of different operation conditions and the optimum synthesis parameters were explored. The specific surface area, surface morphology, species identification, adsorption capacity, and the reuse potentials of the synthesized zeolites were analyzed and evaluated. Experimental results showed that the optimum operation conditions for the synthesis of zeolite from the mixed fly ash were Si/Al=20, alkali/ash=1.5, alkali fusion reaction with NaOH at 800oC for 40 mins, hydrolysis with L/S=200 at 105oC for 24 hr, and hydrothermal synthesis at 105oC for 48 hr. The largest specific surface area of synthesized zeolite could be increased to 943.05m2/g. The influence of different operation parameters on the synthesis of zeolite from mixed fly ash followed the sequence of Si/Al > hydrolysis L/S> hydrothermal time > alkali fusion temperature > alkali/ash ratio. The XRD patterns of synthesized zeolites were identified to be similar with the ZSM-23 zeolite. The adsorption capacities of synthesized zeolite for pollutants were increased as rising the specific surface area of synthesized zeolite. In summary, MSWI fly ash can be treated and reused to synthesize the zeolite with high specific surface area by the alkali fusion and hydrothermal method. The zeolite can be reuse for the adsorption of various pollutants. They have great potential for development.

Keywords: alkali fusion, hydrothermal, fly ash, zeolite

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Authors: Mahjabeen Akbar

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Dental aesthetics and its associated psychosocial influence have a significant impact on individuals. Correcting malocclusions is a key motivating factor for majority patients; however, psychosocial factors have been rarely incorporated in evaluating malocclusions. Therefore, it is necessary to study the psychosocial influence of malocclusion in patients. The study aimed to determine the psychosocial influence of dental aesthetics in dental students by the ‘Psychosocial Impact of Dental Aesthetics Questionnaire’ and self-rated Aesthetic Component of the Index of Orthodontic Treatment Need (IOTN). This was a quantitative study using a cross-sectional study design. One hundred twenty dental students (71 females and 49 males; mean age 24.5) were selected via purposive sampling from July to August 2019. Dental students with no former orthodontic treatment were requested to fill out the ‘Psychosocial Impact of Dental Aesthetics Questionnaire.’ Variables including; self-confidence/insecurity, social influence, psychological influence and self-perception of the need of an orthodontic treatment were evaluated by a sequence of statements, while dental aesthetics were evaluated by using the IOTN Aesthetic Component. To determine the significance, the Kruskal-Wallis test was utilized. The results show that all four variables measuring psychosocial impact indicated significant correlations with the perceived malocclusions with a p-value of less than 0.01. The results conclude there is a strong psychological and social influence of altered dental aesthetics on an individual. Moreover, the relationship between the IOTN-AC grading with the psychosocial wellbeing of an individual stands proven, indicating that the perception of altered dental aesthetics is as important as a factor in treatment need as the amount of malocclusion.

Keywords: dental aesthetics, malocclusion, psychosocial influence, dental students

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Authors: William Li

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Lane-change path planning is a crucial and yet complex task in autonomous driving. The traditional path planning approach based on a system of carefully-crafted rules to cover various driving scenarios becomes unwieldy as more and more rules are added to deal with exceptions and corner cases. This paper proposes to divide the entire path planning to two stages. In the first stage the ego vehicle travels longitudinally in the source lane to reach a safe state. In the second stage the ego vehicle makes lateral lane-change maneuver to the target lane. The paper derives the safe state conditions based on lateral lane-change maneuver calculation to ensure collision free in the second stage. To determine the acceleration sequence that minimizes the time to reach a safe state in the first stage, the paper proposes three schemes, namely, kinetic model based optimization, deep reinforcement learning, and 5G vehicle-to-vehicle (V2V) communications. The paper investigates these schemes via simulation. The model-based optimization is sensitive to the model assumptions. The deep reinforcement learning is more flexible in handling scenarios beyond the model assumed by the optimization. The 5G V2V eliminates uncertainty in predicting future behaviors of surrounding vehicles by sharing driving intents and enabling cooperative driving.

Keywords: lane change, path planning, autonomous driving, deep reinforcement learning, 5G, V2V communications, connected vehicles

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Authors: Nahed Al-Hajeri

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Time and cost is an integral part of every construction plan and can affect each party’s contractual obligations. The performance of both time and cost are usually important to the client and contractor during the project. Almost all construction projects are experiencing time overrun. These time overruns always contributed as expensive to both client and contractor. Construction of any project inside the gathering centers involves complex management skills related to work force, materials, plant, machineries, new technologies etc. It also involves many agencies interdependent on each other like the vendors, structural and functional designers including various types of specialized engineers and it includes support of contractors and specialized contractors. This paper mainly highlights the types of construction delays due to which project suffer time and cost overrun. This paper also speaks about the delay causes and factors that contribute to the construction sequence delay for the oil and gas projects. Construction delay is supposed to be one of the repeated problems in the construction projects and it has an opposing effect on project success in terms of time, cost and quality. Some effective methods are identified to minimize delays in construction projects such as: 1. Site management and supervision, 2. Effective strategic planning, 3. Clear information and communication channel. Our research paper studies the types of delay with some real examples with statistic results and suggests solutions to overcome this problem.

Keywords: non-compensable delay, delays caused by force majeure, compensable delay, delays caused by the owner or the owner’s representative, non-excusable delay, delay caused by the contractor or the contractor’s representative, concurrent delay, delays resulting from two separate causes at the same time

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Authors: Ghulam Muhammad Ali

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Unveiling of genes involved in drought and root architecture using transcriptomic analyses remained fragmented for further improvement of wheat through genome editing. The purpose of this research endeavor was to unveil the variations in different genes implicated in drought tolerance and root architecture in wheat through RNA-seq data analysis. In this study seedlings of 8 days old, 6 cultivars of wheat namely, Batis, Blue Silver, Local White, UZ888, Chakwal 50 and Synthetic wheat S22 were subjected to transcriptomic analysis for root and shoot genes. Total of 12 RNA samples was sequenced by Illumina. Using updated wheat transcripts from Ensembl and IWGC references with 54,175 gene models, we found that 49,621 out of 54,175 (91.5%) genes are expressed at an RPKM of 0.1 or more (in at least 1 sample). The number of genes expressed was higher in Local White than Batis. Differentially expressed genes (DEG) were higher in Chakwal 50. Expression-based clustering indicated conserved function of DRO1and RPK1 between Arabidopsis and wheat. Dendrogram showed that Local White is sister to Chakwal 50 while Batis is closely related to Blue Silver. This study flaunts transcriptomic sequence variations in different cultivars that showed mutations in genes associated with drought that may directly contribute to drought tolerance. DRO1 and RPK1 genes were fetched/isolated for genome editing. These genes are being edited in wheat through CRISPR-Cas9 for yield enhancement.

Keywords: transcriptomic, wheat, genome editing, drought, CRISPR-Cas9, yield enhancement

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Authors: Sarah Devi Silvian, Hanna Shobrina Iqomatul Haq, Fara Cholidatun Nabila, Agustin Krisna Wardani

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Bacteria ability to survive in antibiotic is controlled by the presence of gene that encodes the antibiotic resistance protein. The instability of the antibiotic resistance gene can be observed by exposing the bacteria under the lethal dose of antibiotic. Low concentration of antibiotic can induce mutation, which may take a role in bacterial adaptation through the antibiotic concentration. Lactobacillus casei FNCC 0090 is one of the probiotic bacteria that has an ability to survive in tetracycline by expressing the tetM gene. The aims of this study are to observe the possibilities of mutation happened in L.casei FNCC 0090 by exposing in sub-lethal dose of tetracycline and also observing the instability of the tetM gene by comparing the sequence between the wild type and mutant. L.casei FNCC 0090 has a lethal dose in 60 µg/ml, low concentration is applied to induce the mutation, the range from 10 µg/ml, 15 µg/ml, 30 µg/ml, 45 µg/ml, and 50 µg/ml. L.casei FNCC 0090 is exposed to the low concentration from lowest to the highest concentration to induce the adaptation. Plasmid is isolated from the highest concentration culture which is 50 µg/ml by using modified alkali lysis method with the addition of lysozyme. The tetM gene is isolated by using PCR (Polymerase Chain Reaction) method, then PCR amplicon is purified and sequenced. Sequencing is done on both samples, wild type and mutant. Both sequences are compared and the mutations can be traced in the presence of nucleotides changes. The changing of the nucleotides means that the tetM gene is instable.

Keywords: L. casei FNCC 0090, probiotic, tetM, tetracycline

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

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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

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Authors: Sze Shin Low, Michelle T. T. Tan, Poi Sim Khiew, Hwei-San Loh

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An efficient graphene/zinc oxide (PSE-G/ZnO) platform based on pi-pi stacking, non-covalent interactions for the development of aptamer-based biosensor was presented in this study. As a proof of concept, the DNA recognition capability of the as-developed PSE-G/ZnO enhanced aptamer-based biosensor was evaluated using Coconut Cadang-cadang viroid disease (CCCVd). The G/ZnO nanocomposite was synthesised via a simple, green and efficient approach. The pristine graphene was produced through a single step exfoliation of graphite in sonochemical alcohol-water treatment while the zinc nitrate hexahydrate was mixed with the graphene and subjected to low temperature hydrothermal growth. The developed facile, environmental friendly method provided safer synthesis procedure by eliminating the need of harsh reducing chemicals and high temperature. The as-prepared nanocomposite was characterised by X-ray diffractometry (XRD), scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) to evaluate its crystallinity, morphology and purity. Electrochemical impedance spectroscopy (EIS) was employed for the detection of CCCVd sequence with the use of potassium ferricyanide (K3[Fe(CN)6]). Recognition of the RNA analytes was achieved via the significant increase in resistivity for the double stranded DNA, as compared to single-stranded DNA. The PSE-G/ZnO enhanced aptamer-based biosensor exhibited higher sensitivity than the bare biosensor, attributing to the synergistic effect of high electrical conductivity of graphene and good electroactive property of ZnO.

Keywords: aptamer-based biosensor, graphene/zinc oxide nanocomposite, green synthesis, screen printed carbon electrode

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Authors: Introducing Principles of Land Surveying by Assigning a Practical Project

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A practical project is used in an engineering surveying course to expose sophomore and junior civil engineering students to several important issues related to the use of basic principles of land surveying. The project, which is the design of a two-lane rural highway to connect between two arbitrary points, requires students to draw the profile of the proposed highway along with the existing ground level. Areas of all cross-sections are then computed to enable quantity computations between them. Lastly, Mass-Haul Diagram is drawn with all important parts and features shown on it for clarity. At the beginning, students faced challenges getting started on the project. They had to spend time and effort thinking of the best way to proceed and how the work would flow. It was even more challenging when they had to visualize images of cut, fill and mixed cross sections in three dimensions before they can draw them to complete the necessary computations. These difficulties were then somewhat overcome with the help of the instructor and thorough discussions among team members and/or between different teams. The method of assessment used in this study was a well-prepared-end-of-semester questionnaire distributed to students after the completion of the project and the final exam. The survey contained a wide spectrum of questions from students' learning experience when this course development was implemented to students' satisfaction of the class instructions provided to them and the instructor's competency in presenting the material and helping with the project. It also covered the adequacy of the project to show a sample of a real-life civil engineering application and if there is any excitement added by implementing this idea. At the end of the questionnaire, students had the chance to provide their constructive comments and suggestions for future improvements of the land surveying course. Outcomes will be presented graphically and in a tabular format. Graphs provide visual explanation of the results and tables, on the other hand, summarize numerical values for each student along with some descriptive statistics, such as the mean, standard deviation, and coefficient of variation for each student and each question as well. In addition to gaining experience in teamwork, communications, and customer relations, students felt the benefit of assigning such a project. They noticed the beauty of the practical side of civil engineering work and how theories are utilized in real-life engineering applications. It was even recommended by students that such a project be exercised every time this course is offered so future students can have the same learning opportunity they had.

Keywords: land surveying, highway project, assessment, evaluation, descriptive statistics

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Authors: Yen-Luan Chen

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Maintenance has a great impact on the capacity of production and on the quality of the products, and therefore, it deserves continuous improvement. Maintenance procedure done before a failure is called preventive maintenance (PM). Sequential PM, which specifies that a system should be maintained at a sequence of intervals with unequal lengths, is one of the commonly used PM policies. This article proposes a generalized sequential PM policy for a system subject to shocks with imperfect maintenance and random working time. The shocks arrive according to a non-homogeneous Poisson process (NHPP) with varied intensity function in each maintenance interval. As a shock occurs, the system suffers two types of failures with number-dependent probabilities: type-I (minor) failure, which is rectified by a minimal repair, and type-II (catastrophic) failure, which is removed by a corrective maintenance (CM). The imperfect maintenance is carried out to improve the system failure characteristic due to the altered shock process. The sequential preventive maintenance-last (PML) policy is defined as that the system is maintained before any CM occurs at a planned time Ti or at the completion of a working time in the i-th maintenance interval, whichever occurs last. At the N-th maintenance, the system is replaced rather than maintained. This article first takes up the sequential PML policy with random working time and imperfect maintenance in reliability engineering. The optimal preventive maintenance schedule that minimizes the mean cost rate of a replacement cycle is derived analytically and determined in terms of its existence and uniqueness. The proposed models provide a general framework for analyzing the maintenance policies in reliability theory.

Keywords: optimization, preventive maintenance, random working time, minimal repair, replacement, reliability

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Authors: V. Jagadeesh, K. Venkata Subbaiah, P. Govinda Rao

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This paper explaining about the significance of information technology tools and software packages in supply chain management (SCM) in order to manage the entire supply chain. Managing materials flow and financial flow and information flow effectively and efficiently with the aid of information technology tools and packages in order to deliver right quantity with right quality of goods at right time by using right methods and technology. Information technology plays a vital role in streamlining the sales forecasting and demand planning and Inventory control and transportation in supply networks and finally deals with production planning and scheduling. It achieves the objectives by streamlining the business process and integrates within the enterprise and its extended enterprise. SCM starts with customer and it involves sequence of activities from customer, retailer, distributor, manufacturer and supplier within the supply chain framework. It is the process of integrating demand planning and supply network planning and production planning and control. Forecasting indicates the direction for planning raw materials in order to meet the production planning requirements. Inventory control and transportation planning allocate the optimal or economic order quantity by utilizing shortest possible routes to deliver the goods to the customer. Production planning and control utilize the optimal resources mix in order to meet the capacity requirement planning. The above operations can be achieved by using appropriate information technology tools and software packages for the supply chain management.

Keywords: supply chain management, information technology, business process, extended enterprise

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Authors: Eish Sharma

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Literature around Mathematics education suggests that democratic attitudes can be strengthened through teaching and learning Mathematics. Furthermore, connections between critical education and Mathematics education are observed in the light of critical pedagogy to locate Critical Mathematics Education (CME) as the theoretical framework. Critical pedagogy applied to Mathematics education is identified as one of the key themes subsumed under Critical Mathematics Education. Through the application of critical pedagogy in mathematics, unequal power relations and social injustice can be identified, analyzed, and challenged. The research question is: have educational policies in India viewed the role of critical pedagogy applied to mathematics education (i.e., critical mathematics education) to ensure social justice as an educational aim? The National Curriculum Framework (NCF), 2005 upholds education for democracy and the role of mathematics education in facilitating the same. More than this, NCF 2005 rests on Critical Pedagogy Framework and it recommends that critical pedagogy must be practiced in all dimensions of school education. NCF 2005 visualizes critical pedagogy for social sciences as well as sciences, stating that the science curriculum, including mathematics, must be used as an “instrument for achieving social change to reduce the divide based on economic class, gender, caste, religion, and the region”. Furthermore, the implementation of NCF 2005 led to a reform in the syllabus and textbooks in school mathematics at the national level, and critical pedagogy was applied to mathematics textbooks at the primary level. This intervention led to ethnomathematics and critical mathematics education in the school curriculum in India for the first time at the national level. In October 2022, the Ministry of Education launched the National Curriculum Framework for Foundational Stage (NCF-FS), developed in light of the National Education Policy, 2020, for children in the three to eight years age group. I want to find out whether critical pedagogy-based education and critical pedagogy-based mathematics education are carried forward in NCF 2022. To find this, an argument analysis of specific sections of the National Curriculum Framework 2022 document needs to be executed. Des Gasper suggests two tables: The first table contains four columns, namely, text component, comments on meanings, possible reformulation of the same text, and identified conclusions and assumptions (both stated and unstated). This table is for understanding the components and meanings of the text and is based on Scriven’s model for understanding the components and meanings of words in the text. The second table contains four columns i.e., claim identified, given data, warrant, and stated qualifier/rebuttal. This table is for describing the structure of the argument, how and how well the components fit together and is called ‘George Table diagram based on Toulmin-Bunn Model’.

Keywords: critical mathematics education, critical pedagogy, social justice, etnomathematics

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Authors: S. Srinivasan, E. Cretu

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The information flow (e.g. block-diagram or signal flow graph) paradigm for the design and simulation of Microelectromechanical (MEMS)-based systems allows to model MEMS devices using causal transfer functions easily, and interface them with electronic subsystems for fast system-level explorations of design alternatives and optimization. Nevertheless, the physical bi-directional coupling between different energy domains is not easily captured in causal signal flow modeling. Moreover, models of fundamental components acting as building blocks (e.g. gap-varying MEMS capacitor structures) depend not only on the component, but also on the specific excitation mode (e.g. voltage or charge-actuation). In contrast, the energy flow modeling paradigm in terms of generalized across-through variables offers an acausal perspective, separating clearly the physical model from the boundary conditions. This promotes reusability and the use of primitive physical models for assembling MEMS devices from primitive structures, based on the interconnection topology in generalized circuits. The physical modeling capabilities of Simscape have been used in the present work in order to develop a MEMS library containing parameterized fundamental building blocks (area and gap-varying MEMS capacitors, nonlinear springs, displacement stoppers, etc.) for the design, simulation and optimization of MEMS inertial sensors. The models capture both the nonlinear electromechanical interactions and geometrical nonlinearities and can be used for both small and large signal analyses, including the numerical computation of pull-in voltages (stability loss). Simscape behavioral modeling language was used for the implementation of reduced-order macro models, that present the advantage of a seamless interface with Simulink blocks, for creating hybrid information/energy flow system models. Test bench simulations of the library models compare favorably with both analytical results and with more in-depth finite element simulations performed in ANSYS. Separate MEMS-electronic integration tests were done on closed-loop MEMS accelerometers, where Simscape was used for modeling the MEMS device and Simulink for the electronic subsystem.

Keywords: across-through variables, electromechanical coupling, energy flow, information flow, Matlab/Simulink, MEMS, nonlinear, pull-in instability, reduced order macro models, Simscape

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Authors: Theresa K., Shanmugasundaram R., Kennedy J. S.

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Nutrient supplements are indispensable for raising crops and to reap determining productivity. The nutrient imbalance between replenishment and crop uptake is attempted through the input of inorganic fertilizers. Excessive dumping of inorganic nutrients in soil cause stagnant and decline in yield. Imbalanced N-P-K ratio in the soil exacerbates and agitates the soil ecosystems. The study evaluated the fertilization practices of conventional (CFs), organic and Integrated Nutrient Management system (INM) on soil quality using key indicators and soil quality indices. Twelve rice farming fields of which, ten fields were having conventional cultivation practices, one field each was organic farming based and INM based cultivated under monocropping sequence in the Thondamuthur block of Coimbatore district were fixed and properties viz., physical, chemical and biological were studied for four cropping seasons to determine soil quality index (SQI). SQI was computed for conventional, organic and INM fields. Comparing conventional farming (CF) with organic and INM, CF was recorded with a lower soil quality index. While in organic and INM fields, the higher SQI value of 0.99 and 0.88 respectively were registered. CF₄ received with a super-optimal dose of N (250%) showed a lesser SQI value (0.573) as well as the yield (3.20 t ha⁻¹) and the CF6 which received 125 % N recorded the highest SQI (0.715) and yield (6.20 t ha⁻¹). Likewise, most of the CFs received higher N beyond the level of 125 % except CF₃ and CF₉, which recorded lower yields. CFs which received super-optimal P in the order of CF₆&CF₇>CF₁&CF₁₀ recorded lesser yields except for CF₆. Super-optimal K application also recorded lesser yield in CF₄, CF₇ and CF₉.

Keywords: rice cropping system, soil quality indicators, imbalanced fertilization, yield

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