Search results for: direct DNA sequencing

Authors: Tanveer Hussain, Misbah Hussain, Masroor Ellahi Babar, Muhammad Traiq Pervez, Fiaz Hussain, Sana Zahoor, Rashid Saif

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Interleukin 2 (IL-2) is a cytokine which is produced by activated T cells, play important role in immune response against antigen. It act in both autocrine and paracrine manner. It can stimulate B cells and various other phagocytic cells like monocytes, lymphokine-activated killer cells and natural killer cells. Acting in autocrine fashion, IL-2 protein plays a crucial role in proliferation of T cells. IL-2 triggers the release of pro and anti- inflammatory cytokines by activating several pathways. In present study, exon 1 of IL-2 gene of four local Pakistani breeds (Dera Din Panah, Beetal, Nachi and Kamori) from two provinces was amplified by using reported Ovine IL-2 primers, yielding PCR product of 501 bp. The sequencing of all samples was done to identify the polymorphisms in amplified region of IL-2 gene. Analysis of sequencing data resulted in identification of one novel nucleotide substitution (T→A) in amplified non-coding region of IL-2 gene. Comparison of IL-2 gene sequence of all four breeds with other goat breeds showed high similarity in sequence. While phylogenetic analysis of our local breeds with other mammals showed that IL-2 is a variable gene which has undergone many substitutions. This high substitution rate can be due to the decreased or increased changed selective pressure. These rapid changes can also lead to the change in function of immune system. This pioneering study of Pakistani goat breeds urge for further studies on immune system of each targeted breed for fully understanding the functional role of IL-2 in goat immunity.

Keywords: interleukin 2, mutational analysis, phylogeny, goat breeds, Pakistan

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Authors: Sergio Luiz da Costa Junior, Carolina Fofonka Palomino, Paulo Cesar Lodi

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The use of light landfills is an effective solution for road works in soft ground sites, such as Rio de Janeiro (RJ) and Santos (SP) - the Southeastern Brazilian coast. The technique consists in replacing the topsoil by expandable polystyrene (EPS) geofoam, lined with geomembrane to prevent the attack of chemical products.Thus, knowing the interface shear strength of those materials is important in projects to avoid rupturing the system. The purpose of this paper is to compare the shear strength in the geomembrane-EPS interfaces by the direct shear test. The tests were performed under the dry and saturated condition, and four kind of high-density polyethylene (HDPE) 2,00mm geomembranes were used, smooth and texturized - manufactured in the flat die and blown film process. It was found that the shear strength is directly influenced by the roughness of the geomembrane, showed higher friction angle in the textured geomembrane. The direct shear test, in the saturated condition, also showed smaller friction angle than the now-wetted test.

Keywords: geofoam, geomembrane, soft ground, strength shear

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Authors: M. Imran Hamid, Muzammil Hussain, Yunpeng Wu, Meichun Xiang, Xingzhong Liu

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The rhizosphere microbiome elucidate multiple functioning in the soil suppressiveness against plant pathogens. Soybean rhizosphere microbial communities may involve in the natural suppression of soybean cyst nematode (SCN) populations in disease suppressive soils. To explore these ecological mechanisms of microbes, a long term monoculture suppressive soil were taken into account for further investigation to test the disease suppressive ability by using different treatments. The designed treatments are as, i) suppressive soil (S), ii) conducive soil (C), iii) conducive soil mixed with 10% (w/w) suppressive soil (CS), iv) suppressive soil treated at 80°C for 1 hr (S80), and v) suppressive soil treated with formalin (SF). By using an ultra-high-throughput sequencing approach, we identified the key bacterial and fungal taxa involved in SCN suppression. The Phylum-level investigation of bacteria revealed that Actinobacteria, Bacteroidetes, and Proteobacteria in the rhizosphere soil of soybean seedlings were more abundant in the suppressive soil than in the conducive soil. The phylum-level analysis of fungi in rhizosphere soil indicated that relative abundance of Ascomycota was higher in suppressive soil than in the conducive soil, where Basidiomycota was more abundant. Transferring suppressive soil to conducive soil increased the population of Ascomycota in the conducive soil by lowering the populations of Basidiomycota. The genera, such as, Pochonia, Purpureocillium, Fusarium, Stachybotrys that have been well documented as bio-control agents of plant nematodes were far more in the disease suppressive soils. Our results suggested that the plants engage a subset of functional microbial groups in the rhizosphere for initial defense upon nematode attack and protect the plant roots later on by nematodes to response for suppression of SCN in disease-suppressive soils.

Keywords: disease suppressive soil, high-throughput sequencing, rhizosphere microbiome, soybean cyst nematode

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Authors: Najeeb Ullah Khan

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Background: The receptor activator NF-κβ ligand (RANKL) and Osteoprotegerin (OPG) polymorphisms have been associated with the progression of breast cancer to bone metastasis. Here, we aimed to investigate the association of RANKL and OPG gene polymorphism with breast to bone metastasis in the Pashtun population, Pakistan. Methods: Genomic DNA was obtained from all the study subjects (106 breast cancer, 58 breast to bone metastasis, and 51 healthy controls). RANKL (rs9533156) and OPG (rs2073618, rs3102735) polymorphisms were genotyped using Tetra-ARMS PCR. Results: Our results indicated that the frequencies of OPG (rs3102735) risk allele and genotypes carrying risk allele in breast cancer vs healthy control (C- p=0.005; CC- p=0.0208; TC- p=0.0181), bone metastasis vs healthy control (C- p=0.0211; CC- p=0.0153; TC- p=0.0775), and breast cancer vs breast to bone metastasis (C- p=0.0001; CC- p=0.0001; TC- p=0.001) were found significantly associated with disease risk. However, there was no significant association observed for OPG (rs2073618) risk allele and risk allele containing genotypes in all study groups. Similarly, RANKL (rs9533156) risk alleles and corresponding genotypes in breast cancer vs healthy control (C- p=0.0001; CC- p=0.0001; TC- p=0.0084), bone metastasis vs healthy control (C- p=0.0001; CC- p=0.0001; TC- p=0.5593), and breast cancer vs breast to bone metastasis (C- p=0.0185; CC- p=0.6077; TC- p=0.1436) showed significant association except for the risk allele carrying genotypes in breast cancer to bone metastasis (TC, p=0.1436; CC, p=0.6077). Conclusion: OPG (rs3102735) and RANKL (rs9533156) showed significant association with breast to bone metastasis, while OPG (rs2073618) didn’t show a significant association with breast to bone metastasis in Pashtun population of Pakistan. However, more investigation will be required to disseminate the results while gene sequencing or whole-exome sequencing.

Keywords: breast cancer, bone metastasis, OPG, RANKL, polymorphism

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

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Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease

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Authors: Sandhra M. Pillai

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This article examines the relevance, difficulties, and potential applications of DNA analysis in the criminal justice system. A potent tool for connecting suspects to crime sites, clearing the innocent of wrongdoing, and resolving cold cases, DNA analysis has transformed forensic investigations. The scientific foundations of DNA analysis, including DNA extraction, sequencing, and statistical analysis, are covered in the article. To guarantee accurate and trustworthy findings, it also discusses the significance of quality assurance procedures, chain of custody, and DNA sample storage. DNA analysis has significantly advanced science, but it also brings up substantial moral and legal issues. To safeguard individual rights and uphold public confidence, privacy concerns, possible discrimination, and abuse of DNA information must be properly addressed. The paper also emphasises the effects of the criminal justice system on people and communities while highlighting the necessity of equity, openness, and fair access to DNA testing. The essay describes the obstacles and future directions for DNA analysis. It looks at cutting-edge technology like next-generation sequencing, which promises to make DNA analysis quicker and more affordable. To secure the appropriate and informed use of DNA evidence, it also emphasises the significance of multidisciplinary collaboration among scientists, law enforcement organisations, legal experts, and policymakers. In conclusion, DNA analysis has enormous potential for improving the course of criminal justice. We can exploit the potential of DNA technology while respecting the ideals of justice, fairness, and individual rights by navigating the ethical, legal, and societal issues and encouraging discussion and collaboration.

Keywords: DNA analysis, DNA evidence, reliability, validity, legal frame, admissibility, ethical considerations, impact, future direction, challenges

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

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The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Nayyra Zeb, Fu Qiang, Sundas Rauf

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Foreign Direct Investment (FDI) is often seen as a significant factor of economic development in developing countries like Pakistan. The aim of this article is to investigate the effect of FDI on Pakistan’s economic growth during 1972–2012. Besides FDI, three other variables such as trade openness, political instability and terrorist attacks are also used in this study. The least square method has been applied to check the effect of these variables on GDP of Pakistan. The results show that FDI has a positive significant effect on economic growth of Pakistan.

Keywords: FDI inflows, trade openness, political instability, terrorist attacks

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Authors: Alyaa Abdlwahab

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Cutaneous leishmaniasis represents a serious health problem in Syria; this problem has become noticeably aggravated after the civil war in the country. Leishmania tropica parasite is the main cause of cutaneous leishmaniasis in Syria. In order to control the disease, we need an effective vaccine against leishmania parasite. DNA vaccination remains one of the favorable approaches that have been used to face cutaneous leishmaniasis. Ribosomal protein S4 is responsible for important roles in Leishmania parasite life. DNA vaccine based on S4 gene has been used against infections by many species of Leishmania parasite but leishmania tropica parasite, so this gene represents a good candidate for DNA vaccine construction. After proving the existence of ribosomal protein S4 gene in a Syrian strain of Leishmania tropica (LCED Syrian 01), sequencing it and cloning it into pCI plasmid, BALB/C mice were inoculated with pCI-S4 DNA vaccine. The immune response was determined by monitoring the lesion progression in inoculated BALB/C mice for six weeks after challenging mice with Leishmania tropica (LCED Syrian 01) parasites. IL-12, IFN-γ, and IL-4 were quantified in draining lymph nodes (DLNa) of the immunized BALB/C mice by using the RT-qPCR technique. The parasite burden was calculated in the final week for the footpad lesion and the DLNs of the mice. This study proved the existence and the expression of the ribosomal protein S4 gene in Leishmania tropica (LCED Syrian 01) promastigotes. The sequence of ribosomal protein cDNA S4 gene was determined and published in Genbank; the gene size was 822 bp. Expression was also demonstrated at the level of cDNA. Also, this study revealed that pCI-S4 DNA vaccine induces TH1\TH2 response in immunized mice; this response prevents partially developing a dermal lesion of Leishmania.

Keywords: ribosomal protein S4, DNA vaccine, Leishmania tropica, BALB\c

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Authors: Kouzi Katia

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This paper proposes a Direct Torque Control (DTC) algorithm of dual Stator Induction Motor (DSIM) drive using two approach intelligent techniques: Artificial Neural Network (ANN) approach replaces the switching table selector block of conventional DTC and Mamdani Fuzzy Logic controller (FLC) is used for stator resistance estimation. The fuzzy estimation method is based on an online stator resistance correction through the variations of stator current estimation error and its variation. The fuzzy logic controller gives the future stator resistance increment at the output. The main advantage of suggested algorithm control is to reduce the hardware complexity of conventional selectors, to avoid the drive instability that may occur in certain situation and ensure the tracking of the actual of the stator resistance. The effectiveness of the technique and the improvement of the whole system performance are proved by results.

Keywords: artificial neural network, direct torque control, dual stator induction motor, fuzzy logic estimator, switching table

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Authors: Marulasiddappa H. B., Pushparajesh Viswanathan

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Day by day, the uses of internal combustion engines (ICE) are deteriorating because of pollution and less fuel availability. In the present scenario, the electric vehicle (EV) plays a major role in the place of an ICE vehicle. The performance of EVs can be improved by the proper selection of electric motors. Initially, EV preferred induction motors for traction purposes, but due to complexity in controlling induction motor, permanent magnet synchronous motor (PMSM) is replacing induction motor in EV due to its advantages. Direct torque control (DTC) is one of the known techniques for PMSM drive in EV to control the torque and speed. However, the presence of torque ripple is the main drawback of this technique. Many control strategies are followed to reduce the torque ripples in PMSM. In this paper, the adaptive neuro-fuzzy inference system (ANFIS) controller technique is proposed to reduce torque ripples and settling time. Here the performance parameters like torque, speed and settling time are compared between conventional proportional-integral (PI) controller with ANFIS controller.

Keywords: direct torque control, electric vehicle, torque ripple, PMSM

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Authors: Ek-Uma Imkome, Jintana Yunibhand, Waraporn Chaiyawat

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Background: Persons with schizophrenia patient and misusing methamphetamines suffering from social dysfunction that impact on their quality of life. Knowledge of factors related to social dysfunction will guide the effective intervention. Objectives: To determine the direct effect, indirect effect and total effect of an acerbate Psychotics’ Symptoms, Social Support, Stressful life events, Medication use self-efficacy impact on social dysfunction in Thai schizophrenic patient and methamphetamine misuse. Methods: Data were collected from schizophrenic and methamphetamine misuse patient by self report. A linear structural relationship was used to test the hypothesized path model. Results: The hypothesized model was found to fit the empirical data and explained 54% of the variance of the psychotic symptoms (X² = 114.35, df = 92, p-value = 0.05, X² /df = 1.24, GFI = 0.96, AGFI = 0.92, CFI = 1.00, NFI = 0.99, NNFI = 0.99, RMSEA = 0.02). The highest total effect on social dysfunction was psychotic symptoms (0.67, p<0.05). Medication use self-efficacy had a direct effect on psychotic symptoms (-0.25, p<0.01), and social support had direct effect on medication use self efficacy (0.36, p <0.01). Conclusions: Psychotic symptoms and stressful life events were the significance factors that influenced direct on social dysfunctioning. Therefore, interventions that are designed to manage these factors are crucial in order to enhance social functioning in this population.

Keywords: psychotic symptoms, methamphetamine, schizophrenia, stressful life events, social dysfunction, social support, medication use self efficacy

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Authors: Kyungae Jo, Eun Young Kim, Byungsoo Shin, Kwang Soon Shin, Hyung Joo Suh

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Gamma-aminobutyric acid (GABA) and 5-hydroxytryptophan (5-HTP) are amino acids of digested nutrients or food ingredients and these can possibly be utilized as non-pharmacologic treatment for sleep disorder. We previously investigated the GABA/5-HTP mixture is the principal concept of sleep-promoting and activity-repressing management in nervous system of D. melanogaster. Two experiments in this study were designed to evaluate sleep-promoting effect of GABA/5-HTP mixture, to clarify the possible ratio of sleep-promoting action in the Drosophila invertebrate model system. Behavioral assays were applied to investigate distance traveled, velocity, movement, mobility, turn angle, angular velocity and meander of two amino acids and GABA/5-HTP mixture with caffeine treated flies. In addition, differentially expressed gene (DEG) analyses from next generation sequencing (NGS) were applied to investigate the signaling pathway and functional interaction network of GABA/5-HTP mixture administration. GABA/5-HTP mixture resulted in significant differences between groups related to behavior (p < 0.01) and significantly induced locomotor activity in the awake model (p < 0.05). As a result of the sequencing, the molecular function of various genes has relationship with motor activity and biological regulation. These results showed that GABA/5-HTP mixture administration significantly involved the inhibition of motor behavior. In this regard, we successfully demonstrated that using a GABA/5-HTP mixture modulates locomotor activity to a greater extent than single administration of each amino acid, and that this modulation occurs via the neuronal system, neurotransmitter release cycle and transmission across chemical synapses.

Keywords: sleep, γ-aminobutyric acid, 5-hydroxytryptophan, Drosophila melanogaster

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Authors: Mary Deyo, Zmara Harrison

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This study reports the outcomes of an 8-week experiential learning program for 6 adults with Intellectual and Developmental Disabilities (IDD) at a day habilitation program. The intervention foci for this program include executive function, language learning in the domains of expressive, receptive, and pragmatic language, and quality of life. The interprofessional collaboration aimed at supporting adults with IDD to reach person-centered, functional goals across skill domains is critical. This study is a significant addition to the speech-language pathology literature in that it examines a therapy method that potentially meets this need while targeting domains within the speech-language pathology scope of practice. Communication therapy was provided during highly valued and meaningful hands-on learning experiences, referred to as the Garden Club, which incorporated all aspects of planting and caring for a garden as well as related journaling, sensory, cooking, art, and technology-based activities. Direct care staff and an undergraduate research assistant were trained by SLP to be impactful language guides during their interactions with participants in the Garden Club. SLP also provided direct therapy and modeling during Garden Club. Research methods used in this study included a mixed methods analysis of a literature review, a quasi-experimental implementation of communication therapy in the context of experiential learning activities, Quality of Life participant surveys, quantitative pre- post- data collection and linear mixed model analysis, qualitative data collection with qualitative content analysis and coding for themes. Outcomes indicated overall positive changes in expressive vocabulary, following multi-step directions, sequencing, problem-solving, planning, skills for building and maintaining meaningful social relationships, and participant perception of the Garden Project’s impact on their own quality of life. Implementation of this project also highlighted supports and barriers that must be taken into consideration when planning similar projects. Overall findings support the use of experiential learning projects in day habilitation programs for adults with IDD, as well as additional research to deepen understanding of best practices, supports, and barriers for implementation of experiential learning with this population. This research provides an important contribution to research in the fields of speech-language pathology and other professions serving adults with IDD by describing an interprofessional experiential learning program with positive outcomes for executive function, language learning, and quality of life.

Keywords: experiential learning, adults, intellectual and developmental disabilities, expressive language, receptive language, pragmatic language, executive function, communication therapy, day habilitation, interprofessionalism, quality of life

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Authors: Jadwiga Klukow, Anna Ksykiewicz-Dorota

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An analysis of the distribution of nurses’ working time constitutes vital information for the management in planning employment. The objective of the study was to analyze the distribution of nurses’ working time in an emergency department. The study was conducted in an emergency department of a teaching hospital in Lublin, in Southeast Poland. The catalogue of activities performed by nurses was compiled by means of continuous observation. Identified activities were classified into four groups: Direct care, indirect care, coordination of work in the department and personal activities. Distribution of nurses’ working time was determined by work sampling observation (Tippett) at random intervals. The research project was approved by the Research Ethics Committee by the Medical University of Lublin (Protocol 0254/113/2010). On average, nurses spent 31% of their working time on direct care, 47% on indirect care, 12% on coordinating work in the department and 10% on personal activities. The most frequently performed direct care tasks were diagnostic activities – 29.23% and treatment-related activities – 27.69%. The study has provided information on the complexity of performed activities and utilization of nurses’ working time. Enhancing the effectiveness of nursing actions requires working out a strategy for improved management of the time nurses spent at work. Increasing the involvement of auxiliary staff and optimizing communication processes within the team may lead to reduction of the time devoted to indirect care for the benefit of direct care.

Keywords: emergency nurses, nursing care, workload, work sampling

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Authors: Debjit Ray

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Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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Authors: D. De Matías Batalla

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This paper develops and extended eclectic paradigm to fit the firm internationalization process with the real international business world. The approach is based on Dunning´s, introducing new concepts like mode of entry, international joint venture o international mergers and acquisitions. At the same time is presented a model to describe the Spanish international mergers and acquisitions in order to determinate the most important factor that influence in this type of foreign direct investment.

Keywords: dunning, eclectic paradigm, foreign direct investment, IJV, international business, international management, multinational firms, firm internationalization process, M&A

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Authors: R. Ziaie Moayed, E. Khavaninzadeh, M. Ghorbani Tochaee

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Direct shear test is widely used in soil mechanics experiment to determine the shear strength parameters of granular soils. For analysis of soil stability problems such as bearing capacity, slope stability and lateral pressure on soil retaining structures, the shear strength parameters must be known well. In the present study, shear strength parameters are determined in silty-sand mixtures. Direct shear tests are performed on 161 Firoozkooh sand with different silt content at a relative density of 70% in three vertical stress of 100, 150, and 200 kPa. Wet tamping method is used for soil sample preparation, and the results include diagrams of shear stress versus shear deformation and sample height changes against shear deformation. Accordingly, in different silt percent, the shear strength parameters of the soil such as internal friction angle and dilation angle are calculated and compared. According to the results, when the sample contains up to 10% silt, peak shear strength and internal friction angle have an upward trend. However, if the sample contains 10% to 50% of silt a downward trend is seen in peak shear strength and internal friction angle.

Keywords: shear strength parameters, direct shear test, silty sand, shear stress, shear deformation

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Authors: Farhan Beg, Raymond Moberly

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The Indian subcontinent is facing a massive challenge with regards to energy security in member countries, to provide reliable electricity to facilitate development across various sectors of the economy and consequently achieve the developmental targets. The instability of the current precarious situation is observable in the frequent system failures and blackouts. The deployment of interconnected electricity ‘Supergrid’ designed to carry huge quanta of power across the Indian sub-continent is proposed in this paper. Besides enabling energy security in the subcontinent, it will also provide a platform for Renewable Energy Sources (RES) integration. This paper assesses the need and conditions for a Supergrid deployment and consequently proposes a meshed topology based on Voltage Source High Voltage Direct Current (VSC-HVDC) converters for the Supergrid modeling. Various control schemes for the control of voltage and power are utilized for the regulation of the network parameters. A 3 terminal Multi Terminal Direct Current (MTDC) network is used for the simulations.

Keywords: super grid, wind and solar energy, high voltage direct current, electricity management, load flow analysis

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Authors: Dali Gaganidze, Ekaterine Abashidze

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Potato is one of the main agricultural crops in Georgia. Georgia produces early and late potato varieties in almost all regions. In traditional potato growing regions (Svaneti, Samckhet javaheti and Tsalka), the yield is higher than 30-35 t/ha. Among the plant pests that limit potato production and quality, the potato cyst nematodes (PCN) are harmful around the world. Yield losses caused by PCN are estimated up to 30%. Rout surveys conducted in two geographically distinct regions of Georgia producing potatoes - Samtskhe - Javakheti and Svaneti revealed potato cyst nematode Globodera rostochiensi. The aim of the study was the Phylogenetic analyses of Globodera rostochiensi revealed in Georgia by the amplification and sequencing of 28S gen in the D3 region and intergenic ITS1-15.8S-ITS2 region. Identification of all the samples from the two Globodera populations (Samtskhe - Javakheti and Svaneti), i.e., G. rostochiensis (20 isolates) were confirmed by conventional multiplex PCR with ITS 5 universal and PITSp4, PITSr3 specific primers of the cyst nematodes’ (G. pallida, G. rostochiensis). The size of PCR fragment 434 bp confirms that PCN samples from two populations, Samtskhe- Javakheti and Svaneti, belong to G. rostochiensi . The ITS1–5.8S-ITS2 regions were amplified using prime pairs: rDNA1 ( 5’ -TTGATTACGTCCCTGCCCTTT-3’ and rDNA2( 5’ TTTCACTCGCCGTTACTAAGG-3’), D3 expansion regions were amplified using primer pairs: D3A (5’ GACCCCTCTTGAAACACGGA-3’) and D3B (5’-TCGGAAGGAACCAGCTACTA-3’. PCR products of each region were cleaned up and sequenced using an ABI 3500xL Genetic Analyzer. Obtained sequencing results were analyzed by computer program BLASTN (https://blast.ncbi.nlm.nih.gov/Blast.cg). Phylogenetic analyses to resolve the relationships between the isolates were conducted in MEGA7 using both distance- and character-based methods. Based on analysis of G.rostochiensis isolate`s D3 expansion regions are grouped in three major clades (A, B and C) on the phylogenetic tree. Clade A is divided into three subclades; clade C is divided into two subclades. Isolates from the Samtckhet-javakheti population are in subclade 1 of clade A and isolates in subclade 1 of clade C. Isolates) from Svaneti populations are in subclade 2 of clade A and in clad B. In Clade C, subclade two is presented by three isolates from Svaneti and by one isolate (GL17) from Samckhet-Javakheti. . Based on analysis of G.rostochiensis isolate`s ITS1–5.8S-ITS2 regions are grouped in two main clades, the first contained 20 Georgian isolates of Globodera rostochiensis from Svaneti . The second clade contained 15 isolates of Globodera rostochiensis from Samckhet javakheti. Our investigation showed of high genetic variation of D3 and ITS1–5.8S-ITS2 region of rDNA of the isolates of G. rostochiensis from different geographic origins (Svameti, Samckhet-Javakheti) of Georgia. Acknowledgement: The research has been supported by the Shota Rustaveli National Scientific Foundation of Georgia : Project # FR17_235

Keywords: globodera rostochiensi, PCR, phylogenetic tree, sequencing

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Authors: Haleh Hamidpour

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Since the seismic damageability of structures is controlled by the inelastic deformation capacities of structural elements, seismic design of structure based on force analogy methods is not appropriate. In recent year, the basic approach of design codes have been changed from force-based approach to displacement-based. In this regard, a Direct Displacement-Based Design (DDBD) and a Performance-Based Plastic Design (PBPD) method are proposed. In this study, the efficiency of these two methods on seismic performance of structures is evaluated through a sample 12-story reinforced concrete moment frame. The building is designed separately based on the DDBD and the PBPD methods. Once again the structure is designed by the traditional force analogy method according to the FEMA P695 regulation. Different design method results in different structural elements. Seismic performance of these three structures is evaluated through nonlinear static and nonlinear dynamic analysis. The results show that the displacement-based design methods accommodate the intended performance objectives better than the traditional force analogy method.

Keywords: direct performance-based design, ductility demands, inelastic seismic performance, yield mechanism

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Authors: S. Muthuraja Soundrapandian, C.K. Subramaniam

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A micro Direct Methanol Fuel Cell (DMFC) of 1 cm2 active area with selective sensor materials to sense methanol for redox, has been developed. Among different Pt alloys, Pt-Sn/C was able to produce high current density and repeatability. Membrane Elecctrode Assembly (MEA) of anode catalyst Pt-Sn/C was prepared with nafion as active membrane and Pt black as cathode catalyst. The sensor’s maximum ability to detect the trace levels of methanol in ppm has been analyzed. A compact sensor set up has also been made and the characterization studies were carried out. The acceptable value of current density was derived by the cell and the results are able to fulfill the needs of DMFC technology for the practical applications.

Keywords: DMFC, sensor, MEA, Pt-Sn

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Authors: Jin Young Kim, Kwon Kyoo Kang

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The SGR1 (STAYGREEN1) protein is a critical regulator of plant leaves in chlorophyll degradation and senescence. The functions and mechanisms of tomato SGR1 action are poorly understood and worthy of further investigation. To investigate the function of the SGR1 gene, we generated a SGR1-knockout (KO) null line via clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene editing and conducted RNA sequencing and gas chromatography tandem mass spectrometry (GC-MS/MS) analysis to identify the differentially expressed genes. The SlSGR1 (Solanum lycopersicum SGR1) knockout null line clearly showed a turbid brown color with significantly higher chlorophyll and carotenoid content compared to wild-type (WT) fruit. Differential gene expression analysis revealed 728 differentially expressed genes (DEGs) between WT and sgr1 #1-6 line, including 263 and 465 downregulated and upregulated genes, respectively, for which fold change was >2, and the adjusted p-value was <0.05. Most of the DEGs were related to photosynthesis and chloroplast function. In addition, the pigment, carotenoid changes in sgr1 #1-6 line was accumulated of key primary metabolites such as sucrose and its derivatives (fructose, galactinol, raffinose), glycolytic intermediates (glucose, G6P, Fru6P) and tricarboxylic acid cycle (TCA) intermediates (malate and fumarate). Taken together, the transcriptome and metabolite profiles of SGR1-KO lines presented here provide evidence for the mechanisms underlying the effects of SGR1 and molecular pathways involved in chlorophyll degradation and carotenoid biosynthesis.

Keywords: tomato, CRISPR/Cas9, null line, RNA-sequencing, metabolite profiling

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Authors: Sneha Shankar, Orlando Buendia, Will Evans

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Alpha-1 antitrypsin deficiency (AATD) is a rare, genetic, and multisystemic condition. Underdiagnosis is common, leading to chronic pulmonary and hepatic complications, increased resource utilization, and additional costs to the healthcare system. Currently, there is limited evidence of the direct medical costs of AATD diagnosis in the UK. This study explores the economic impact of AATD patients during the 3 years before diagnosis and to identify the major cost drivers using primary and secondary care electronic health record (EHR) data. The 3 years before diagnosis time period was chosen based on the ability of our tool to identify patients earlier. The AATD algorithm was created using published disease criteria and applied to 148 known AATD patients’ EHR found in a primary care database of 936,148 patients (413,674 Biobank and 501,188 in a single primary care locality). Among 148 patients, 9 patients were flagged earlier by the tool and, on average, could save 3 (1-6) years per patient. We analysed 101 of the 148 AATD patients’ primary care journey and 20 patients’ Hospital Episode Statistics (HES) data, all of whom had at least 3 years of clinical history in their records before diagnosis. The codes related to laboratory tests, clinical visits, referrals, hospitalization days, day case, and inpatient admissions attributable to AATD were examined in this 3-year period before diagnosis. The average cost per patient was calculated, and the direct medical costs were modelled based on the mean prevalence of 100 AATD patients in a 500,000 population. A deterministic sensitivity analysis (DSA) of 20% was performed to determine the major cost drivers. Cost data was obtained from the NHS National tariff 2020/21, National Schedule of NHS Costs 2018/19, PSSRU 2018/19, and private care tariff. The total direct medical cost of one hundred AATD patients three years before diagnosis in primary and secondary care in the UK was £3,556,489, with an average direct cost per patient of £35,565. A vast majority of this total direct cost (95%) was associated with inpatient admissions (£3,378,229). The DSA determined that the costs associated with tier-2 laboratory tests and inpatient admissions were the greatest contributors to direct costs in primary and secondary care, respectively. This retrospective study shows the role of EHRs in calculating direct medical costs and the potential benefit of new technologies for the early identification of patients with AATD to reduce the economic burden in primary and secondary care in the UK.

Keywords: alpha-1 antitrypsin deficiency, costs, digital health, early diagnosis

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Authors: R. B. Ogunrinde, C. C. Jibunoh

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In this paper, a spectral decomposition method is developed for the direct integration of stiff and nonstiff homogeneous linear (ODE) systems with linear, constant, or zero right hand sides (RHSs). The method does not require iteration but obtains solutions at any random points of t, by direct evaluation, in the interval of integration. All the numerical solutions obtained for the class of systems coincide with the exact theoretical solutions. In particular, solutions of homogeneous linear systems, i.e. with zero RHS, conform to the exact analytical solutions of the systems in terms of t.

Keywords: spectral decomposition, linear RHS, homogeneous linear systems, eigenvalues of the Jacobian

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Authors: Alexandre H. Okano, Pedro M. D. Agrícola, Daniel G. Da S. Machado, Luiz I. Do N. Neto, Luiz F. Farias Junior, Paulo H. D. Nascimento, Rickson C. Mesquita, John F. Araujo, Eduardo B. Fontes, Hassan M. Elsangedy, Shinsuke Shimojo, Li M. Li

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The prefrontal cortex is involved in the reward system and the insular cortex integrates the afferent inputs arriving from the body’ systems and turns into feelings. Therefore, modulating neuronal activity in these regions may change individuals’ perception in a given situation such as exercise. We tested whether transcranial direct current stimulation (tDCS) change cerebral oxygenation and pleasure during exercise. Fourteen volunteer healthy adult men were assessed into five different sessions. First, subjects underwent to a maximum incremental test on a cycle ergometer. Then, subjects were randomly assigned to a transcranial direct current stimulation (2mA for 15 min) intervention in a cross over design in four different conditions: anode and cathode electrodes on T3 and Fp2 targeting the insular cortex, and Fpz and F4 targeting prefrontal cortex, respectively; and their respective sham. These sessions were followed by 30 min of moderate intensity exercise. Brain oxygenation was measured in prefrontal cortex with a near infrared spectroscopy. Perceived exertion and pleasure were also measured during exercise. The asymmetry in prefrontal cortex oxygenation before the stimulation decreased only when it was applied over this region which did not occur after insular cortex or sham stimulation. Furthermore, pleasure was maintained during exercise only after prefrontal cortex stimulation (P > 0.7), while there was a decrease throughout exercise (P < 0.03) during the other conditions. We conclude that tDCS over the prefrontal cortex changes brain oxygenation in ventromedial prefrontal cortex and maintains perceived pleasure during exercise. Therefore, this technique might be used to enhance effective responses related to exercise.

Keywords: affect, brain stimulation, dopamine neuromodulation, pleasure, reward, transcranial direct current stimulation

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Authors: Ese Urhie, Bosede Olopade, Muyiwa Oladosun, Henry Okodua

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In the past three and half decades, aside from the fact that the contribution of the industrial sector to gross domestic product in Nigeria has nose-dived, its performance has also been highly unstable. Investment funds needed to develop the industrial sector usually come from both internal and external sources. The internal sources include surplus generated within the industrial sector and surplus diverted from other sectors of the economy. It has been observed that due to the small size of the industrial sector in developing countries, very limited funds could be raised for further investment. External sources of funds which many currently industrialized and some ‘newly industrializing countries’ have benefited from including direct and indirect investment by foreign capitalists; foreign aid and loans; and investments by nationals living abroad. Foreign direct investment inflow in Nigeria has been declining since 2009 in both absolute and relative terms. High level of human capital has been identified as one of the crucial factors that explain the miraculous growth of the ‘Asian Tigers’. Its low level has also been identified as the major cause for the low level of FDI flow to Nigeria in particular and Africa in general. There has been positive, but slow improvement in human capital indicators in Nigeria in the past three decades. In spite of this, foreign direct investment inflow has not only been low; it has declined drastically in recent years. i) Why has the improvement in human capital in Nigeria failed to attract more FDI inflow? ii) To what extent does the level of human capital influence FDI inflow in Nigeria? iii) Is there a threshold of human capital stock that guarantees sustained inflow of FDI? iv) Does the quality of human capital matter? v) Does the influence of other (negative) factors outweigh the benefits of human capital? Using time series secondary data, a system of equations is employed to evaluate the effect of human capital on FDI inflow in Nigeria on one hand and the effect of FDI on the level of industrialization on the other. A weak relationship between human capital and FDI is expected, while a strong relationship between FDI and industrial growth is expected from the result.

Keywords: human capital, foreign direct investment, industrialization, gross domestic product

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Authors: Wafa Toumi, Alessandro Ripalti, Luigi Ricciardiello, Dalila Gargouri, Jamel Kharrat, Abderraouf Cherif, Ahmed Bouhafa, Slim Jarboui, Mohamed Zili, Ridha Khelifa

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Background & aims: Colorectal cancer (CRC) is one of the most common malignancies throughout the world. Several risk factors, both genetic and environmental, including viral infections, have been linked to colorectal carcinogenesis. A few studies report the detection of human polyomavirus JC (JCV) DNA and transformation antigen (T-Ag) in a fraction of the colorectal tumors studied and suggest an association of this virus with CRC. In order to investigate whether such an association of JCV with CRC will hold in a different epidemiological setting, we looked for the presence of JCV DNA and T-Ag expression in a group of Tunisian CRC patients. Methods: Fresh colorectal mucosa biopsies were obtained from 17 healthy volunteers and from both colorectal tumors and adjacent normal tissues of 47 CRC patients. DNA was extracted from fresh biopsies or from formalin-fixed, paraffin-embedded tissue sections using the Invitrogen Purelink Genomic DNA mini Kit. A simple PCR and a nested PCR were used to amplify a region of the T-Ag gene. The obtained PCR products revealed a 154 bp and a 98 bp bands, respectively. Specificity was confirmed by sequencing of the PCR products. T-Ag expression was determined by immunohistochemical staining using a mouse monoclonal antibody (clone PAb416) directed against SV40 T-Ag that cross reacts with JCV T-Ag. Results: JCV DNA was found in 12 (25%) and 22 (46%) of the CRC tumors by simple PCR and by nested PCR, respectively. All paired adjacent normal mucosa biopsies were negative for viral DNA. Sequencing of the DNA amplicons obtained confirmed the authenticity of T-Ag sequences. Immunohistochemical staining showed nuclear T-Ag expression in all 22 JCV DNA- positive samples and in 3 additional tumor samples which appeared DNA-negative by PCR. Conclusions: These results suggest an association of JCV with a subpopulation of Tunisian colorectal tumors.

Keywords: colorectal cancer, immunohistochemistry, Polyomavirus JC, PCR

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Authors: Meimei Shi

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Objectives: The identification of endangered species, especially simultaneous detection of multiple species in complex samples, plays a critical role in alleged wildlife crime incidents and prevents illegal trade. This study was to develop a multi-locus DNA metabarcoding method for endangered animal species identification. Methods: Several pairs of universal primers were designed according to the mitochondria conserved gene regions. Experimental mixtures were artificially prepared by mixing well-defined species, including endangered species, e.g., forest musk, bear, tiger, pangolin, and sika deer. The artificial samples were prepared with 1-16 well-characterized species at 1% to 100% DNA concentrations. After multiplex-PCR amplification and parameter modification, the amplified products were analyzed by capillary electrophoresis and used for NGS library preparation. The DNA metabarcoding was carried out based on Illumina MiSeq amplicon sequencing. The data was processed with quality trimming, reads filtering, and OTU clustering; representative sequences were blasted using BLASTn. Results: According to the parameter modification and multiplex-PCR amplification results, five primer sets targeting COI, Cytb, 12S, and 16S, respectively, were selected as the NGS library amplification primer panel. High-throughput sequencing data analysis showed that the established multi-locus DNA metabarcoding method was sensitive and could accurately identify all species in artificial mixtures, including endangered animal species Moschus berezovskii, Ursus thibetanus, Panthera tigris, Manis pentadactyla, Cervus nippon at 1% (DNA concentration). In conclusion, the established species identification method provides technical support for customs and forensic scientists to prevent the illegal trade of endangered animals and their products.

Keywords: DNA metabarcoding, endangered animal species, mitochondria nucleic acid, multi-locus

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