Search results for: gene frequency

Authors: Yan Pang, Xiang Wang, Zhaomiao Liu

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Droplet microfluidics, in which nanoliter to picoliter droplets acted as individual compartments, are common to a diverse array of applications such as analytical chemistry, tissue engineering, microbiology and drug discovery. The droplet generation in a simplified two dimension T-shape microchannel with the main channel width of 50 μm and the side channel width of 25 μm, is simulated to investigate effects of the forced fluctuation of the side wall on the droplet generation and flow. The periodic fluctuations are applied on a length of the side wall in the main channel of the T-junction with the deformation shape of the double-clamped beam acted by the uniform force, which varies with the flow time and fluctuation periods, forms and positions. The fluctuations under most of the conditions expand the distribution range of the droplet size but have a little effect on the average size, while the shape of the fixed side wall changes the average droplet size chiefly. Droplet sizes show a periodic pattern along the relative time when the fluctuation is forced on the side wall near the T-junction. The droplet emerging frequency is not varied by the fluctuation of the side wall under the same flow rate and geometry conditions. When the fluctuation period is similar with the droplet emerging period, the droplet size shows a nice stability as the no fluctuation case.

Keywords: droplet generation, droplet size, flow flied, forced fluctuation

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Authors: Nony Rahadiva

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The development of housing in urban areas can not be separated from the high rate of population growth from both natural population growth and population growth due to migration. The development is bounded by urban land area so that construction of flats become a development priority. Quality of residential flats are influenced by the patterns of behavior of its inhabitants. The frequency of contact between the occupants become one of the effects of good social relations, but harmful activity can degrade the environment, especially in flats. One of the social relationships that can be seen on the flats development is the residents in Kutobedah flat built in Malang city. Problems that occur in that place is unfavorable flat management due to social activities such as daily activities and also the neighboring activities of apartment dwellers who tend not to pay attention to the environment. Based on these problems we can do a study on social interaction in Kutobedah flat and its influence on the management of flat facilities and infrastructures. This research was carried out by submitting a questionnaire to the residents of the apartment based social activities , operations and maintenance of the flats. By using a weighted analysis, we can find that social interaction tenants is high, but the level of infrastructure and facilities management of the tenants is low so it is needed to counsel the residents how to use and maintain the infrastructure properly.

Keywords: activities, flat, infrastructure management, social interaction

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Authors: Orpita U. Laz, Ataur Rahman

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Climate change will affect various aspects of hydrological cycle such as rainfall. A change in rainfall will affect flood magnitude and frequency in future which will affect the design and operation of hydraulic structures. In this paper, trends in sub-hourly, sub-daily, and daily extreme rainfall events from 18 rainfall stations located in Tasmania, Australia are examined. Two non-parametric tests (Mann-Kendall and Spearman’s Rho) are applied to detect trends at 10%, 5%, and 1% significance levels. Sub-hourly (6, 12, 18, and 30 minutes) annual maximum rainfall events have been found to experience statistically significant upward trends at 10 % level of significance. However, sub-daily durations (1 hour, 3 and 12 hours) exhibit decreasing trends and no trends exists for longer duration rainfall events (e.g. 24 and 72 hours). Some of the durations (e.g. 6 minutes and 6 hours) show similar results (with upward trends) for both the tests. For 12, 18, 60 minutes and 3 hours durations both the tests show similar downward trends. This finding has important implication for Tasmania in the design of urban infrastructure where shorter duration rainfall events are more relevant for smaller urban catchments such as parking lots, roof catchments and smaller sub-divisions.

Keywords: climate change, design rainfall, Mann-Kendall test, trends, Spearman’s Rho, Tasmania

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Authors: Eriko Ochiai, Fumiko Satoh, Keiko Miyashita, Yu Kakimoto, Motoki Osawa

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Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims.

Keywords: postmortem genetic testing, sudden death, SIDS, next generation sequencing

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Authors: Adriana B. Ribeiro, Camila B. Araujo, Frank L. Bueno, Luiz Eduardo V. Silva, Caroline V. Fortes, Helio C. Salgado, Rubens Fazan Jr., Claudia H. L. da Silva

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Denture-related stomatitis (DRS) has recently been associated with deleterious cardiovascular effects, including hypertension. This study evaluated salivary parameters, blood pressure (BP) and heart rate variability (HRV), before and after DRS treatment in edentulous patients (n=14). Collection of unstimulated and stimulated saliva, as well as blood pressure (BP) measurements and electrocardiogram recordings were performed before and after 10 days of DRS treatment. The salivary flow (mL/min) was found similar at both times while pH was smaller (more neutral) after treatment (7.3 ± 2.2 vs. 7.1 ± 0.24). Systolic BP (mmHg) showed a trend, but not a significant reduction after DRS treatment (158 ± 25.68 vs. 148 ± 16,72, p=0,062) while diastolic BP was found similar in both times (86 ± 13.93 and 84 ± 9.38). Overall HRV, measured by standard deviation of RR intervals was not affected by DRS treatment (24 ± 4 vs 18 ± 2 ms), but differences of successive RR intervals (an index of parasympathetic cardiac modulation) increased after the treatment (26 ± 4 vs 19 ± 2 ms). Moreover, another index of vagal modulation of the heart, the power of RR interval spectra at high-frequency, was also markedly higher after DRS treatment (236 ± 63 vs 135 ± 32 ms²). Such findings strongly suggest that DRS is linked to an autonomic imbalance with sympathetic overactivity, which is markedly deleterious, increasing cardiovascular risk and the incidence of diseases such as hypertension. Acknowledgment: This study is supported by FAPESP, CNPq.

Keywords: biofilm, denture stomatitis, HRV, blood pressure

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Authors: Philippa Saunders, Claire Fletcher

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INTRODUCTION: Prostate cancer is the most prevalent malignancy affecting Western males. It is initially an androgen-dependent disease: androgens bind to the androgen receptor and drive the expression of genes that promote proliferation and evasion of apoptosis. Despite reduced androgen dependence in advanced prostate cancer, androgen receptor signaling remains a key driver of growth. Androgen deprivation therapy (ADT) is, therefore, a first-line treatment approach and works well initially, but resistance inevitably develops. Abiraterone and Enzalutamide are drugs widely used in ADT and are androgen synthesis and androgen receptor signaling inhibitors, respectively. The shortage of other treatment options means acquired resistance to these drugs is a major clinical problem. MicroRNAs (miRs) are important mediators of post-transcriptional gene regulation and show altered expression in cancer. Several have been linked to the development of resistance to ADT. Manipulation of such miRs may be a pathway to breakthrough treatments for advanced prostate cancer. This study aimed to validate ADT resistance-implicated miRs and their clinically relevant targets. MATERIAL AND METHOD: Small RNA-sequencing of Abiraterone- and Enzalutamide-resistant C42 prostate cancer cells identified subsets of miRs dysregulated as compared to parental cells. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) was used to validate altered expression of candidate ADT resistance-implicated miRs 195-5p, 497-5p and 29a-5p in ADT-resistant and -responsive prostate cancer cell lines, patient-derived xenografts (PDXs) and primary prostate cancer explants. RESULTS AND DISCUSSION: This study suggests a possible role for miR-497-5p in the development of ADT resistance in prostate cancer. MiR-497-5p expression was increased in ADT-resistant versus ADT-responsive prostate cancer cells. Importantly, miR-497-5p expression was also increased in Enzalutamide-treated, castrated (ADT-mimicking) PDXs versus intact PDXs. MiR-195-5p was also elevated in ADT-resistant versus -responsive prostate cancer cells, while there was a drop in miR-29a-5p expression. Candidate clinically relevant targets of miR-497-5p in prostate cancer were identified by mining AGO-PAR-CLIP-seq data sets and may include AVL9 and FZD6. CONCLUSION: In summary, this study identified microRNAs that are implicated in prostate cancer resistance to androgen deprivation therapy and could represent novel therapeutic targets for advanced disease.

Keywords: microRNA, androgen deprivation therapy, Enzalutamide, abiraterone, patient-derived xenograft

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Authors: Arezou Hajhashemi, Karim Asgari, Masoud Etemadifar, Maryam Keyvani, Ali Hekmatnia

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Multiple Sclerosis (MS) is one of the most prevalent demyelinating diseases in CNS. As in other chronic cerebral diseases, impairment in cognitive functioning and in memory is popular. Because of the inflammatory and demyelinating nature of the disease, the localization of plaques in different parts of the Prefrontal and Limbic System, may lead to memorial symptoms. This investigation was intended to study relationship between frequency of plaques and memorial symptoms arising from dysfunction limbic system and prefrontal of patients with MS. The sample was selected randomly from patients with MS with memory problem, who have been referred to Isfahan Multiple Sclerosis Society. Brain System Test and Memory Test was administered to the sample, and their MRI's were analyzed by specialist in order to indentify two different parts of plaques. The data was analyzed by SPSS. The results showed that there were significant relationship between MS plaques and prefrontal's dysfunction and memorial symptom related to prefrontal area; however, there were no significant relationship between MS plaques and limbic system's dysfunction and memorial symptoms related to limbic system area. The results of this study suggest that memorial symptoms due to injury regions of the brain have the most significant relationship to prefrontal. Better judgment about these results needs more studies in future.

Keywords: multiple sclerosis, magnetic image, brain injury, behavior disorder

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Authors: Shalini TV, Gangadharan GG, Sriranjini S Jaideep, ASN Seshasayee, Awadhesh Pandit

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Introduction: Prakriti (body-mind constitution of an individual) is a conventional, customized and unique understanding of which is essential for the personalized medicine described in Ayurveda, Indian System of Medicine. Based on the Doshas( functional, bio humoral unit in the body), individuals are categorized into three major Prakriti- Vata, Pitta, and Kapha. The human gut microbiome hosts plenty of highly diverse and metabolically active microorganisms, mainly dominated by the bacteria, which are known to influence the physiology of an individual. Few researches have shown the correlation between the Prakriti and the biochemical parameters. In this study, an attempt was made to explore any correlation between the Prakriti (phenotype of an individual) with the Genetic makeup of the gut microbiome in healthy individuals. Materials and methods: 270 multi-ethnic, healthy volunteers of both sex with the age group between 18 to 40 years, with no history of antibiotics in the last 6 months were recruited into three groups of Vata, Pitta, and Kapha. The Prakriti of the individual was determined using Ayusoft, a software designed by CDAC, Pune, India. The volunteers were subjected to initial screening for the assessment of their height, weight, Body Mass Index, Vital signs and Blood investigations to ensure they are healthy. The stool and saliva samples of the recruited volunteers were collected as per the standard operating procedure developed, and the bacterial DNA was isolated using Qiagen kits. The extracted DNA was subjected to 16s rRNA sequencing using the Illumina kits. The sequencing libraries are targeting the variable V3 and V4 regions of the 16s rRNA gene. Paired sequencing was done on the MiSeq system and data were analyzed using the CLC Genomics workbench 11. Results: The 16s rRNA sequencing of the V3 and V4 regions showed a diverse pattern in both the oral and stool microbial DNA. The study did not reveal any specific pattern of bacterial flora amongst the Prakriti. All the p-values were more than the effective alpha values for all OTUs in both the buccal cavity and stool samples. Therefore, there was no observed significant enrichment of an OTU in the patient samples from either the buccal cavity or stool samples. Conclusion: In healthy volunteers of multi-ethnicity, due to the influence of the various factors, the correlation between the Prakriti and the gut microbiome was not seen.

Keywords: gut microbiome, ayurveda Prakriti, sequencing, multi-ethnic urban population

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Authors: Oswaldo Otero, Eduardo A. Orozco, Ana M. Herrera

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In this work, we present results from analytical and numerical studies of the electron acceleration by a TE₀₁₁ cylindrical microwave mode in a static homogeneous magnetic field under electron cyclotron resonance (ECR) condition. The stability of the orbits is analyzed using the particle orbit theory. In order to get a better understanding of the interaction wave-particle, we decompose the azimuthally electric field component as the superposition of right and left-hand circular polarization standing waves. The trajectory, energy and phase-shift of the electron are found through a numerical solution of the relativistic Newton-Lorentz equation in a finite difference method by the Boris method. It is shown that an electron longitudinally injected with an energy of 7 keV in a radial position r=Rc/2, being Rc the cavity radius, is accelerated up to energy of 90 keV by an electric field strength of 14 kV/cm and frequency of 2.45 GHz. This energy can be used to produce X-ray for medical imaging. These results can be used as a starting point for study the acceleration of electrons in a magnetic field changing slowly in time (GYRAC), which has some important applications as the electron cyclotron resonance ion proton accelerator (ECR-IPAC) for cancer therapy and to control plasma bunches with relativistic electrons.

Keywords: Boris method, electron cyclotron resonance, finite difference method, particle orbit theory, X-ray

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Authors: D. Shakirah Shukor, A. Aminudin, Hashim U. A., Waziralilah N. Fathiah, T. Vikneshvaran

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The interior noise control is essential to be explored due to the interior acoustic analysis is significant in the systems such as automobiles, aircraft, air-handling system and diesel engine exhausts system. In this research, experimental work was undertaken for canceling an active noise in the rectangular enclosure. The rectangular enclosure was fabricated with multiple speakers and microphones inside the enclosure. A software program using digital signal processing is implemented to evaluate the proposed method. Experimental work was conducted to obtain the acoustic behavior and characteristics of the rectangular enclosure and noise cancellation based on active noise control in low-frequency range. Noise is generated by using multispeaker inside the enclosure and microphones are used for noise measurements. The technique for noise cancellation relies on the principle of destructive interference between two sound fields in the rectangular enclosure. One field is generated by the original or primary sound source, the other by a secondary sound source set up to interfere with, and cancel, that unwanted primary sound. At the end of this research, the result of output noise before and after cancellation are presented and discussed. On the basis of the findings presented in this research, an active noise cancellation in the rectangular enclosure is worth exploring in order to improve the noise control technologies.

Keywords: active noise control, digital signal processing, noise cancellation, rectangular enclosure

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Authors: M. Khaledi Pour, P. Akbartehrani, M. Amini, M. Khani, M. Mohajeri Tehrani, R. Radi, B. Shokri

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Diabetic Foot Ulcer (DFU) is one of the costly severe complications of diabetes. Neuropathy and Peripheral Arterial Disease (PAD) due to diabetes are significant causes of this complication. In 10 years the patients with DFUs are twice as likely to die as patients without DFUs. Cold Atmospheric Plasma (CAP) is a promising tool for medical purposes. CAP generate reactive species at room temperature and are effective in killing bacteria and fibroblast proliferation. These CAP-based tools produce NO, which has bactericidal and angiogenesis properties. It also showed promising effects in the DFUs surface reduction and the time to wound closure. In this paper, we evaluated the effect of the Argon Plasma Jet (APJ) on the healing process of the Wagner Grade 2 DFUs in a randomized clinical trial. The 20 kHz sinusoidal voltage frequency derives the APJ. Patients (n=20) were randomly double-blinded assigned into two groups. These groups receive the standard care (SC, n=10) and the standard care with APJ treatment (SC+APJ, n=10) for five sessions in four weeks. The results showed that the APJ treatment along standard care could reduce the wound surface by 20 percent more than the standard care. Also, It showed a more influential role in controlling wound infection.

Keywords: argon plasma jet, cold atmospheric plasma, diabetes, diabetic foot ulcer

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Authors: Ahmad Zahran, Ahmed Herzallah, Ahmad Ahmad, Mahran Quraan

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Generation of high DC voltages is necessary for testing the insulation material of high voltage AC transmission lines with long lengths. The harmonic and ripple contents of the output DC voltage supplied by high voltage DC circuits require the use of costly capacitors to smooth the output voltage after rectification. This paper proposes a new modular multiplier high voltage DC generator with embedded Cockcroft-Walton circuits that achieve a negligible harmonic and ripple contents of the output DC voltage without the need for costly filters to produce a nearly constant output voltage. In this new topology, Cockcroft-Walton modules are connected in series to produce a high DC output voltage. The modules are supplied by low input AC voltage sources that have the same magnitude and frequency and shifted from each other by a certain angle to eliminate the harmonics from the output voltage. The small ripple factor is provided by the smoothing column capacitors and the phase shifted input voltages of the cascaded modules. The constituent harmonics within each module are determined using Fourier analysis. The viability of the proposed DC generator for testing purposes and the effectiveness of the cascaded connection are confirmed by numerical simulations using MATLAB/Simulink.

Keywords: Cockcroft-Walton circuit, harmonics, ripple factor, HVDC generator

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Authors: Victoria L. Chester, Usha Kuruganti

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The forest industry is a major economic sector of Canada and also one of the most dangerous industries for workers. The use of mechanized mobile forestry harvesting machines has successfully reduced the incidence of injuries in forest workers related to manual labor. However, these machines have also created additional concerns, including a high machine operation learning curve, increased the length of the workday, repetitive strain injury, cognitive load, physical and mental fatigue, and increased postural loads due to sitting in a confined space. It is critical to obtain objective performance data for employers to develop appropriate work practices for this industry, however ergonomic field studies of this industry are lacking mainly due to the difficulties in obtaining comprehensive data while operators are cutting trees in the woods. The purpose of this study was to establish a measurement and experimental protocol to examine the effects of worker skill level and movement training speed (joystick crane speed) on harvesting performance using a forestry simulator. A custom wrist angle measurement device was developed as part of the study to monitor Euler angles during operation of the simulator. The device of the system consisted of two accelerometers, a Bluetooth module, three 3V coin cells, a microcontroller, a voltage regulator and an application software. Harvesting performance and crane data was provided by the simulator software and included tree to frame collisions, crane to tree collisions, boom tip distance, number of trees cut, etc. A pilot study of 3 operators with various skill levels was tested to identify factors that distinguish highly skilled operators from novice or intermediate operators. Dependent variables such as reaction time, math skill, past work experience, training movement speed (e.g. joystick control speeds), harvesting experience level, muscle activity, and wrist biomechanics were measured and analyzed. A 10-channel wireless surface EMG system was used to monitor the amplitude and mean frequency of 10 upper extremity muscles during pre and postperformance on the forestry harvest stimulator. The results of the pilot study showed inconsistent changes in median frequency pre-and postoperation, but there was the increase in the activity of the flexor carpi radialis, anterior deltoid and upper trapezius of both arms. The wrist sensor results indicated that wrist supination and pronation occurred more than flexion and extension with radial-ulnar rotation demonstrating the least movement. Overall, wrist angular motion increased as the crane speed increased from slow to fast. Further data collection is needed and will help industry partners determine those factors that separate skill levels of operators, identify optimal training speeds, and determine the length of training required to bring new operators to an efficient skill level effectively. In addition to effective and employment training programs, results of this work will be used for selective employee recruitment strategies to improve employee retention after training. Further, improved training procedures and knowledge of the physical and mental demands on workers will lead to highly trained and efficient personnel, reduced risk of injury, and optimal work protocols.

Keywords: EMG, forestry, human factors, wrist biomechanics

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Authors: Waziralilah N. Fathiah, A. Aminudin, U. Alyaa Hashim, T. Vikneshvaran D. Shakirah Shukor

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This paper presents the experimental analysis conducted on a structure borne noise in a rectangular enclosure prototype made by joining of sheet aluminum metal and plywood. The study is significant as many did not realized the annoyance caused by structural borne-noise. In this study, modal analysis is carried out to seek the structure’s behaviour in order to identify the characteristics of enclosure in frequency domain ranging from 0 Hz to 200 Hz. Here, numbers of modes are identified and the characteristic of mode shape is categorized. Modal experiment is used to diagnose the structural behaviour while microphone is used to diagnose the sound. Spectral testing is performed on the enclosure. It is acoustically excited using shaker and as it vibrates, the vibrational and noise responses sensed by tri-axis accelerometer and microphone sensors are recorded respectively. Experimental works is performed on each node lies on the gridded surface of the enclosure. Both experimental measurement is carried out simultaneously. The modal experimental results of the modal modes are validated by simulation performed using MSC Nastran software. In pursuance of reducing the structure borne-noise, mitigation method is used whereby the stiffener plates are perpendicularly placed on the sheet aluminum metal. By using this method, reduction in structure borne-noise is successfully made at the end of the study.

Keywords: enclosure, modal analysis, sound analysis, structure borne-noise

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Authors: Warsa Melles

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This study examines the way second-generation Eritrean immigrants living in the French-speaking part of Switzerland behave linguistically and culturally. The aim of this research is to demonstrate how the participants deal with their bilingualism (Tigrinya and French). More precisely, how does their language use correlates with their socio-cultural attitudes and how do these aspects (re)construct their identity? Data for this research was collected via, questionnaires and semi-structured interviews. Participants were asked to answer questions regarding their linguistic habits, their perception on being bilingual and their cultural identity. The major findings demonstrate that generation 2 relates more with the host country’s language since French is used as the main language in their daily interactions. On the other hand, due to the fact that they have never lived in Eritrea yet were raised by Eritrean born parents in a foreign country, it is more difficult for them to unanimously identify with just one culture. In that sense, intergenerational transmission plays a major role in the perception of identity. All the participants have at least a basic knowledge of Tigrinya, but the use of languages varies according to the purpose. Proficiency in the native language and sense of belonging can be correlated with the frequency of visits to Eritrea. In conclusion, the question of identity in the second-generation Eritrean community cannot be given a categorical and clear-cut answer instead, the new-self image that this social group aims to build is shaped by different factors that are essential to take into consideration.

Keywords: biculturalism, identity, language, migration

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Authors: Oshma Chakoory, Sophie Comtet-Marre, Pierre Peyret

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Metagenomic classifiers are widely used for the taxonomic profiling of metagenomic data and estimation of taxa relative abundance. Small subunit rRNA genes are nowadays a gold standard for the phylogenetic resolution of complex microbial communities, although the power of this marker comes down to its use as full-length. We benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then built a pipeline called RiboTaxa to generate a highly sensitive and specific metataxonomic approach. Using metagenomics data, RiboTaxa gave the best results compared to other tools (Kraken2, Centrifuge (1), METAXA2 (2), PhyloFlash (3)) with precise taxonomic identification and relative abundance description, giving no false positive detection. Using real datasets from various environments (ocean, soil, human gut) and from different approaches (metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not seen by current bioinformatics analysis opening new biological perspectives in human and environmental health. In a study focused on corals’ health involving 20 metagenomic samples (4), an affiliation of prokaryotes was limited to the family level with Endozoicomonadaceae characterising healthy octocoral tissue. RiboTaxa highlighted 2 species of uncultured Endozoicomonas which were dominant in the healthy tissue. Both species belonged to a genus not yet described, opening new research perspectives on corals’ health. Applied to metagenomics data from a study on human gut and extreme longevity (5), RiboTaxa detected the presence of an uncultured archaeon in semi-supercentenarians (aged 105 to 109 years) highlighting an archaeal genus, not yet described, and 3 uncultured species belonging to the Enorma genus that could be species of interest participating in the longevity process. RiboTaxa is user-friendly, rapid, allowing microbiota structure description from any environment and the results can be easily interpreted. This software is freely available at https://github.com/oschakoory/RiboTaxa under the GNU Affero General Public License 3.0.

Keywords: metagenomics profiling, microbial diversity, SSU rRNA genes, full-length phylogenetic marker

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Authors: Sandisiwe Mangali, Graeme Bradley

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Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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Authors: M'Hamed Boulakroune, Mouloud Challal, Hassiba Louazene, Saida Fentiz

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This paper presents a new ultra wideband (UWB) microstrip bandpass filter (BPF) at microwave frequencies. The first one is based on multiple-mode resonator (MMR) and rectangular-shaped defected ground structure (DGS). This filter, which is compact size of 25.2 x 3.8 mm2, provides in the pass band an insertion loss of 0.57 dB and a return loss greater than 12 dB. The second structure is a tunable bandpass filters using planar patch resonators based on diode varactor. This filter is formed by a triple mode circular patch resonator with two pairs of slots, in which the varactors are connected. Indeed, this filter is initially centered at 2.4 GHz, the center frequency of the tunable patch filter could be tuned up to 1.8 GHz simultaneously with the bandwidth, reaching high tuning ranges. Lossless simulations were compared to those considering the substrate dielectric, conductor losses, and the equivalent electrical circuit model of the tuning element in order to assess their effects. Within these variations, simulation results showed insertion loss better than 2 dB and return loss better than 10 dB over the passband. The proposed filters presents good performances and the simulation results are in satisfactory agreement with the experimentation ones reported elsewhere.

Keywords: defected ground structure, diode varactor, microstrip bandpass filter, multiple-mode resonator

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Authors: Amit Verma, Pardeep Kaur

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In software development organizations, Component based Software engineering (CBSE) is emerging paradigm for software development and gained wide acceptance as it often results in increase quality of software product within development time and budget. In component reusability, main challenges are the right component identification from large repositories at right time. The major objective of this work is to provide efficient algorithm for storage and effective retrieval of components using neural network and parameters based on user choice through clustering. This research paper aims to propose an algorithm that provides error free and automatic process (for retrieval of the components) while reuse of the component. In this algorithm, keywords (or components) are extracted from software document, after by applying k mean clustering algorithm. Then weights assigned to those keywords based on their frequency and after assigning weights, ANN predicts whether correct weight is assigned to keywords (or components) or not, otherwise it back propagates in to initial step (re-assign the weights). In last, store those all keywords into repositories for effective retrieval. Proposed algorithm is very effective in the error correction and detection with user base choice while choice of component for reusability for efficient retrieval is there.

Keywords: component based development, clustering, back propagation algorithm, keyword based retrieval

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Authors: Abdullah Tahir

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The omission of regular medications in surgical patients poses a significant challenge in healthcare settings and is associated with increased morbidity during hospital stays. Human factors such as high workload, poor communication, and emotional stress are known to contribute to these omissions, particularly evident in the surgical assessment unit (SAU) due to its high patient burden and long wait times. This study aimed to quantify and address the issue by implementing targeted interventions to enhance compliance in prescribing regular medications for surgical patients at Stoke Mandeville Hospital, United Kingdom. Data were collected on 14 spontaneous days between April and May 2023, and the frequency of prescription omissions was recorded using a tally chart. Subsequently, informative posters were introduced in the SAU, and presentations were given to the surgical team to emphasize the importance of compliance in this area. The interventions were assessed using a second data collection cycle, again over 14 spontaneous days in May 2023. Results demonstrated an improvement from 40% (60 out of 150) to 74% (93 out of 126) of patients having regular medications prescribed at the point of clerking. These findings highlight the efficacy of frequent prompts and awareness-raising interventions in increasing workforce compliance and addressing the issue of prescription omissions in the SAU.

Keywords: prescription omissions, quality improvement, regular medication, surgical assessment unit

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Authors: Amir AlAmeeri, Mohamed Ibrahim

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Various data points are constantly being measured in the production system, and due to the nature of the wells, these data points, such as pressure, temperature, water cut, etc.., fluctuations are constant, which requires high frequency monitoring and collection. It is a very difficult task to analyze these parameters manually using spreadsheets and email. An automated system greatly enhances efficiency, reduce errors, the need for constant emails which take up disk space, and frees up time for the operator to perform other critical tasks. Various production data is being recorded in an oil field, and this huge volume of data can be seen as irrelevant to some, especially when viewed on its own with no context. In order to fully utilize all this information, it needs to be properly collected, verified and stored in one common place and analyzed for surveillance and monitoring purposes. This paper describes how data is recorded by different parties and departments in the field, and verified numerous times as it is being loaded into a repository. Once it is loaded, a final check is done before being entered into a production monitoring system. Once all this is collected, various calculations are performed to report allocated production. Calculated production data is used to report field production automatically. It is also used to monitor well and surface facility performance. Engineers can use this for their studies and analyses to ensure field is performing as it should be, predict and forecast production, and monitor any changes in wells that could affect field performance.

Keywords: automation, oil production, Cheleken, exploration and production (E&P), Caspian Sea, allocation, forecast

Procedia PDF Downloads 151

Authors: Hamed Ahari, Behrouz Akbari Adreghani, Vadood Razavilar, Amirali Anvar, Sima Moradi, Hourieh Shalchi

Abstract:

Considering the ever increasing population and industrialization of the developmental trend of humankind's life, we are no longer able to detect the toxins produced in food products using the traditional techniques. This is due to the fact that the isolation time for food products is not cost-effective and even in most of the cases, the precision in the practical techniques like the bacterial cultivation and other techniques suffer from operator errors or the errors of the mixtures used. Hence with the advent of nanotechnology, the design of selective and smart sensors is one of the greatest industrial revelations of the quality control of food products that in few minutes time, and with a very high precision can identify the volume and toxicity of the bacteria. Methods and Materials: In this technique, based on the bacterial antibody connection to nanoparticle, a sensor was used. In this part of the research, as the basis for absorption for the recognition of bacterial toxin, medium sized silica nanoparticles of 10 nanometer in form of solid powder were utilized with Notrino brand. Then the suspension produced from agent-linked nanosilica which was connected to bacterial antibody was positioned near the samples of distilled water, which were contaminated with Staphylococcus aureus bacterial toxin with the density of 10-3, so that in case any toxin exists in the sample, a connection between toxin antigen and antibody would be formed. Finally, the light absorption related to the connection of antigen to the particle attached antibody was measured using spectrophotometry. The gene of 23S rRNA that is conserved in all Staphylococcus spp., also used as control. The accuracy of the test was monitored by using serial dilution (l0-6) of overnight cell culture of Staphylococcus spp., bacteria (OD600: 0.02 = 107 cell). It showed that the sensitivity of PCR is 10 bacteria per ml of cells within few hours. Result: The results indicate that the sensor detects up to 10-4 density. Additionally, the sensitivity of the sensors was examined after 60 days, the sensor by the 56 days had confirmatory results and started to decrease after those time periods. Conclusions: Comparing practical nano biosensory to conventional methods like that culture and biotechnology methods(such as polymerase chain reaction) is accuracy, sensitiveness and being unique. In the other way, they reduce the time from the hours to the 30 minutes.

Keywords: exotoxin, nanobiosensor, recognition, Staphylococcus aureus

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Authors: Mehrdad Kamali-Sanzighi, Maziar Kamali-Sanzighi

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The aim of this investigation is to study the phytoplankton and saprobic index at warm water fish ponds in the East of Golestan province, Gonbade Kavous city. Phytoplankton and ciliate sampling were done monthly during one season of culture. Finally, 39 genera from 7 classes of phytoplankton and 4 genera from the ciliate group were identified. Although, among different classes, Chlorophyceae, Cyanophyceae, Bacillariophyceae, Charophyceae, Chrysophyceae, Dinophyceae, and Euglenophyceae had the highest and lowest frequency percent of phytoplankton community with 23, 21, 20, 14, 11, 6 and 5 percent respectively. The results show that there are no significant differences between the saprobic index of different ponds (P > 0.05). But there are significant differences between the saprobic index value of different months and seasons during season culture (P < 0.05). Also, in current research, the saprobic index indicated the ß-mesosaprob water quality level. There was a general tends of decrease in the saprobic index value from the beginning to the end of the culture season. Parameters such as biomass increase of grower fishes, an increase of introduced chemical fertilizer and manure sedimentation, uneaten fish feed, fish fecal, and no regular exchangeable water resources are some of these changes' reasons.

Keywords: fish pond, Golestan Province, saprobi index, phytoplankton, water quality

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Authors: C. -L. Huang, J. -H. Ho

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Social media has become more and more important in our life. Many enterprises promote their services and products to fans via the social media. The positive or negative sentiment of feedbacks from fans is very important for enterprises to improve their products, services, and promotion activities. The purpose of this paper is to understand the sentiment of the fan’s responses by analyzing the responses posted by fans on Facebook. The entity and aspect of fan’s responses were analyzed based on a predefined ontology. The ontology for cell phone sentiment analysis consists of aspect categories on the top level as follows: overall, shape, hardware, brand, price, and service. Each category consists of several sub-categories. All aspects for a fan’s response were found based on the ontology, and their corresponding sentimental terms were found using lexicon-based approach. The sentimental scores for aspects of fan responses were obtained by summarizing the sentimental terms in responses. The frequency of 'like' was also weighted in the sentimental score calculation. Three famous cell phone fan pages on Facebook were selected as demonstration cases to evaluate performances of the proposed methodology. Human judgment by several domain experts was also built for performance comparison. The performances of proposed approach were as good as those of human judgment on precision, recall and F1-measure.

Keywords: opinion mining, ontology, sentiment analysis, text mining

Procedia PDF Downloads 227

Authors: Kamran Jawed, Anu Jose Mattam, Zia Fatma, Saima Wajid, Malik Z. Abdin, Syed Shams Yazdani

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Worldwide demand of natural and sustainable fuels and chemicals have encouraged researchers to develop microbial platform for synthesis of short chain fatty acids as they are useful precursors to replace petroleum-based fuels and chemicals. In this study, we evaluated the role of fatty acid synthesis and β-oxidation cycle of Escherichia coli to produce butyric acid, a 4-carbon short chain fatty acid, with the help of three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron. We found that E. coli strain transformed with gene for TesBT and grown in presence of 8 g/L glucose produced maximum butyric acid titer at 1.46 g/L, followed by that of TesBF at 0.85 g/L and TesAT at 0.12 g/L, indicating that these thioesterases were efficiently converting short chain fatty acyl-ACP intermediate of fatty acid synthesis pathway into the corresponding acid. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. Deletion of genes for fatty acyl-CoA synthetase and acyl-CoA dehydrogenase, which are involved in initiating the fatty acid degradation cycle, and overexpression of FadR, which is a dual transcriptional regulator and exerts negative control over fatty acid degradation pathway, reduced up to 30% of butyric acid titer. This observation suggested that β-oxidation pathway is working synergistically with fatty acid synthesis pathway in production of butyric acid. Moreover, accelerating the fatty acid elongation cycle by overexpressing acetyl-CoA carboxyltransferase (Acc) and 3-hydroxy-acyl-ACP dehydratase (FabZ) or by deleting FabR, the transcription suppressor of elongation, did not improve the butyric acid titer, rather favored the long chain fatty acid production. Finally, a balance between cell growth and butyric acid production was achieved with the use of phosphorous limited growth medium and 14.3 g/L butyric acid, and 17.5 g/L total free fatty acids (FFAs) titer was achieved during fed-batch cultivation. We have engineered an E. coli strain which utilizes the intermediate of both fatty acid synthesis and degradation pathway, i.e. butyryl-ACP and -CoA, to produce butyric acid from glucose. The strategy used in this study resulted in highest reported titers of butyric acid and FFAs in engineered E. coli.

Keywords: butenoic acid, butyric acid, Escherichia coli, fed-batch fermentation, short chain fatty acids, thioesterase

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Authors: David Taillis, Oussama Becissa, Julien Gabaston, Jean-Michel Merillon, Tristan Richard, Stephanie Cluzet

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Nowadays, there is a strong pressure to reduce the phytosanitary inputs of synthetic chemistry in vineyards. It is, therefore, necessary to find viable alternatives in order to protect the vine against its major diseases. For this purpose, we suggest the use of a plant extract enriched in antimicrobial compounds. Being produced from vine trunks and roots, which are co-products of wine production, the extract produced is part of a circular economy. The antimicrobial molecules present in this plant material are polyphenols and, more particularly, stilbenes, which are derived from a common base, the resveratrol unit, and that are well known vine phytoalexins. The stilbenoids were extracted from trunks and roots (30/70, w/w) by a double extraction with ethyl acetate followed by enrichment by liquid-liquid extraction. The produced extract was characterized by UHPLC-MS, then its antimicrobial activities were tested on Plasmopara viticola and Botrytis cinerea in the laboratory and/or in greenhouse and in vineyard. The major compounds were purified, and their antimicrobial activity was evaluated on B. cinerea. Moreover, after its spraying, the effect of the stilbene extract on the plant defence status was evaluated by analysis of defence gene expression. UHPLC-MS analysis revealed that the extract contains 50% stilbenes with resveratrol, ε-viniferin and r-viniferin as major compounds. The extract showed antimicrobial activities on P. viticola with IC₅₀ and IC₁₀₀ respectively of 90 and 300 mg/L in the laboratory. In addition, it inhibited 40% of downy mildew development in greenhouse. However, probably because of the sensitivity of stilbenes to the environment, such as UV degradation, no activity has been observed in vineyard towards P. viticola development. For B. cinerea, the extract IC50 was 123 mg/L, with resveratrol and ε-viniferin being the most active stilbenes (IC₅₀ of 88 and 142 mg/L, respectively). The analysis of the expression of defence genes revealed that the extract can induce the expression of some defence genes 24, 48, and 72 hours after treatment, meaning that the extract has a defence-stimulating effect at least for the first three days after treatment. In conclusion, we produced a plant extract enriched in stilbenes with antimicrobial properties against two major grapevine pathogenic agents P. viticola and B. cinerea. In addition, we showed that this extract displayed eliciting activity of plant defences. This extract can therefore represent, after formulation development, a viable eco-friendly alternative for vineyard protection. Subsequently, the effect of the stilbenoid extract on primary metabolism will be evaluated by quantitative NMR.

Keywords: antimicrobial, bioprotection, grapevine, Plasmopara viticola, stilbene

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Authors: Hatice Karakoyun, Mustafa Akdag

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This study has been made to examine the attitudes of pre-school teachers towards values education. The study has been made as a general scanning model. The study’s working group contains 108 pre-school teachers who worked in Diyarbakır, Turkey. In this study Values Education Attitude Scale (VEAS), which developed by Yaşaroğlu (2014), was used. In order to analyze the data for sociodemographic structure, percentage and frequency values were examined. The Kolmogorov-Smirnov method was used in determination of the normal distribution of data. During analyzing the data, KolmogorovSimirnov test and the normal curved histograms were examined to determine which statistical analyzes would be applied on the scale and it was found that the distribution was not normal. Thus, the Mann Whitney U analysis technique which is one of the nonparametric statistical analysis techniques were used to test the difference of the scores obtained from the scale in terms of independent variables. According to the analyses, it seems that pre-school teachers’ attitudes toward values education are positive. According to the scale with the highest average, it points out that pre-school teachers think that values education is very important for students’ and children’s future. The variables included in the scale (gender, seniority, age group, education, school type, school place) seem to have no effect on the pre-school teachers’ attitude grades which joined to the study.

Keywords: attitude scale, pedagogy, pre-school teacher, values education

Procedia PDF Downloads 238

Authors: Farhan Beg

Abstract:

A space vector based pulse width modulation control technique for the three-phase PWM converter is proposed in this paper. The proposed control scheme is based on a synchronous reference frame model. High performance and efficiency is obtained with regards to the DC bus voltage and the power factor considerations of the PWM rectifier thus leading to low losses. MATLAB/SIMULINK are used as a platform for the simulations and a SIMULINK model is presented in the paper. The results show that the proposed model demonstrates better performance and properties compared to the traditional SPWM method and the method improves the dynamic performance of the closed loop drastically. For the space vector based pulse width modulation, sine signal is the reference waveform and triangle waveform is the carrier waveform. When the value of sine signal is larger than triangle signal, the pulse will start producing to high; and then when the triangular signals higher than sine signal, the pulse will come to low. SPWM output will change by changing the value of the modulation index and frequency used in this system to produce more pulse width. When more pulse width is produced, the output voltage will have lower harmonics contents and the resolution will increase.

Keywords: power factor, SVPWM, PWM rectifier, SPWM

Procedia PDF Downloads 326

Authors: Wenjuan Du, Jingtian Bi, Tong Wang, Haifeng Wang

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Grid connection of a large-scale wind farm affects power system small-signal angular stability in two aspects. Firstly, connection of the wind farm brings about the change of load flow and configuration of a power system. Secondly, the dynamic interaction is introduced by the wind farm with the synchronous generators (SGs) in the power system. This paper proposes a method to assess the two aspects of the effect of the wind farm on power system small-signal angular stability. The effect of the change of load flow/system configuration brought about by the wind farm can be examined separately by displacing wind farms with constant power sources, then the effect of the dynamic interaction of the wind farm with the SGs can be also computed individually. Thus, a clearer picture and better understanding on the power system small-signal angular stability as affected by grid connection of the large-scale wind farm are provided. In the paper, an example power system with grid connection of a wind farm is presented to demonstrate the proposed approach.

Keywords: power system small-signal angular stability, power system low-frequency oscillations, electromechanical oscillation modes, wind farms, double fed induction generator (DFIG)

Procedia PDF Downloads 475

Authors: Khaliun Nyambayar, Nomindari Azzaya, Batkhuyag Purevjav

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Pharmacovigilance was officially introduced in Mongolia in 2003, in accordance with the Health Minister Order 183 for the registry of adverse drug reactions (ADR), approved in 2006 and was reviewed in 2010. This study was designed to evaluate the incidence and common types of adverse drug reactions among hospitalized children, the frequency of adverse drug reaction reported by health care providers, and the follow-up processes resulting from adverse drug reactions. A retrospective study of paediatric patients who experienced an adverse drug reaction from 2015 to 2019, extracted from the “yellow” card at the State Research Center for Maternal and Child Health, (city). A total of 417 adverse drug reactions were reported with an overall incidence was 80 (21.5%). Adverse reactions resulting from the use of antibiotics (particularly gentamycin, cephalosporins, and vancomycin) were usually mild. ADR’s were reported by physicians and nurses (93.8%), pharmacists (6.25%). Although documentation of physician notification occurred for 93% of adverse drug reactions, only 29% of cases were documented in the patient's medical chart, 13% included follow-up education for individuals involved, and 10% were updated in the allergy profile of the hospital computer system. Measures to improve the detection and reporting of adverse drug reactions by all health care professionals should be improved, to enhance our understanding of the nature and impact of these reactions in children.

Keywords: adverse drug reaction, pediatric, yellow card, Mongolia

Procedia PDF Downloads 105