Search results for: A/H1N1 influenza antigen

Authors: Young Kwon Yang, In Sung Kang, Jung Ha Hwang, Jin Chul Park

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The present study is a foundational study for performance improvements on isolation wards to prevent proliferation of secondary infection of infectious diseases such as SARS, H1N1, and MERS inside hospitals. Accordingly, the present study conducted an analysis of the effect of sealing mechanisms and filling of openings on ensuring air tightness performance in isolation wards as well as simulation on air currents in improved isolation wards. The study method is as follows. First, previous studies on aerial infection type and mechanism were reviewed, and the review results were utilized as basic data of analysis on simulation of air current. Second, national and international legislations and regulations in relation to isolation wards as well as case studies on developed nations were investigated in order to identify the problems in isolation wards in Korea and improvement plans. Third, construction and facility plans were compared and analyzed between general and isolation wards focusing on large general hospitals in Korea, thereby conducting comparison and analysis on the performance and effects of air-tightness of general and isolation wards through CFD simulations. The study results showed that isolation wards had better air-tightness performance than that of general wards.

Keywords: AII Room, air-borne infection, CFD, computational fluid dynamics.

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Authors: Majid Forghani, Michael Khachay

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In genetics, the impact of neighboring amino acids on a target site is referred as the nearest-neighbor effect or simply neighbor effect. In this paper, a new method called wavelet particle decomposition representing the one-dimensional neighbor effect using wavelet packet decomposition is proposed. The main idea lies in known dependence of wavelet packet sub-bands on location and order of neighboring samples. The method decomposes the value of a signal sample into small values called particles that represent a part of the neighbor effect information. The results have shown that the information obtained from the particle decomposition can be used to create better model variables or features. As an example, the approach has been applied to improve the correlation of test and reference sequence distance with titer in the hemagglutination inhibition assay.

Keywords: Antigenic variants, neighbor effect, wavelet packet, wavelet particle decomposition.

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

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Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.

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Authors: Hany Mahgoub

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This paper presents a system for discovering association rules from collections of unstructured documents called EART (Extract Association Rules from Text). The EART system treats texts only not images or figures. EART discovers association rules amongst keywords labeling the collection of textual documents. The main characteristic of EART is that the system integrates XML technology (to transform unstructured documents into structured documents) with Information Retrieval scheme (TF-IDF) and Data Mining technique for association rules extraction. EART depends on word feature to extract association rules. It consists of four phases: structure phase, index phase, text mining phase and visualization phase. Our work depends on the analysis of the keywords in the extracted association rules through the co-occurrence of the keywords in one sentence in the original text and the existing of the keywords in one sentence without co-occurrence. Experiments applied on a collection of scientific documents selected from MEDLINE that are related to the outbreak of H5N1 avian influenza virus.

Keywords: Association rules, information retrieval, knowledgediscovery in text, text mining.

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Authors: Tomohiro Hachino, Kengo Nagatomo, Hitoshi Takata

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This paper deals with an on-line identification method of continuous-time Hammerstein systems by using the radial basis function (RBF) networks and immune algorithm (IA). An unknown nonlinear static part to be estimated is approximately represented by the RBF network. The IA is efficiently combined with the recursive least-squares (RLS) method. The objective function for the identification is regarded as the antigen. The candidates of the RBF parameters such as the centers and widths are coded into binary bit strings as the antibodies and searched by the IA. On the other hand, the candidates of both the weighting parameters of the RBF network and the system parameters of the linear dynamic part are updated by the RLS method. Simulation results are shown to illustrate the proposed method.

Keywords: Continuous-time System, Hammerstein System, OnlineIdentification, Immune Algorithm, RBF network.

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Authors: Yuhong Lu

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Graves’ Disease (GD), an autoimmune health condition caused by the over reactiveness of the thyroid, affects about 1 in 200 people worldwide. GD is not caused by one specific single nucleotide polymorphism (SNP) or gene mutation, but rather determined by multiple factors, each differing from each other. Malfunction of the genes in Human Leukocyte Antigen (HLA) family tend to play a major role in autoimmune diseases, but other genes, such as LOC101929163, have functions that still remain ambiguous. Currently, little studies were done to study GD, resulting in inconclusive results. This study serves not only to introduce background knowledge about GD, but also to organize and pinpoint the major SNPs and genes that are potentially related to the occurrence of GD in humans. Collected from multiple sources from genome-wide association studies (GWAS) Central, the potential SNPs related to the causes of GD are included in this study. This study has located the genes that are related to those SNPs and closely examines a selected sample. Using the data from this study, scientists will then be able to focus on the most expressed genes in GD patients and develop a treatment for GD.

Keywords: CTLA4, Graves’ Disease, HLA, single nucleotide polymorphism, SNP.

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Authors: Uun Yanuhar

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The purpose of research was to know the role of immunogenic protein of 49 kDa from V.alginolyticus which capable to initiate molecule expression of MHC Class II in receptor of Cromileptes altivelis. The method used was in vivo experimental research through testing of immunogenic protein 49 kDa from V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams) using 3 times booster by injecting an immunogenic protein in a intramuscular manner. Response of expressed MHC molecule was shown using immunocytochemistry method and SEM. Results indicated that adhesin V.alginolyticus 49 kDa which have immunogenic character could trigger expression of MHC class II on receptor of grouper and has been proven by staining using immunocytochemistry and SEM with labeling using antibody anti MHC (anti mouse). This visible expression based on binding between epitopes antigen and antibody anti MHC in the receptor. Using immunocytochemistry, intracellular response of MHC to in vivo induction of immunogenic adhesin from V.alginolyticus was shown.

Keywords: C.altivelis, immunogenic, MHC, V.alginolyticus.

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Authors: N. Hussain, G. Jaffery, A.N. Sabri, S. Hasnain

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The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.

Keywords: American College of Rheumatology criteria, autoimmune disease, Cytotoxic T Lymphocyte Antigen-4, Polymerase Chain Reaction, Systemic Lupus Erythematosus

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Authors: Natasha Hussain, Maleeha Aslam, Robina Farooq

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Hepatitis B and hepatitis C are among the most significant hepatic infections all around the world that may lead to hepatocellular carcinoma. This study is first time performed at the blood transfussion centre of Omar hospital, Lahore. It aims to determine the sero-prevalence of these diseases by screening the apparently healthy blood donors who might be the carriers of HBV or HCV and pose a high risk in the transmission. It also aims the comparison between the sensitivity of two diagnostic tests; chromatographic immunoassay – one step test device and Enzyme Linked Immuno Sorbant Assay (ELISA). Blood serum of 855 apparently healthy blood donors was screened for Hepatitis B surface antigen (HBsAg) and for anti HCV antibodies. SPSS version 12.0 and X2 (Chi-square) test were used for statistical analysis. The seroprevalence of HCV was 8.07% by the device method and by ELISA 9.12% and that of HBV was 5.6% by the device and 6.43% by ELISA. The unavailability of vaccination against HCV makes it more prevalent. Comparing the two diagnostic methods, ELISA proved to be more sensitive.

Keywords: ELISA, Sensitivity comparison of diagnostic tests, seroprevalence of Hepatitis B and C

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Authors: Permphan Dharmasaroja

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Acute disseminated encephalomyelitis (ADEM) has been reported to develop after a hymenoptera sting, but its pathogenesis is not known in detail. Myelin basic protein (MBP)- specific T cells have been detected in the blood of patients with ADEM, and a proportion of these patients develop multiple sclerosis (MS). In an attempt to understand the mechanisms underlying ADEM, molecular mimicry between hymenoptera venom peptides and the human immunodominant MBP peptide was scrutinized, based on the sequence and structural similarities, whether it was the root of the disease. The results suggest that the three wasp venom peptides have low sequence homology with the human immunodominant MBP residues 85-99. Structural similarity analysis among the three venom peptides and the MS-related HLA-DR2b (DRA, DRB1*1501)-associated immunodominant MHC binding/TCR contact residues 88-93, VVHFFK showed that hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and antigen 5 residues 109-114 showed a high degree of similarity 83.3%, 100%, and 83.3% respectively. In conclusion, some wasp venom peptides, particularly phospholipase A1, may potentially act as the molecular motifs of the human 3HLA-DR2b-associated immunodominant MBP88-93, and possibly present a mechanism for induction of wasp sting-associated ADEM.

Keywords: central nervous system, Hymenoptera, myelin basicprotein, molecular mimicry.

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Authors: Asma Meziti, Hicham Meziti, Kaouthar Boudiaf, Benboubetra Mustapha, Hemama Bouriche.

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Nigella sativa L. is an aromatic plant belonging to the family Ranunculaceae. It has been used traditionally, especially in the middle East and India, for the treatment of asthma, cough, bronchitis, headache, rheumatism, fever, influenza and eczema. Several biological activities have been reported in Nigella sativa seeds, including antioxidant. In this context we tried to estimate the antioxidant activity of various extracts prepared from Nigella sativa seeds, methanolic extract (ME), chloroformic extract (CE), hexanic extract (HE : fixed oil), ethyl acetate extract (EAE) water extract (WE). The Folin-Ciocalteu assay showed that CE and EAE contained high level of phenolic compounds 81.31 and 72.43μg GAE/mg of extract respectively. Similarly, the CE and EAE exhibited the highest DPPH radical scavenging activity, with IC50 values of 106.56μg/ml and 121.62μg/ml respectively. In addition, CE and HE showed the most scavenging activity against superoxide radical generated in the PMS-NADH-NBT system with respective IC50 values of 361.86 μg/ml and 371.80 μg/ml, which is comparable to the activity of the standard antioxidant BHT (344.59 μg/ml). Ferrous ion chelating capacity assay showed that WE, EAE and ME are the most active with 40.57, 39.70 and 22.02 mg EDTA-E/g of extract. The inhibition of linoleic acid/ß-carotene coupled oxidation was estimated by ßcarotene bleaching assay, this showed a highest relative antioxidant activity with CE and EAE (69.82% of inhibition). The antioxidant activities of the methanolic extract and the fixed oil are confirmed by an in vivo assay in mice, the daily oral administration of methanolic extract (500 and 800 mg/kg/day) and fixed oil (2 and 4 ml/kg/day) during 21 days, resulted in a significant enhancement of the blood total antioxidant capacity (measured by KRL test) and the plasmatic antioxidant capacity towards DPPH radical.

Keywords: Antioxidant Capacity, Chelating, Phenolic Compounds, Nigella Sativa, Scavenger

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Authors: Abu Salim Mustafa

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Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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Authors: Amean A. Yasir, Zainab Kh. A. Al-Mahdi Al-Amean

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In both developed and developing countries, obesity among women is increasing, but in different patterns and at very different speeds. It may have a negative effect on health, leading to reduced life expectancy and/or increased health problems. This research studied the age distribution among obese women, the types of overweight and obesity, and the extent of the problem of overweight/obesity and the obesity etiological factors among women in Hillah city in central Iraq. A total of 322 overweight and obese women were included in the study, those women were randomly selected. The Body Mass Index was used as indicator for overweight/ obesity. The incidence of overweight/obesity among age groups were estimated, the etiology factors included genetic, environmental, genetic/environmental and endocrine disease. The overweight and obese women were screened for incidence of infection and/or diseases. The study found that the prevalence of 322 overweight and obese women in Hillah city in central Iraq was 19.25% and 80.78%, respectively. The obese women types were recorded based on BMI and WHO classification as class-1 obesity (29.81%), class-2 obesity (24.22%) and class-3 obesity (26.70%), the result was discrepancy non-significant, P value < 0.05. The incidence of overweight in women was high among those aged 20-29 years (90.32%), 6.45% aged 30-39 years old and 3.22% among ≥ 60 years old, while the incidence of obesity was 20.38% for those in the age group 20-29 years, 17.30% were 30-39 years, 23.84% were 40-49 years, 16.92% were 50-59 years group and 21.53% were ≥ 60 years age group. These results confirm that the age can be considered as a significant factor for obesity types (P value < 0.0001). The result also showed that the both genetic factors and environmental factors were responsible for incidents of overweight or obesity (84.78%) p value < 0.0001. The results also recorded cases of different repeated infections (skin infection, recurrent UTI and influenza), cancer, gallstones, high blood pressure, type 2 diabetes, and infertility. Weight stigma and bias generally refers to negative attitudes; Obesity can affect quality of life, and the results of this study recorded depression among overweight or obese women. This can lead to sexual problems, shame and guilt, social isolation and reduced work performance. Overweight and Obesity are real problems among women of all age groups and is associated with the risk of diseases and infection and negatively affects quality of life. This result warrants further studies into the prevalence of obesity among women in Hillah City in central Iraq and the immune response of obese women.

Keywords: Obesity, overweight, Iraq, body mass index.

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Authors: Moustafa Osman Mohammed

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This paper introduces topological order in descried social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. Topological order is important in describing the physical systems for exploiting optical systems and improving photonic devices. The stats of topologically order have some interesting properties of topological degeneracy and fractional statistics that reveal the entanglement origin of topological order, etc. Topological ideas in photonics form exciting developments in solid-state materials, that being; insulating in the bulk, conducting electricity on their surface without dissipation or back-scattering, even in the presence of large impurities. A specific type of autopoiesis system is interrelated to the main categories amongst existing groups of the ecological phenomena interaction social and medical sciences. The hypothesis, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for exchange photon energy with molecules without changes in topology (i.e., chemical transformation into products do not propagate any changes or variation in the network topology of physical configuration). The engineering topology of a biosensor is based on the excitation boundary of surface electromagnetic waves in photonic band gap multilayer films. The device operation is similar to surface Plasmonic biosensors in which a photonic band gap film replaces metal film as the medium when surface electromagnetic waves are excited. The use of photonic band gap film offers sharper surface wave resonance leading to the potential of greatly enhanced sensitivity. So, the properties of the photonic band gap material are engineered to operate a sensor at any wavelength and conduct a surface wave resonance that ranges up to 470 nm. The wavelength is not generally accessible with surface Plasmon sensing. Lastly, the photonic band gap films have robust mechanical functions that offer new substrates for surface chemistry to understand the molecular design structure, and create sensing chips surface with different concentrations of DNA sequences in the solution to observe and track the surface mode resonance under the influences of processes that take place in the spectroscopic environment. These processes led to the development of several advanced analytical technologies, which are automated, real-time, reliable, reproducible and cost-effective. This results in faster and more accurate monitoring and detection of biomolecules on refractive index sensing, antibody–antigen reactions with a DNA or protein binding. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other in order to form unique spatial structure and dynamics of biological molecules for providing the environment mutual contribution in investigation of changes due the pathogenic archival architecture of cell clusters.

Keywords: autopoiesis, engineering topology, photonic system molecular structure, biosensor

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