Search results for: gene concordance factor confidence

Authors: Fadzil Ahmad, Noor Ashidi Mat Isa

Abstract:

This study introduces an improved genetic algorithm procedure that focuses search around near optimal solution corresponded to a group of elite chromosome. This is achieved through a novel crossover technique known as Segmented Multi Chromosome Crossover. It preserves the highly important information contained in a gene segment of elite chromosome and allows an offspring to carry information from gene segment of multiple chromosomes. In this way the algorithm has better possibility to effectively explore the solution space. The improved GA is applied for the automatic and simultaneous parameter optimization and feature selection of artificial neural network in pattern recognition of medical problem, the cancer and diabetes disease. The experimental result shows that the average classification accuracy of the cancer and diabetes dataset has improved by 0.1% and 0.3% respectively using the new algorithm.

Keywords: genetic algorithm, artificial neural network, pattern clasification, classification accuracy

Procedia PDF Downloads 474

Authors: Sheila M. Wicks, Gail Mahady, Udesh Patel, Joanna Michel, Armando Caceres

Abstract:

Introduction: The genus piperaceae contains approximately 1000 species of herbs scrubs small trees and hanging vines distributed in both hemispheres. During our ethno medical work in Guatemala of the 27 plant families documented for us e by the Qeqchi Maya for reproductive disorders the most prominent were the Piperaceae (15%) and Menispermiaceae. Our Previous work showed that extracts from form Piper and Cissampelos species bound to both and progesterone and the estrogen receptors. In this work active extracts from Piper aeruginosibaccum Trelease, P auritum, P tuerckheimii and Cissampels tropaeolifolia were tested in functionalized cell based assays including a SEAP reporter gene and by qPCR of ER-responsive gene expression in MCF-7cells. In the reporter gene assay P aeruginosibaccum was estrogenic and enhanced E2 EFFECTS IN MCF-7 CELLS. P. tuerckheimi was not estrogenic alone but significantly enhanced the effects of E2 on SEAP reporter gene expression. Both altered mRNA expression of E2 responsive genes in MCF-7. Methods: this is collaborative project between University of Illinois at Chicago and University of San Carlos Guatemala City. 144 spices of plants were collected in Guatemala of which 57 used to treat a variety of women's reproductive health. The Genus Piperaraceae contains approximately 1000 species of herbs scrubs and small trees. Active extracts of the plants were tested in functionalized in cell-based bioassays including SEAP reporter genes. Results demonstrated altered mRNA expression of E2 responsive genes in MC-7 cells plants were collected in Guatemala of which 57 used. Conclusion of the 5 plants tested all were shown to contain components of binding to estrogenic receptor to a greater or lesser degree. These effects support the use of QEqchi Maya women in Guatemala for reproductive.

Keywords: reporter genes, MC7, guatemala piperaceae, reproductive health

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Authors: Nadia Naseem, Farwa Batool, Nasir Mehmood, AbdulHannan Nagi

Abstract:

Background: The incidence and mortality of breast cancer vary significantly in geographically distinct populations. In Pakistan, breast cancer has shown an increase in incidence in young females and is characterized by more aggressive behavior. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. This study investigated the TP53 mutations in molecular subtypes of both nodes negative and positive breast cancer in young Pakistani patients. Material and Methods: p53, Estrogen Receptor (ER), Progesterone Receptor (PR), Her-2 neu and Ki 67 expressions were analyzed immunohistochemically in a series of 75 node negative (A) and 75 node positive (B) young (aged: 19-40 years) breast cancer patients diagnosed between 2014 to 2017 at two leading hospitals of Punjab, Pakistan. Tumor tissue specimens and peripheral blood samples were examined for TP53 mutations by direct sequencing of the gene (exons 4-9). The relation of TP53 mutations to these markers and clinicopathological data was investigated. Results: Mean age of the patients was 32.4 + 9.1 SD. Invasive breast carcinoma was the most frequent histological variant (A=92%, B=94.6%). Grade 3 carcinoma was the commonest grade (A=72%, B=81.3%). Triple negative cases (ER-, PR-, Her-2) formed most of the molecular subtypes (A=44%, B=50.6%). A total of 17.2% (A: 6.6%, B: 10.6%) patients showed TP53 mutations. Mutations were significantly more frequent in triple negative cases (A: 74.8%, B: 62.2%) compared to HER2-positive patients (P < 0.0001). In the multivariate analysis of the whole patient group, the independent prognosticator were triple negative cases (P=0.021), TP53 overexpression by IHC (P=0.001) and advanced-stage disease (P=0.007). No statistically significant correlation between TP53 mutations and clinicopathological parameters was found (P < 0.05). Conclusions: It is concluded that TP53 mutations are infrequently present in breast carcinoma of young Pakistani population and there was no significant correlation between p53 mutation and early onset disease. Immunohistochemically detected TP53 expression in our resource-constrained to set up can be beneficial in predicting mutations at the younger age in our population.

Keywords: immunohistochemistry (IHC), invasive breast carcinoma (IBC), Pakistan, TP53

Procedia PDF Downloads 158

Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia(CIN)and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, p53, miR-146a, rs2910164, polymorphism

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Authors: Balthazar Temu, Zhao Yan, Bogdan-Petrin Ratiu, Sang Soon Oh, Qiang Li

Abstract:

Nanowire based Photonic Crystal Surface Emitting Lasers (PCSELs) reported in the literature have been designed using a triangular, square or honeycomb patterns. The triangular and square pattern PCSELs have limited degrees of freedom in tuning the design parameters which hinders the ability to design high quality factor (Q-factor) devices. Nanowire based PCSELs designed using triangular and square patterns have been reported with the lasing thresholds of 130 kW/〖cm〗^2 and 7 kW/〖cm〗^2 respectively. On the other hand the honeycomb pattern gives more degrees of freedom in tuning the design parameters, which can allow one to design high Q-factor devices. A deformed honeycomb pattern device was reported with lasing threshold of 6.25 W/〖cm〗^2 corresponding to a simulated Q-factor of 5.84X〖10〗^5.Despite this achievement, the design principles which can lead to realization of even higher Q-factor honeycomb pattern PCSELs have not yet been investigated. In this work we show that through deforming the honeycomb pattern and tuning the heigh and lattice constants of the nanowires, it is possible to achieve even higher Q-factor devices. Considering three different band edge modes, we investigate how the resonance wavelength changes as the device is deformed, which is useful in designing high Q-factor devices in different wavelength bands. We eventually establish the design and simulation of honeycomb PCSELs operating around the wavelength of 960nm , in the O and the C band with Q-factors up to 7X〖10〗^7. We also investigate the Q-factors of undeformed device, and establish that the mode at the band edge close to 960nm can attain highest Q-factor of all the modes when the device is undeformed and the Q-factor degrades as the device is deformed. This work is a stepping stone towards the fabrication of very high Q-factor, nanowire based honey comb PCSELs, which are expected to have very low lasing threshold.

Keywords: designing nanowire PCSEL, designing PCSEL on silicon substrates, low threshold nanowire laser, simulation of photonic crystal lasers

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, sport performance, Slovakia

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Authors: Emily Moore, Dora Amos, Tracy Ellimah, Natasha Parrott

Abstract:

Postoperative haematoma is a well-recognised complication of thyroid surgery with an incidence of 1-5%. Haematoma formation causes progressive airway obstruction, necessitating emergency bedside haematoma evacuation in up to ¼ of patients. ENT UK, BAETS and DAS have developed consensus guidelines to improve perioperative care, recommending that all healthcare staff interacting with patients undergoing thyroid surgery should be trained in managing post-thyroidectomy haematoma. The aim was to assess the effectiveness of a hybrid simulation model in improving clinician’s confidence in dealing with this surgical emergency. A hybrid simulation was designed, consisting of a standardised patient wearing a part-task trainer to mimic a post-thyroidectomy haematoma in a real patient. The part-task trainer was an adapted C-spine collar with layers of silicone representing the skin and strap muscles and thickened jelly representing the haematoma. Both the skin and strap muscle layers had to be opened in order to evacuate the haematoma. Boxes have been implemented into the appropriate post operative areas (recovery and surgical wards), which contain a printed algorithm designed to assist in remembering a sequence of steps for haematoma evacuation using the ‘SCOOP’ method (skin exposure, cut sutures, open skin, open muscles, pack wound) along with all the necessary equipment to open the front of the neck. Small-group teaching sessions were delivered by ENT and anaesthetic trainees to members of the multidisciplinary team normally involved in perioperative patient care, which included ENT surgeons, anaesthetists, recovery nurses, HCAs and ODPs. The DESATS acronym of signs and symptoms to recognise (difficulty swallowing, EWS score, swelling, anxiety, tachycardia, stridor) was highlighted. Then participants took part in the hybrid simulation in order to practice this ‘SCOOP’ method of haematoma evacuation. Participants were surveyed using a Likert scale to assess their level of confidence pre- and post teaching session. 30 clinicians took part. Confidence (agreed/strongly agreed) in recognition of post thyroidectomy haematoma improved from 58.6% to 96.5%. Confidence in management improved from 27.5% to 89.7%. All participants successfully decompressed the haematoma. All participants agreed/strongly agreed, that the sessions were useful for their learning. Multidisciplinary team simulation teaching is effective at significantly improving confidence in both the recognition and management of postoperative haematoma. Hybrid simulation sessions are useful and should be incorporated into training for clinicians.

Keywords: thyroid surgery, haematoma, teaching, hybrid simulation

Procedia PDF Downloads 96

Authors: Hossein Rassi, Marjan Moradi fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human Papillomavirus (HPV) infection is the leading risk factor for Cervical Intraepithelial Neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33, and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, miR-146a rs2910164 polymorphism, p53 polymorphism, intraepithelial, neoplasia, HPV

Procedia PDF Downloads 398

Authors: D. P. Rajesh, H. N. Anjanayappa, P. Nayana, S. Benakappa

Abstract:

The present study deals with length-weight relationship of Atropus atropos for which no information is available on this aspect from Mangalore coast. Therefore the present investigation was undertaken. Fish samples were collected from fish landing center (Mangalore) and fish market. The regression co-efficient of male was found to be lower than female. From this observation it may be opined that female gained more weight with increase in length compared to male. Data on seasonal variation in condition factor (Kn) showed that Kn values were more or less similar in both the sexes, indicating almost identical metabolic activity. Gonadal development and high feeding intensity are the factors which influenced the condition factor. The seasonal fluctuations in the relative condition factor of both the sexes could be attributed to the sexual cycle, food intake and environmental factors. From the present study, it can be inferred that the variation in the condition of Atropus atropos was due to feeding activity and gonadal maturity.

Keywords: Atropus atropos, length-weight relationship, Mangalore coast, relative condition factor, Kn

Procedia PDF Downloads 344

Authors: Ha T. T. Ly, Truc B. Truc, Hai N. Truong, Mai P. T. Nguyen, Ngoc D. Ngo, Khanh V. Tran, Hai T. Le

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Beta thalassemia is one of the most common inherited blood disorders, which is characterized by decreased or absent in beta globin expression. Patients with Beta thalassemia whose anemia is not so severe as to necessitate transfusions are said to have thalassemia intermedia. Objective: The goal of this study is prenatal diagnosis for pregnancy woman with Beta thalassemia intermedia and her husband with Beta thalassemia carrier at high risk of Beta thalassemia major in Northern of Vietnam. Material and method: The family has a 6 years-old compound heterozygous thalassemia major for CD71/72(+A) and Hbb:c. -78A>G/nt-28(A>G) male child. The father was heterozygous for CD71/72(+A) mutation which is Beta plus type and the mother was compound heterozygosity of two different variants, namely, Hbb: c. -78A>G/nt-28(A>G) and CD26(A-G) HbE. Prenatal Beta thalassemia mutation detection in fetal DNA was carried out using multiplex Amplification-refractory mutation system ARMS-PCR and confirmed by direct Sanger-sequencing Hbb gene. Prenatal diagnoses were perfomed by amniotic fluid sampling from pregnant woman in the 16-18th week of pregnancy after the genotypes of parents of the probands were identified. Result: When amniotic fluid sample was analyzed for Beta globin gene (Hbb), we found that the genotype is heterozygous for CD71/72(+A) and CD26(A-G) HbE. This genotype is different from the 1st child of this family. Conclusion: Prenatal diagnosis helps the parents to know the genotype and the thalassemia status of the fetus, so they can have early decision on their pregnancy. Genetic diagnosis provided a useful method in diagnosis for familial members in pedigree, genetic counseling and prenatal diagnosis.

Keywords: beta thalassemia intermedia, Hbb gene, pedigree, prenatal diagnosis

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

Abstract:

Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Shubhita Mathur, Ritika Kar Bahal, Priyanka Chauhan, Anil K. Tyagi

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Mycobacterium tuberculosis, the causative agent of human tuberculosis, is a major cause of mortality. Bacillus Calmette-Guérin (BCG), the only licensed vaccine available for protection against tuberculosis confers highly variable protection ranging from 0%-80%. Thus, novel vaccine strains need to be evaluated for their potential as a vaccine against tuberculosis. We had previously constructed a triple gene mutant of M. tuberculosis (MtbΔmms), having deletions in genes encoding for phosphatases mptpA, mptpB, and sapM that are involved in host-pathogen interaction. Though vaccination with Mtb∆mms strain induced protection in the lungs of guinea pigs, the mutant strain was not able to control the hematogenous spread of the challenge strain to the spleens. Additionally, inoculation with Mtb∆mms resulted in some pathological damage to the spleens in the early phase of infection. In order to overcome the pathology caused by MtbΔmms in the spleens of guinea pigs and also to control the dissemination of the challenge strain, MtbΔmms was genetically modified by disrupting bioA gene to generate MtbΔmmsb strain. Further, in vivo attenuation of MtbΔmmsb was evaluated, and its protective efficacy was assessed against virulent M. tuberculosis challenge in guinea pigs. Our study demonstrates that Mtb∆mmsb mutant was highly attenuated for growth and virulence in guinea pigs. Vaccination with Mtb∆mmsb mutant generated significant protection in comparison to sham-immunized animals at 4 and 12 weeks post-infection in lungs and spleens of the infected animals. Our findings provide evidence that deletion of genes involved in signal transduction and biotin biosynthesis severely attenuates the pathogen and the single immunization with the auxotroph was able to provide significant protection as compared to sham-immunized animals. The protection imparted by Mtb∆mmsb fell short in comparison to the protection observed in BCG-immunized animals. This study nevertheless indicates the importance of attenuated multiple gene deletion mutants of M. tuberculosis in generating protection against tuberculosis.

Keywords: Mycobacterium tuberculosis, BCG, MtbΔmmsb, bioA, guinea pigs

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Authors: Fiston Masudi Tambwe, Lwanga Charles, Arfang Badji, Unzimai Innocent

Abstract:

The development of maize varieties combining Provitamin A (PVA), high yield, and Striga resistance is an effective and affordable strategy to contribute to food security in sub-Saharan Africa, where maize is a staple food crop. There has been limited research on introgressing PVA genes into Striga-resistant maize genotypes. The objectives of this study were to: i) determine the mode of gene action controlling PVA carotenoid accumulation in Striga-resistant maize, ii) identify Striga-resistant maize hybrids with high PVA content and stable yield, and iii) validate the presence of PVA functional markers in offspring. Six elite, Striga-resistant inbred females were crossed with six high-PVA inbred males in a North Carolina Design II and their offspring were evaluated in four environments, following a 5x8 alpha lattice design with four hybrid checks. Results revealed that both additive and non-additive gene action control carotenoid accumulation in the present study, with a predominance of non-additive gene effects for PVA. Hybrids STR1004xCLHP0352 and STR1004xCLHP0046 - identified as Striga-resistant because they supported fewer Striga plants – were the highest-yielding genotypes with a moderate PVA concentration of 5.48 and 5.77 µg/g, respectively. However, those two hybrids were not stable in terms of yield across all environments. Hybrid STR1007xCLHP0046, however, supported fewer Striga plants, had a yield of 4.52 T/ha, a PVA concentration of 4.52 µg/g, and was also stable. Gel-based marker systems of CrtRB1 and LCYE were used to screen the hybrids and favorable alleles of CrtRB1 primers were detected in 20 hybrids, confirming good levels of PVA carotenoids. Hybrids with favorable alleles of LCYE had the highest concentration of non-PVA carotenoids. These findings will contribute to the development of high-yielding PVA-rich maize varieties in Uganda.

Keywords: gene action, stability, striga resistance, provitamin A markers, beta-carotene hydroxylase 1, CrtRB1, beta-carotene, beta-cryptoxanthin, lycopene epsilon cyclase, LCYE

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Authors: L. M. Al-Harbi, A. M. Shokry, J. S. M. Sabir, A. Chaudhary, J. Manikandan, K. S. Saini

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Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations.

Keywords: breast cancer, molecular biology, ecology, environment

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Authors: Sameer Jung Karki, Gokhan Saygili

Abstract:

The allowable bearing capacity of foundation systems is determined by applying a factor of safety to the ultimate bearing capacity. Conventional ultimate bearing capacity calculations routines are based on deterministic input parameters where the nonuniformity and inhomogeneity of soil and site properties are not accounted for. Hence, the laws of mathematics like probability calculus and statistical analysis cannot be directly applied to foundation engineering. It’s assumed that the Factor of Safety, typically as high as 3.0, incorporates the uncertainty of the input parameters. This factor of safety is estimated based on subjective judgement rather than objective facts. It is an ambiguous term. Hence, a probabilistic analysis of the bearing capacity of an isolated footing on a clayey soil is carried out by using the Monte Carlo Simulation method. This simulated model was compared with the traditional discrete model. It was found out that the bearing capacity of soil was found higher for the simulated model compared with the discrete model. This was verified by doing the sensitivity analysis. As the number of simulations was increased, there was a significant % increase of the bearing capacity compared with discrete bearing capacity. The bearing capacity values obtained by simulation was found to follow a normal distribution. While using the traditional value of Factor of safety 3, the allowable bearing capacity had lower probability (0.03717) of occurring in the field compared to a higher probability (0.15866), while using the simulation derived factor of safety of 1.5. This means the traditional factor of safety is giving us bearing capacity that is less likely occurring/available in the field. This shows the subjective nature of factor of safety, and hence probability method is suggested to address the variability of the input parameters in bearing capacity equations.

Keywords: bearing capacity, factor of safety, isolated footing, montecarlo simulation

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Authors: Omogoriola Hannah Omoloye

Abstract:

Fish is a key ingredient on the global menu, a vital factor in the global environment and an important basis for livelihood worldwide1. The length – weight relationships (LWRs) is of great importance in fishery assessment2,3. Its importance is pronounced in estimated the average weight at a given length group4 and in assessing the relative well being of a fish population5. Length and weight measurement in conjunction with age data can give information on the stock composition, age at maturity, life span, mortality, growth and production4,5,6,7. In addition, the data on length and weight can also provides important clues to climatic and environmental changes and the change in human consumption practices8,9. However, the size attained by the individual fish may also vary because of variation in food supply, and these in turn may reflect variation in climatic parameters and in the supply of nutrient or in the degree of competition for food. Environment deterioration, for example, may reduce growth rates and will cause a decrease in the average age of the fish. The condition factor and the relative condition factor10 are the quantitative parameters of the well being state of the fish and reflect recent feeding condition of the fish. It is based on the hypothesis that heavier fish of a given length are in better condition11. This factor varies according to influences of physiological factors, fluctuating according to different stages of the development. Condition factor has been used as an index of growth and feeding intensity12. Condition factor decrease with increase in length 12,13 and also influences the reproductive cycle in fish14. The objective here is to determine the length-weight relationships and condition factor for direct use in fishery assessment and for future comparisons between populations of the same species at different locations. To provide quantitative information on the biology of marine fish species trawl from Nigeria coastal water.

Keywords: condition factor, growth pattern, marine fish species, Nigerian Coastal water

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Authors: S. Yeo, M. Mathur

Abstract:

Introduction: Obesity, defined as a Body Mass Index (BMI) of more than or equal to 30kg/m, is associated with an increased risk of complications during pregnancy and delivery. During labour, obese mothers often require greater intervention and have higher rates of caesarean section. Despite a low overall rate of serious complications following caesarean section, a high BMI predisposes to a higher risk of postoperative complications. Our study, therefore, aimed to investigate the impact of antenatal obesity on adverse outcomes following caesarean section, particularly wound-related infections. Materials and Methods: A retrospective cohort study of all caesarean deliveries during the first quarter of a chosen year was undertaken in our hospital, which is a tertiary referral centre with > 12,000 deliveries per year. Patients’ health records and data from our hospital’s electronic labour and delivery database were reviewed. Data analysis was performed using the Statistical Package for the Social Sciences (SPSS), and odds ratios plus adjusted odd ratios were calculated with 95% confidence intervals (CI). Results: A total of 1829 deliveries were reviewed during our study period. Of these, 180 (9.8%) patients were obese. The rate of caesarean delivery was 48.9% in obese patients versus 28.1% in non-obese patients. Post-operatively, 17% of obese patients experienced wound infection versus 0.2% of non-obese patients. Obese patients were also more likely to experience major postpartum haemorrhage (4.6% vs. 0.2%) and postpartum pyrexia (18.2% vs. 5.0%) in comparison to non-obese patients. Conclusions: Obesity is a significant risk factor in the development of postoperative complications following caesarean section. Wound infection remains a major concern for obese patients undergoing major surgery and results in extensive morbidity during the postnatal period. Postpartum infection can prolong recovery and affect maternal mental health, leading to reduced perinatal bonding with long-term implications on breastfeeding and parenting confidence. This study supports the need for the development of standardized protocols specifically for obese patients undergoing caesarean section. Multidisciplinary team care, in conjunction with anaesthesia, family physicians, and plastic surgery counterparts, early on in the antenatal journey, may be beneficial where wound complications are anticipated and to minimize the burden of postoperative infection in obese mothers.

Keywords: pregnancy, obesity, caesarean, infection

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Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

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Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, HPV18, p53 codon 72 polymorphism, miR-146a rs2910164 polymorphism

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Authors: Sahil Imtiyaz

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One of the biggest challenges has emerged from the ever-expanding, dynamic, and instantaneously changing space-Big Data; and to find a data point and inherit wisdom to this space is a hard task. In this paper, we reduce the space of big data in Hamiltonian formalism that is in concordance with Ising Model. For this formulation, we simulate the system using dye laser in FORTRAN and analyse the dynamics of the data point in energy well of rhodium atom. After mapping the photon intensity and pulse width with energy and potential we concluded that as we increase the energy there is also increase in probability of tunnelling up to some point and then it starts decreasing and then shows a randomizing behaviour. It is due to decoherence with the environment and hence there is a loss of ‘quantumness’. This interprets the efficiency parameter and the extent of quantum evolution. The results are strongly encouraging in favour of the use of ‘Topological Property’ as a source of information instead of the qubit.

Keywords: big data, optimization, quantum evolution, hamiltonian, dye laser, fermionic computations

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Authors: Maryam Najafi, Mahdi Rajabi

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Although the rural cooperatives are an effective way for rural development in Iran, their potential is not applied effectively. The investigation of the failures of rural cooperatives helps the authorities to improve the routine procedures and eliminate the current barriers to the success of these cooperatives, and to remove the defects in order to have a more efficient policy. Therefore, this research aims to prioritize the failure factors of rural cooperatives in Isfahan province via the survey research method. For this purpose, the effective factors of these failures were investigated by the available research documents and then by the new information which was obtained from 20 questionnaires from the experts of Central Organization Rural Cooperatives in Isfahan province. The questionnaire results were analyzed by Analytical Hierarchy Process (AHP), Excel, and Expert Choice software. The results of this research showed that the most important failure factor of these cooperatives is the lack of the participation culture of cooperative members and then the performance of Central Organization Rural Cooperatives, and also loss of confidence of the members in the cooperation.

Keywords: cooperative, rural cooperatives, failure factors, analytical hierarchy process

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Authors: Lydia Foucan, Christine Rambhojan, Rachel Billy, Christophe Armand, Carl-Thony Michel, Jean-Marc Lacorte, Laurent Larifla

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Leptin, an adipocyte-derived hormone, modulates insulin secretion and action via the leptin receptor (LEPR) that is expressed in pancreatic beta cells, adipose tissue, and muscle. Several polymorphisms have been described in the human LEPR gene including p.K109R (rs1137100), p.Q223R (rs1137101) and p.K656N (rs1805094) polymorphisms. The role of these polymorphisms is not yet studied in Guadeloupian population. Our aim was to explore the association of LEPR polymorphisms (K109R, Q223R and K656N) with leptin levels and obesity in non-diabetic Afro-Caribbean subjects. Genotypic analysis of the three polymorphisms was performed in 425 subjects using TaqMan and KASPar Assays. Serum leptin was measured with ELISA kits Biovendor® (RD191001100). Logistic regressions were used for assessment of statistical associations. Mean age was 47.6 ± 12.7 years. Among the participants, 238 (56 %) were women, 124 (30%) were obese and 155 (36.5%) had abdominal obesity. Carriers of LEPR K656N rs1805094 rare allele had significant higher frequencies of obesity (P = 0.007), abdominal obesity (P = 0.004) and metabolic syndrome (P = 0.021) but mean leptin level was not significantly different between both groups (P = 0.075). Odds ratios, adjusted for age and sex associated with presence of rs1805094 rare allele were 1.8 (1.1-2.9), P = 0.012 for obesity, 2.0 (1.2-3.3), P = 0.008 for abdominal obesity and 1.8 (1.1-3.0), P = 0.031 for MetS. No significant association was found with K109R, Q223R. These findings suggest that the K656N polymorphism (but not the K109R or Q223R polymorphism) of LEPR is associated with obesity, abdominal obesity and metabolic syndrome in this Afro-Caribbean non-diabetic population.

Keywords: Afro-Caribbean, leptin levels, leptin receptor gene polymorphisms, obesity

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Authors: S. Sreeja, Radhakrishnan R. Nair, Noble Gracious, Sreeja S. Nair, M. Radhakrishna Pillai

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Background: Tacrolimus is a potent immunosuppressant clinically used for the long term treatment of antirejection of transplanted organs in liver and kidney transplant recipients though dose optimization is poorly managed. However, So far no study has been carried out on the South Indian kidney transplant patients. The objective of this study is to evaluate the potential influence of a functional polymorphism in CYP3A5*3 gene on tacrolimus physiological availability/dose ratio in South Indian renal transplant patients. Materials and Methods: Twenty five renal transplant recipients receiving tacrolimus were enrolled in this study. Their body weight, drug dosage, and therapeutic concentration of Tacrolimus were observed. All patients were on standard immunosuppressive regime of Tacrolimus-Mycophenolate mofetil along with steroids on a starting dose of Tac 0.1 mg/kg/day. CYP3A5 genotyping was performed by PCR followed with RFLP. Conformation of RFLP analysis and variation in the nucleotide sequence of CYP3A5*3 gene were determined by direct sequencing using a validated automated generic analyzer. Results: A significant association was found between tacrolimus per dose/kg/d and CYP3A5 gene (A6986G) polymorphism in the study population. The CYP3A5 *1/*1, *1/*3 and *3/*3 genotypes were detected in 5 (20 %), 5 (20 %) and 15 (60 %) of the 25 graft recipients, respectively. CYP3A5*3 genotypes were found to be a good predictor of tacrolimus Concentration/Dose ratio in kidney transplant recipients. Significantly higher L/D was observed among non-expressors 9.483 ng/mL(4.5- 14.1) as compared with the expressors 5.154 ng/mL (4.42-6.5 ) of CYP3A5. Acute rejection episodes were significantly higher for CYP3A5*1 homozygotes compared to patients with CYP3A5*1/*3 and CYP3A5*3/*3 genotypes (40 % versus 20 % and 13 %, respectively ). The dose normalized TAC concentration (ng/ml/mg/kg) was significantly lower in patients having CYP3A5*1/*3 polymorphism. Conclusion: This is the first study to extensively determine the effect of CYP3A5*3 genetic polymorphism on tacrolimus pharmacokinetics in South Indian renal transplant recipients and also shows that majority of our patients carry mutant allele A6986G in CYP3A5*3 gene. Identification of CYP3A5 polymorphism prior to transplantation could contribute to evaluate the appropriate initial dosage of tacrolimus for each patient.

Keywords: kidney transplant patients, CYP3A5 genotype, tacrolimus, RFLP

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Authors: Elena Ivany, Leanne Aitken

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Little is known about the delivery of end-of-life care in cardiac intensive care unit (CICU) settings. The aims of this study were to highlight the nurse-identified barriers and facilitators to delivering end-of-life care in the CICU, and to identify whether any of the barriers and/or facilitators are specific to the CICU setting. This was an exploratory qualitative study utilizing semi-structured individual interviews as the data collection method and inductive thematic analysis to structure the data. Six CICU nurses took part in the study. Five key themes were identified, each theme including both barriers and facilitators. The five key themes are as follows: patient-centered care, emotional challenges, reaching concordance, nursing contribution and the surgical intensive care unit.

Keywords: end-of-life, cardiovascular disease, cardiac surgery, critical care

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Authors: Mahsa Taghavi

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In the treatment of breast cancer, tamoxifen is a regularly prescribed medication. The effect of tamoxifen on breast cancer patients' EMT pathways was studied. In this study to see if it had any effect on the cancer cells' resistance to tamoxifen and to look for specific miRNAs associated with EMT. In this work, we used continuous and integrated bioinformatics analysis to choose the optimal GEO datasets. Once we had sorted the gene expression profile, we looked at the mechanism of signaling, the ontology of genes, and the protein interaction of each gene. In the end, we used the GEPIA database to confirm the candidate genes. after that, I investigated critical miRNAs related to candidate genes. There were two gene expression profiles that were categorized into two distinct groups. Using the expression profile of genes that were lowered in the EMT pathway, the first group was examined. The second group represented the polar opposite of the first. A total of 253 genes from the first group and 302 genes from the second group were found to be common. Several genes in the first category were linked to cell death, focal adhesion, and cellular aging. Two genes in the second group were linked to cell death, focal adhesion, and cellular aging. distinct cell cycle stages were observed. Finally, proteins such as MYLK, SOCS3, and STAT5B from the first group and BIRC5, PLK1, and RAPGAP1 from the second group were selected as potential candidates linked to tamoxifen's influence on the EMT pathway. hsa-miR-1204 and hsa-miR-639 have a very close relationship with the candidates genes according to the node degrees and betweenness index. With this, the action of tamoxifen on the EMT pathway was better understood. It's important to learn more about how tamoxifen's target genes and proteins work so that we can better understand the drug.

Keywords: tamoxifen, breast cancer, bioinformatics analysis, EMT, miRNAs

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Authors: Debasish Nandy

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India’s foreign policy towards all of her neighbor countries is determinate on the basis of multi-dimensional factors. India’s relations with its South Asian neighbor can be classified into three categories. In the first category, there are four countries -Sri Lanka, Bangladesh, Nepal, and Afghanistan- whose bilateral relationships have encompassed cooperation, irritants, problems and crisis at different points in time. With Pakistan, the relationship has been perpetually adversarial. The third category includes Bhutan and Maldives whose relations are marked by friendship and cooperation, free of any bilateral problems. It is needless to say that Jawaharlal Nehru emphasized on friendly relations with the neighboring countries. The subsequent Prime Ministers of India especially I.K. Gujral had advocated in making of peaceful and friendly relations with the subcontinental countries. He had given a unique idea to foster bilateral relations with the neighbors. His idea is known as ‘Gujral Doctrine’. A dramatical change has been witnessed in Indian foreign policy since 1991.In the post-Cold War period, India’s national security has been vehemently threatened by terrorism, which originated from Pakistan-Afghanistan and partly Bangladesh. India has required a cooperative security, which can be made by mutual understanding among the South Asian countries. Additionally, the countries of South Asia need to evolve the concept of ‘Cooperative Security’ to explain the underlying logic of regional cooperation. According to C. Rajamohan, ‘cooperative security could be understood, as policies of governments, which see themselves as former adversaries or potential adversaries to shift from or avoid confrontationist policies.’ A cooperative security essentially reflects a policy of dealing peacefully with conflicts, not merely by abstention from violence or threats but by active engagement in negotiation, a search for practical solutions and with a commitment to preventive measures. Cooperative assumes the existence of a condition in which the two sides possess the military capabilities to harm each other. Establishing cooperative security runs into a complex process building confidence. South Asian nations often engaged with hostility to each other. Extra-regional powers have been influencing their powers in this region since a long time. South Asian nations are busy to purchase military equipment. In spite of weakened economic systems, these states are spending a huge amount of money for their security. India is the big power in this region in every aspect. The big states- small states syndrome is a negative factor in this respect. However, India will have to an initiative to extended ‘track II diplomacy’ or soft diplomacy for its security as well as the security of this region.Confidence building measures could help rejuvenate not only SAARC but also build trust and mutual confidence between India and its neighbors in South Asia. In this paper, I will focus on different aspects of India’s policy towards it, South-Asian neighbors. It will also be searched that how India is dealing with these countries by using a mixed type of diplomacy – both idealistic and realistic points of view. Security and cooperation are two major determinants of India’s foreign policy towards its South Asian neighbors.

Keywords: bilateral, diplomacy, infiltration, terrorism

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Authors: Stefanie Siebenhütter

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Male and female speakers use language differently and with varying confidence levels. This paper contrasts gendered differences in language use with socioeconomic status and age factors. It specifically examines how Kui minority language use and competence are conditioned by the variable of gender and discusses potential reasons for this variation by examining gendered language awareness and sociolinguistic attitudes. Moreover, it discusses whether women in Kui society function as 'leaders of linguistic change', as represented in Labov’s sociolinguistic model. It discusses whether societal role expectations in collectivistic cultures influence the model of linguistic change. The findings reveal current Kui speaking preferences and give predictions on the prospective language use, which is a stable situation of multilingualism because the current Kui speakers will socialize and teach the prospective Kui speakers in the near future. It further confirms that Lao is losing importance in Kui speaker’s (female’s) daily life.

Keywords: gender, identity construction, language change, minority language, multilingualism, sociolinguistics, social Networks

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Authors: Li-Te Lin, Chia-Jung Li, Kuan-Hao Tsui

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Cuproptosis, a newly identified cell death mechanism, has attracted attention for its association with various diseases. However, the genetic interplay between cuproptosis and ovarian aging remains largely unexplored. This study aims to address this gap by analyzing datasets related to ovarian aging and cuproptosis. Spatial transcriptome analyses were conducted in the ovaries of both young and aged female mice to elucidate the role of FDX1. Comprehensive bioinformatics analyses, facilitated by R software, identified FDX1 as a potential cuproptosis-related gene with implications for ovarian aging. Clinical infertility biopsies were examined to validate these findings, showing consistent results in elderly infertile patients. Furthermore, pharmacogenomic analyses of ovarian cell lines explored the intricate association between FDX1 expression levels and sensitivity to specific small molecule drugs. Spatial transcriptome analyses revealed a significant reduction in FDX1 expression in aging ovaries, supported by consistent findings in biopsies from elderly infertile patients. Pharmacogenomic investigations indicated that modulating FDX1 could influence drug responses in ovarian-related therapies. This study pioneers the identification of FDX1 as a cuproptosis-related gene linked to ovarian aging. These findings not only contribute to understanding the mechanisms of ovarian aging but also position FDX1 as a potential diagnostic biomarker and therapeutic target. Further research may establish FDX1's pivotal role in advancing precision medicine and therapies for ovarian-related conditions.

Keywords: cuproptosis, FDX1, ovarian aging, biomarker

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Authors: J. Adeppa, S. Samanta, O. K. Raina

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Fasciolosis is a widespread economically important parasitic infection throughout the world caused by Fasciola hepatica and F. gigantica. In order to identify novel immunogen conferring significant protection against fasciolosis, currently, research has been focused on the defined antigens viz. glutathione S-transferase, fatty acid binding protein, cathepsin-L, fluke hemoglobin, paramyosin, myosin and F. hepatica- Kunitz Type Molecule. Among various antigens, GST which plays a crucial role in detoxification processes, i.e. phase II defense mechanism of this parasite, has a unique position as a novel vaccine candidate and a drug target in the control of this disease. For producing the antigens in large quantities and their purification to complete homogeneity, the recombinant DNA technology has become an important tool to achieve this milestone. RT- PCR was carried out using F. gigantica total RNA as template, and an amplicon of 657 bp GST gene was obtained. TA cloning vector was used for cloning of this gene, and the presence of insert was confirmed by blue-white selection for recombinant colonies. Sequence analysis of the present isolate showed 99.1% sequence homology with the published sequence of the F. gigantica GST gene of cattle origin (accession no. AF112657), with six nucleotide changes at 72, 74, 423, 513, 549 and 627th bp found in the present isolate, causing an overall change of 4 amino acids. The 657 bp GST gene was cloned at BamH1 and HindIII restriction sites of the prokaryotic expression vector pPROEXHTb in frame with six histidine residues and expressed in E. coli DH5α. Recombinant protein was purified from the bacterial lysate under non-denaturing conditions by the process of sonication after lysozyme treatment and subjecting the soluble fraction of the bacterial lysate to Ni-NTA affinity chromatography. Western blotting with rabbit hyper-immune serum showed immuno-reactivity with 25 kDa recombinant GST. Recombinant protein detected F. gigantica experimental as well as field infection in buffaloes by dot-ELISA. However, cross-reactivity studies on Fasciola gigantica GST antigen are needed to evaluate the utility of this protein in the serodiagnosis of fasciolosis.

Keywords: fasciola gigantic, fasciola hepatica, GST, RT- PCR

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Authors: Manpreet Kaur, Badaruddoza, Sandeep Kaur Brar

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The increasing prevalence of adolescent obesity is one of the major causes to be hypertensive in adulthood. Various statistical methods have been applied to examine the performance of anthropometric indices for the identification of adverse cardiovascular risk profile. The present work was undertaken to determine the significant traditional risk factors through principal component factor analysis (PCFA) among population based Punjabi adolescents aged 10-18 years. Data was collected among adolescent children from different schools situated in urban areas of Punjab, India. Principal component factor analysis (PCFA) was applied to extract orthogonal components from anthropometric and physiometric variables. Association between components were explained by factor loadings. The PCFA extracted four factors, which explained 84.21%, 84.06% and 83.15% of the total variance of the 14 original quantitative traits among boys, girls and combined subjects respectively. Factor 1 has high loading of the traits that reflect adiposity such as waist circumference, BMI and skinfolds among both sexes. However, waist circumference and body mass index are the indicator of abdominal obesity which increases the risk of cardiovascular diseases. The loadings of these two traits have found maximum in girls adolescents (WC=0.924; BMI=0.905). Therefore, factor 1 is the strong indicator of atherosclerosis in adolescents. Factor 2 is predominantly loaded with blood pressures and related traits (SBP, DBP, MBP and pulse rate) which reflect the risk of essential hypertension in adolescent girls and combined subjects, whereas, factor 2 loaded with obesity related traits in boys (weight and hip circumferences). Comparably, factor 3 is loaded with blood pressures in boys and with height and WHR in girls, while factor 4 contains high loading of pulse pressure among boys, girls and combined group of adolescents.

Keywords: adolescent obesity, cvd, hypertension, punjabi population

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Authors: Sahar Nasr, Lin Li, Edwin Wang

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Bladder cancer (BLCA) is known as the 13th cause of death among cancer patients worldwide, and ~575,000 new BLCA cases are diagnosed each year. Urothelial carcinoma (UC) is the most prevalent subtype among BLCA patients, which can be categorized into muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Currently, various therapeutic options are available for UC patients, including (1) transurethral resection followed by intravesical instillation of chemotherapeutics or Bacillus Calmette-Guérin for NMIBC patients, (2) neoadjuvant platinum-based chemotherapy (NAC) plus radical cystectomy is the standard of care for localized MIBC patients, and (3) systematic chemotherapy for metastatic UC. However, conventional treatments may lead to several challenges for treating patients. As an illustration, some patients may suffer from recurrence of the disease after the first line of treatment. Recently, immune checkpoint therapy (ICT) has been introduced as an alternative treatment strategy for the first or second line of treatment in advanced or metastatic BLCA patients. Although ICT showed lucrative results for a fraction of BLCA patients, ~80% of patients were not responsive to it. Therefore, novel treatment methods are required to augment the ICI response rate within BLCA patients. It has been shown that the infiltration of T-cells into the tumor microenvironment (TME) is positively correlated with the response to ICT within cancerous patients. Therefore, the goal of this study is to enhance the infiltration of cytotoxic T-cells into TME through the identification of target genes within the tumor that are responsible for the non-T-cell inflamed TME and their inhibition. BLCA bulk RNA-sequencing data from The Cancer Genome Atlas (TCGA) and immune score for TCGA samples were used to determine the Pearson correlation score between the expression of different genes and immune score for each sample. The genes with strong negative correlations were selected (r < -0.2). Thereafter, the correlation between the expression of each gene and survival in BLCA patients was calculated using the TCGA data and Cox regression method. The genes that are common in both selected gene lists were chosen for further analysis. Afterward, BLCA bulk and single-cell RNA-sequencing data were ranked based on the expression of each selected gene and the top and bottom 25% samples were used for pathway enrichment analysis. If the pathways related to the T-cell infiltration (e.g., antigen presentation, interferon, or chemokine pathways) were enriched within the low-expression group, the gene was included for downstream analysis. Finally, the selected genes will be used to calculate the correlation between their expression and the infiltration rate of the activated CD+8 T-cells, natural killer cells and the activated dendric cells. A list of potential target genes has been identified and ranked based on the above-mentioned analysis and criteria. SUN-1 got the highest score within the gene list and other identified genes in the literature as benchmarks. In conclusion, inhibition of SUN1 may increase the tumor-infiltrating lymphocytes and the efficacy of ICI in BLCA patients. BLCA tumor cells with and without SUN-1 CRISPR/Cas9 knockout will be injected into the syngeneic mouse model to validate the predicted SUN-1 effect on increasing tumor-infiltrating lymphocytes.

Keywords: data analysis, gene expression analysis, gene identification, immunoinformatic, functional genomics, transcriptomics

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