Search results for: complete genome sequencing

Authors: Debbarma Asis, Guha Chandan

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Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

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Authors: Andika Bagaskara, Andhika Rizki Pratama, Lalu Arya Repatmaja, Septhian Ditaputra Raharja

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The power transformer is one of the critical things in system transmission. Regular testing of the power transformer is very important to maintain the reliability of the power. One of the causes of the failure of the transformer is the breakdown of insulation caused by the presence of voids in the equipment that is electrified. As a result of the voids that occur in this power transformer equipment, it can cause partial discharge. Several methods were used to determine the occurrence of damage to the power transformer equipment, such as Sweep Frequency Response Analysis (SFRA) and Tan Delta. In Inter Bus Transformer (IBT) 500/150 kV Cirata Extra High Voltage (EHV) Substation, a breakdown occurred in the T-phase tertiary bushing. From the lessons learned in this case, a complete electrical test was carried out. From the results of the complete electrical test, there was a suspicion of deterioration in the post-breakdown SFRA results. After overhaul and inspection, traces of voids were found on the tertiary bushing, which indicated a breakdown in the tertiary bushing of the IBT 500/150kV Cirata Substation transformer.

Keywords: void, bushing, SFRA, Tan Delta

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Authors: Harshith Gowda K. S, Tejaskumar N, Shubhanga R. B, Gowtham N, Deekshith Gowda H. S

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Phasor measurement units (PMU) are playing an important role in the current power system for state estimation. It is necessary to have complete observability of the power system while minimizing the cost. For this purpose, the optimal location of the phasor measurement units in the power system is essential. In a bus system, zero injection buses need to be evaluated to minimize the number of PMUs. In this paper, the optimization problem is formulated using mixed integer programming to obtain the optimal location of the PMUs with increased observability. The formulation consists of with and without zero injection bus as constraints. The formulated problem is simulated using a CPLEX solver in the GAMS software package. The proposed method is tested on IEEE 30, IEEE 39, IEEE 57, and IEEE 118 bus systems. The results obtained show that the number of PMUs required is minimal with increased observability.

Keywords: PMU, observability, mixed integer programming (MIP), zero injection buses (ZIB)

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Authors: Gabrielle Holt

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This paper is looking to prove the efficacy of the Schulte Holt IOL Toric Calculator Processor (Schulte Holt ITCP). It has been completed using manually inputted data into the Barrett Toric Calculator and comparing the number of minutes taken to complete the Toric calculations, the number of errors identified during completion, and distractions during completion. It will then compare that data to the number of minutes taken for the Schulte Holt ITCP to complete also, using the Barrett method, as well as the number of errors identified in the Schulte Holt ITCP. The data clearly demonstrate a momentous advantage to the Schulte Holt ITCP and notably reduces time spent doing Toric Calculations, as well as reducing the number of errors. With the ever-growing number of cataract surgeries taking place around the world and the waitlists increasing -the Schulte Holt IOL Toric Calculator Processor may well demonstrate a way forward to increase the availability of ophthalmologists and ophthalmic staff while maintaining patient safety.

Keywords: Toric, toric lenses, ophthalmology, cataract surgery, toric calculations, Barrett

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Authors: M. Chaichanyut, S. Tungjitkusolmun

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This paper is concerned with microwave (MW) ablation for a liver cancer tissue by using helix antenna. The antenna structure supports the propagation of microwave energy at 2.45 GHz. A 1½ turn spiral catheter-based microwave antenna applicator has been developed. We utilize the three-dimensional finite element method (3D FEM) simulation to analyze where the tissue heat flux, lesion pattern and volume destruction during MW ablation. The configurations of helix antenna where Helix air-core antenna and Helix Dielectric-core antenna. The 3D FEMs solutions were based on Maxwell and bio-heat equations. The simulation protocol was power control (10 W, 300s). Our simulation result, both helix antennas have heat flux occurred around the helix antenna and that can be induced the temperature distribution similar (teardrop). The region where the temperature exceeds 50°C the microwave ablation was successful (i.e. complete destruction). The Helix air-core antenna and Helix Dielectric-core antenna, ablation zone or axial ratios (Widest/length) were respectively 0.82 and 0.85; the complete destructions were respectively 4.18 cm³ and 5.64 cm³.

Keywords: liver cancer, Helix antenna, finite element, microwave ablation

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Authors: Mohan Kotamrazu

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Cyclone Hudhud which battered the city of Visakhapatnam on 12^th October, 2014, damaged many buildings, public amenities and infrastructure facilities along the Visakha- Bheemili coastal corridor. More than half the green cover of the city was wiped out. Majority of the trees along the coastal corridor suffered from complete or partial damage. In order to understand the different ways that trees incurred damage during the cyclone, a damage assessment study was carried out by the author. The areas covered by this study included two university campuses, several parks and residential colonies which bore the brunt of the cyclone. Post disaster attempts have been made to restore many of the trees that have suffered from partial or complete damage from the effects of extreme winds. This paper examines the various ways that trees incurred damage from the cyclone Hudhud and presents some examples of the restoration efforts carried out by educational institutions, public parks and religious institutions of the city of Visakhapatnam in the aftermath of the devastating cyclone.

Keywords: defoliaton, salt spray damage, uprooting and wind throw, restoration

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Authors: Arsyam Mawardi, Sony Suhandono, Azzania Fibriani, Fifi Fitriyah Masduki

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Malaria is an infectious disease caused by Plasmodium sp. This disease has a high prevalence in Indonesia, especially in Jayapura. The vaccine that is currently being developed has not been effective in overcoming malaria. This is due to the high polymorphism in the Plasmodium genome especially in areas that encode Plasmodium surface proteins. Merozoite Surface Protein 1 (MSP1) Plasmodium falciparum is a surface protein that plays a role in the invasion process in human erythrocytes through the interaction of Glycophorin A protein receptors and sialic acid in erythrocytes with Reticulocyte Binding Proteins (RBP) and Duffy Adhesion Protein (DAP) ligands in merozoites. MSP1 can be targeted to be a specific antigen and predicted epitope area which will be used for the development of diagnostic and malaria vaccine therapy. MSP1 consists of 17 blocks, each block is dimorphic, and has been marked as the K1 and MAD20 alleles. Exceptions only in block 2, because it has 3 alleles, among others K1, MAD20 and RO33. These polymorphisms cause allelic variations and implicate the severity of patients infected P. falciparum. In addition, polymorphism of MSP1 in Jayapura isolates has not been reported so it is interesting to be further identified and projected as a specific antigen. Therefore, in this study, we analyzed the allele polymorphism as well as detected the MSP1 epitope antigen candidate on block 2 P. falciparum. Clinical samples of selected malaria patients followed the consecutive sampling method, examining malaria parasites with blood preparations on glass objects observed through a microscope. Plasmodium DNA was isolated from the blood of malarial positive patients. The block 2 MSP1 gene was amplified using PCR method and cloned using the pGEM-T easy vector then transformed to TOP'10 E.coli. Positive colonies selection was performed with blue-white screening. The existence of target DNA was confirmed by PCR colonies and DNA sequencing methods. Furthermore, DNA sequence analysis was done through alignment and formation of a phylogenetic tree using MEGA 6 software and insilico analysis using IEDB software to predict epitope candidate for P. falciparum. A total of 15 patient samples have been isolated from Plasmodium DNA. PCR amplification results show the target gene size about ± 1049 bp. The results of MSP1 nucleotide alignment analysis reveal that block 2 MSP1 genes derived from the sample of malarial patients were distributed in four different allele family groups, K1 (7), MAD20 (1), RO33 (0) and MSP1_Jayapura (10) alleles. The most commonly appears of the detected allele is MSP1_Jayapura single allele. There was no significant association between sex variables, age, the density of parasitemia and alel variation (Mann Whitney, U > 0.05), while symptomatic signs have a significant difference as a trigger of detectable allele variation (U < 0.05). In this research, insilico study shows that there is a new epitope antigen candidate from the MSP1_Jayapura allele and it is predicted to be recognized by B cells with 17 amino acid lengths in the amino acid sequence 187 to 203.

Keywords: epitope candidate, insilico analysis, MSP1 P. falciparum, polymorphism

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Authors: Niklas Ravn-Boess, Nainita Bhowmick, Takamitsu Hattori, Shohei Koide, Christopher Park, Dimitris Placantonakis

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Background: Glioblastoma (GBM) is the most common and deadly primary brain malignancy in adults. Tumor propagation, brain invasion, and resistance to therapy critically depend on GBM stem-like cells (GSCs); however, the mechanisms that regulate GSC self-renewal are incompletely understood. Given the aggressiveness and poor prognosis of GBM, it is imperative to find biomarkers that could also translate into novel drug targets. Along these lines, we have identified a cell surface antigen, CD97 (ADGRE5), an adhesion G protein-coupled receptor (GPCR), that is expressed on GBM cells but is absent from non-neoplastic brain tissue. CD97 has been shown to promote invasiveness, angiogenesis, and migration in several human cancers, but its frequency of expression and functional role in regulating GBM growth and survival, and its potential as a therapeutic target has not been investigated. Design: We assessed CD97 mRNA and protein expression in patient derived GBM samples and cell lines using publicly available RNA-sequencing datasets and flow cytometry, respectively. To assess CD97 function, we generated shRNA lentiviral constructs that target a sequence in the CD97 extracellular domain (ECD). A scrambled shRNA (scr) with no predicted targets in the genome was used as a control. We evaluated CD97 shRNA lentivirally transduced GBM cells for Ki67, Annexin V, and DAPI. We also tested CD97 KD cells for their ability to self-renew using clonogenic tumorsphere formation assays. Further, we utilized synthetic Abs (sAbs) generated against the ECD of CD97 to test for potential antitumor effects using patient-derived GBM cell lines. Results: CD97 mRNA expression was expressed at high levels in all GBM samples available in the TCGA cohort. We found high levels of surface CD97 protein expression in 6/6 patient-derived GBM cell cultures, but not human neural stem cells. Flow cytometry confirmed downregulation of CD97 in CD97 shRNA lentivirally transduced cells. CD97 KD induced a significant reduction in cell growth in 3 independent GBM cell lines representing mesenchymal and proneural subtypes, which was accompanied by reduced (~20%) Ki67 staining and increased (~30%) apoptosis. Incubation of GBM cells with sAbs (20 ug/ ml) against the ECD of CD97 for 3 days induced GSC differentiation, as determined by the expression of GFAP and Tubulin. Using three unique GBM patient derived cultures, we found that CD97 KD attenuated the ability of GBM cells to initiate sphere formation by over 300 fold, consistent with an impairment in GSC self-renewal. Conclusion: Loss of CD97 expression in patient-derived GBM cells markedly decreases proliferation, induces cell death, and reduces tumorsphere formation. sAbs against the ECD of CD97 reduce tumorsphere formation, recapitulating the phenotype of CD97 KD, suggesting that sAbs that inhibit CD97 function exhibit anti-tumor activity. Collectively, these findings indicate that CD97 is necessary for the proliferation and survival of human GBM cells and identify CD97 as a promising therapeutically targetable vulnerability in GBM.

Keywords: adhesion GPCR, CD97, GBM stem cell, glioblastoma

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Authors: Corey F. Fitzgerald

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This study provides a comprehensive examination of the biomechanical sequencing inherent in pitching motions, coupled with an advanced methodology for interpreting gathered data to inform programming strategies. The analysis is conducted utilizing state-of-the-art biomechanical laboratory equipment capable of detecting subtle changes and deviations, facilitating highly informed decision-making processes. Through this presentation, the intricate dynamics of pitching sequences are meticulously discussed to highlight the complex movement patterns accessible and actionable for performance enhancement purposes in the weight room.

Keywords: sport science, applied biomechanics, strength and conditioning, applied research

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Doaa Abbas Zaher

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For the past two decades demand for knowledge has been increasing. Management of society’s knowledge has far reaching effects to economic growth through increased capacity to complete viable activities. Organizations use information technology to effect organizational change. This is a challenge for the less developed nations whose capacity to integrate knowledge in core functions is limited. This creates organizational problems as there is global competition amongst organizations. Cross-cultural perceptions influence difference knowledge Management. This study provides a cross-cultural analysis on the influence in knowledge culture in Japan and Saudi Arabia to effect change in organizations. Since different countries adopt different knowledge management strategies, this dictates the state of organizational development through enriched organizational culture. The research uses a mixed approach design to collect data from primary and secondary sources. Primary source will use the questionnaires while secondary sources uses case analysis from books, articles, reports, and journals. The study will take a period of three years to come up with a complete paper.

Keywords: knowledge management, organizational culture, information, society knowledge

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Authors: Mohammad Mozammel Haque

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A clause is a sentence or a part of a sentence having a subject and a principal verb; it may or may not express a complete thought. But, a sentence is a group of words arranged orderly, and it has a complete thought. Clause and sentence are interrelated with each other. It is really quite impossible to decide whether a sentence is simple, complex or compound without having an idea about clauses. Correspondingly, knowing whether a clause is main or subordinate without having an idea about sentence is equally not easy. It is even a task somewhat difficult task for a teacher to teach sentences and clauses in a classroom, unconnectedly or independently. When discussing types of sentences, the teacher must talk about clauses. Likewise, he/she must confer sentences when he teaches clauses in a classroom. This paper aims at discussing types of clauses and sentences in detail, and showing their interrelationship. It also shows that it is requisite to discuss clauses when teaching sentences in the same class, and that the students also have trouble understanding the one without having, at least, a little idea about the other. Ardent and practical paradigms from the books selected for various skill courses in the English Department of Jazan University have also been discussed in this paper.

Keywords: clause, correlation, dependent, independent, interrelationship, sentence

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Authors: Lina Wu, Ye Li

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An equivalent relation between a harmonic form and a closed co-closed form is established on a complete non-compact manifold. This equivalence has been generalized for a differential k-form ω from Lq spaces to non-Lq spaces when q=2 in the context of p-balanced growth where p=2. Especially for a simple differential k-form on a complete non-compact manifold, the equivalent relation has been verified with the extended scope of q for from finite q-energy in Lq spaces to infinite q-energy in non-Lq spaces when with 2-balanced growth. Generalized Hadamard Theorem, Cauchy-Schwarz Inequality, and Calculus skills including Integration by Parts as well as Convergent Series have been applied as estimation techniques to evaluate growth rates for a differential form. In particular, energy growth rates as indicated by an appropriate power range in a selected test function lead to a balance between a harmonic differential form and a closed co-closed differential form. Research ideas and computational methods in this paper could provide an innovative way in the study of broadening Lq spaces to non-Lq spaces with a wide variety of infinite energy growth for a differential form.

Keywords: closed forms, co-closed forms, harmonic forms, L^q spaces, p-balanced growth, simple differential k-forms

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Authors: Shameel Pervez, Saad Aziz Durrani, Ibatsam Khokhar

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Pectinase is an enzyme that breaks down pectin, a compound responsible for structural integrity of the plant. Pectin is difficult to break down mechanically and the cost is very high, that is why many industries including food industries use pectinase enzyme produced by microbes for pectin breakdown. Apple (Malus domestica) is an important fruit in terms of market value. Every year, millions of apples are wasted due to post-harvest rot caused by fungi. Fungi are natural decomposers of our ecosystem and are infamous for post-harvest rot of apple fruit but at the same time they are prized for their high production of valuable extracellular enzymes such as pectinase. In this study, fungi belonging to different genus were isolated from rotten apples. Rotten samples of apple were picked from different markets of Lahore. After surface sterilization, the rotten parts were cut into small pieces and placed onto MEA media plates for three days. Afterwards, distinct colonies were picked and purified by sub-culturing. The isolates were identified to genus level through the study of basic colony morphology and microscopic features. The isolates were then subjected to screening for pectinase activity on MS media to compare pectinase production and were then subsequently tested for pathogenic activity through wound suspension method to evaluate the pathogenic activity of isolates in comparison with their pectinolytic activity. A total of twelve fungal strains were isolates from rotten apples. They were belonging to genus Penicillium, Alternaria, Paecilomyces and Rhizopus. Upon screening for pectinolytic activity, isolates Pen 1, Pen 4, and Rz showed high pectinolytic activity and were further subjected to DNA isolation and partial sequencing for species identification. The results of partial sequencing were combined with in-depth study of morphological features revealing Pen 1 as Penicillium janthinellum, Pen 4 as Penicillium griseofulvum, and Rz as Rhizopus microsporus. Pathogenic activity of all twelve isolates was evaluated. Penicillium spp. were highly pathogenic and destructive and same was the case with Paecilomyces sp. and Rhizopus sp. However, Alternaria spp. were found to be more consistent in their pathogenic activity, on all types of apples.

Keywords: apple, pectinase, fungal pathogens, penicillium, rhizopus

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Authors: Sanjeev Kumar Sharma, Arnab Mondal, Ranjit Kumar Upadhyay

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Excitable cells often produce different oscillatory activities that help us to understand the transmitting and processing of signals in the neural system. We consider a FitzHugh-Rinzel (FH-R) model and studied the different dynamics of the model by considering the parameter c as the predominant parameter. The model exhibits different types of neuronal responses such as regular spiking, mixed-mode bursting oscillations (MMBOs), elliptic bursting, etc. Based on the bifurcation diagram, we consider the three regimes (MMBOs, elliptic bursting, and quiescent state). An analytical treatment for the occurrence of the supercritical Hopf bifurcation is studied. Further, we extend our study to a network of a hundred neurons by considering the bi-directional synaptic coupling between them. In this article, we investigate the alternation of spiking propagation and bursting phenomena of an uncoupled and coupled FH-R neurons. We explore that the complete graph of heterogenous desynchronized neurons can exhibit different types of bursting oscillations for certain coupling strength. For higher coupling strength, all the neurons in the network show complete synchronization.

Keywords: excitable neuron model, spiking-bursting, stability and bifurcation, synchronization networks

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Authors: Seung-Won Lee, JongSoo Lee, Won-Jik Yang, Hyung-Joon Kim

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A capacity spectrum method (CSM), one of methodologies to evaluate seismic fragilities of building structures, has been long recognized as the most convenient method, even if it contains several limitations to predict the seismic response of structures of interest. This paper proposes the procedure to estimate seismic fragility curves using an incremental dynamic analysis (IDA) rather than the method adopting a CSM. To achieve the research purpose, this study compares the seismic fragility curves of a 5-story reinforced concrete (RC) moment frame obtained from both methods, an IDA method and a CSM. Both seismic fragility curves are similar in slight and moderate damage states whereas the fragility curve obtained from the IDA method presents less variation (or uncertainties) in extensive and complete damage states. This is due to the fact that the IDA method can properly capture the structural response beyond yielding rather than the CSM and can directly calculate higher mode effects. From these observations, the CSM could overestimate seismic vulnerabilities of the studied structure in extensive or complete damage states.

Keywords: seismic fragility curve, incremental dynamic analysis, capacity spectrum method, reinforced concrete moment frame

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Authors: Yelin Zhao, Xinxiu Li, Martin Smelik, Oleg Sysoev, Firoj Mahmud, Dina Mansour Aly, Mikael Benson

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Background: Early diagnosis of pancreatic cancer is clinically challenging due to vague, or no symptoms, and lack of biomarkers. Polygenic risk score (PRS) scores may provide a valuable tool to assess increased or decreased risk of PC. This study aimed to develop such PRS by filtering genetic variants identified by GWAS using transcriptional programs identified by single-cell RNA sequencing (scRNA-seq). Methods: ScRNA-seq data from 24 pancreatic ductal adenocarcinoma (PDAC) tumor samples and 11 normal pancreases were analyzed to identify differentially expressed genes (DEGs) in in tumor and microenvironment cell types compared to healthy tissues. Pathway analysis showed that the DEGs were enriched for hundreds of significant pathways. These were clustered into 40 “programs” based on gene similarity, using the Jaccard index. Published genetic variants associated with PDAC were mapped to each program to generate program PRSs (pPRSs). These pPRSs, along with five previously published PRSs (PGS000083, PGS000725, PGS000663, PGS000159, and PGS002264), were evaluated in a European-origin population from the UK Biobank, consisting of 1,310 PDAC participants and 407,473 non-pancreatic cancer participants. Stepwise Cox regression analysis was performed to determine associations between pPRSs with the development of PC, with adjustments of sex and principal components of genetic ancestry. Results: The PDAC genetic variants were mapped to 23 programs and were used to generate pPRSs for these programs. Four distinct pPRSs (P1, P6, P11, and P16) and two published PRSs (PGS000663 and PGS002264) were significantly associated with an increased risk of developing PC. Among these, P6 exhibited the greatest hazard ratio (adjusted HR[95% CI] = 1.67[1.14-2.45], p = 0.008). In contrast, P10 and P4 were associated with lower risk of developing PC (adjusted HR[95% CI] = 0.58[0.42-0.81], p = 0.001, and adjusted HR[95% CI] = 0.75[0.59-0.96], p = 0.019). By comparison, two of the five published PRS exhibited an association with PDAC onset with HR (PGS000663: adjusted HR[95% CI] = 1.24[1.14-1.35], p < 0.001 and PGS002264: adjusted HR[95% CI] = 1.14[1.07-1.22], p < 0.001). Conclusion: Compared to published PRSs, scRNA-seq-based pPRSs may be used not only to assess increased but also decreased risk of PDAC.

Keywords: cox regression, pancreatic cancer, polygenic risk score, scRNA-seq, UK biobank

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Ethel E. Phiri, Lionel Hartzenberg, Percy Chimwamuromba, Emmanuel Nepolo, Jens Kossmann, James R. Lloyd

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Orphan crops are underresearched and underutilized food plant species that have not been categorized as major food crops, but have the potential to be economically and agronomically significant. They have been documented to have the ability to tolerate extreme environmental conditions. However, limited research has been conducted to uncover their potential as food crop species. The New Partnership for Africa’s Development (NEPAD) has classified Marama bean, Tylosema esculentum, as an orphan crop. The plant is one of the 101 African orphan crops that must have their genomes sequenced, assembled, and annotated in the foreseeable future. Marama bean is a perennial leguminous plant that primarily grows in poor, arid soils in southern Africa. The plants produce large tubers that can weigh as much as 200kg. While the foliage provides fodder, the tuber is carbohydrate rich and is a staple food source for rural communities in Namibia. Also, the edible seeds are protein- and oil-rich. Marama Bean plants respond rapidly to increased temperatures and severe water scarcity without extreme consequences. Advances in molecular biology and biotechnology have made it possible to effectively transfer technologies between model- and major crops to orphan crops. In this research, the aim was to assemble the first transcriptomic analysis of Marama Bean RNA-sequence data. Many model plant species have had their genomes sequenced and their transcriptomes assembled. Therefore the availability of transcriptome data for a non-model crop plant species will allow for gene identification and comparisons between various species. The data has been sequenced using the Ilumina Hiseq 2500 sequencing platform. Data analysis is underway. In essence, this research will eventually evaluate the potential use of Marama Bean as a crop species to improve its value in agronomy. data for a non-model crop plant species will allow for gene identification and comparisons between various species. The data has been sequenced using the Ilumina Hiseq 2500 sequencing platform. Data analysis is underway. In essence, this researc will eventually evaluate the potential use of Marama bean as a crop species to improve its value in agronomy.

Keywords: 101 African orphan crops, RNA-Seq, Tylosema esculentum, underutilised crop plants

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Authors: Tamar Lin, Nufar Buchshtab, Yifat Elharar, Julian Nicenboim, Rotem Edgar, Iddo Weiner, Lior Zelcbuch, Ariel Cohen, Sharon Kredo-Russo, Inbar Gahali-Sass, Naomi Zak, Sailaja Puttagunta, Merav Bassan

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Background: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder that is characterized by dry skin and flares of eczematous lesions and intense pruritus. Multiple lines of evidence suggest that AD is associated with increased colonization by Staphylococcus aureus, which contributes to disease pathogenesis through the release of virulence factors that affect both keratinocytes and immune cells, leading to disruption of the skin barrier and immune cell dysfunction. The aim of the current study is to develop a bacteriophage-based product that specifically targets S. aureus. Methods: For the discovery of phage, environmental samples were screened on 118 S. aureus strains isolated from skin samples, followed by multiple enrichment steps. Natural phages were isolated, subjected to Next-generation Sequencing (NGS), and analyzed using proprietary bioinformatics tools for undesirable genes (toxins, antibiotic resistance genes, lysogeny potential), taxonomic classification, and purity. Phage host range was determined by an efficiency of plating (EOP) value above 0.1 and the ability of the cocktail to completely lyse liquid bacterial culture under different growth conditions (e.g., temperature, bacterial stage). Results: Sequencing analysis demonstrated that the 118 S. aureus clinical strains were distributed across the phylogenetic tree of all available Refseq S. aureus (~10,750 strains). Screening environmental samples on the S. aureus isolates resulted in the isolation of 50 lytic phages from different genera, including Silviavirus, Kayvirus, Podoviridae, and a novel unidentified phage. NGS sequencing confirmed the absence of toxic elements in the phages’ genomes. The host range of the individual phages, as measured by the efficiency of plating (EOP), ranged between 41% (48/118) to 79% (93/118). Host range studies in liquid culture revealed that a subset of the phages can infect a broad range of S. aureus strains in different metabolic states, including stationary state. Combining the single-phage EOP results of selected phages resulted in a broad host range cocktail which infected 92% (109/118) of the strains. When tested in vitro in a liquid infection assay, clearance was achieved in 87% (103/118) of the strains, with no evidence of phage resistance throughout the study (24 hours). A S. aureus host was identified that can be used for the production of all the phages in the cocktail at high titers suitable for large-scale manufacturing. This host was validated for the absence of contaminating prophages using advanced NGS methods combined with multiple production cycles. The phages are produced under optimized scale-up conditions and are being used for the development of a topical formulation (BX005) that may be administered to subjects with atopic dermatitis. Conclusions: A cocktail of natural phages targeting S. aureus was effective in reducing bacterial burden across multiple assays. Phage products may offer safe and effective steroid-sparing options for atopic dermatitis.

Keywords: atopic dermatitis, bacteriophage cocktail, host range, Staphylococcus aureus

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Authors: Angela U. Makolo

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Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: Artem Kim, Clara Savary, Christele Dubourg, Wilfrid Carre, Houda Hamdi-Roze, Valerie Dupé, Sylvie Odent, Marie De Tayrac, Veronique David

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Holoprosencephaly (HPE) is a rare congenital brain malformation resulting from the incomplete separation of the two cerebral hemispheres. It is characterized by a wide phenotypic spectrum and a high degree of locus heterogeneity. Genetic defects in 16 genes have already been implicated in HPE, but account for only 30% of cases, suggesting that a large part of genetic factors remains to be discovered. HPE has been recently redefined as a complex multigenic disorder, requiring the joint effect of multiple mutational events in genes belonging to one or several developmental pathways. The onset of HPE may result from accumulation of the effects of multiple rare variants in functionally-related genes, each conferring a moderate increase in the risk of HPE onset. In order to decipher the genetic basis of HPE, unconventional patterns of inheritance involving multiple genetic factors need to be considered. The primary objective of this study was to uncover possible disease causing combinations of multiple rare variants underlying HPE by performing trio-based Whole Exome Sequencing (WES) of familial cases where no molecular diagnosis could be established. 39 families were selected with no fully-penetrant causal mutation in known HPE gene, no chromosomic aberrations/copy number variants and without any implication of environmental factors. As the main challenge was to identify disease-related variants among a large number of nonpathogenic polymorphisms detected by WES classical scheme, a novel variant prioritization approach was established. It combined WES filtering with complementary gene-level approaches: transcriptome-driven (RNA-Seq data) and clinically-driven (public clinical data) strategies. Briefly, a filtering approach was performed to select variants compatible with disease segregation, population frequency and pathogenicity prediction to identify an exhaustive list of rare deleterious variants. The exome search space was then reduced by restricting the analysis to candidate genes identified by either transcriptome-driven strategy (genes sharing highly similar expression patterns with known HPE genes during cerebral development) or clinically-driven strategy (genes associated to phenotypes of interest overlapping with HPE). Deeper analyses of candidate variants were then performed on a family-by-family basis. These included the exploration of clinical information, expression studies, variant characteristics, recurrence of mutated genes and available biological knowledge. A novel bioinformatics pipeline was designed. Applied to the 39 families, this final integrated workflow identified an average of 11 candidate variants per family. Most of candidate variants were inherited from asymptomatic parents suggesting a multigenic inheritance pattern requiring the association of multiple mutational events. The manual analysis highlighted 5 new strong HPE candidate genes showing recurrences in distinct families. Functional validations of these genes are foreseen.

Keywords: complex genetic disorder, holoprosencephaly, multiple rare variants, whole exome sequencing

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Authors: Lalita Khuna, Sugalya Amatachaya, Pipatana Amatachaya, Thiwabhorn Thaweewannakij, Pattra Wattanapan

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The five times sit-to-stand test (FTSST) has been widely used to quantify lower extremity motor strength (LEMS), dynamic balance ability, and risk of falls in many individuals. Recently, it has been used in ambulatory patients with spinal cord injury (SCI) but variously using with or without hands according to patients’ ability. This difference might affect the validity of the test in these individuals. Thus, this study assessed the concurrent validity of the FTSST in ambulatory individuals with SCI, separately for those who could complete the test with or without hands using LEMS and standard functional measures as gold standards. Moreover, the data of the tests from those who completed the FTSST with and without hands were compared. A total of 56 ambulatory participants with SCI who could complete sit-to-stand with or without hands were assessed for the time to complete the FTSST according to their ability. Then they were assessed for their LEMS scores and functional abilities, including the 10-meter walk test (10MWT), the walking index for spinal cord injury II (WISCI II), the timed up and go test (TUGT), and the 6-minute walk test (6MWT). The Mann-Whitney U test was used to compare the different findings between the participants who performed the FTSST with and without hands. The Spearman rank correlation coefficient (ρ) was applied to analyze the levels of correlation between the FTSST and standard tests (LEMS scores and functional measures). There were significant differences in the data between the participants who performed the test with and without hands (p < 0.01). The time to complete the FTSST of the participants who performed the test without hands showed moderate to strong correlation with total LEMS scores and all functional measures (ρ = -0.71 to 0.69, p < 0.001). On the contrary, the FTSST data of those who performed the test with hands were significantly correlated only with the 10MWT, TUGT, and 6MWT (ρ = -0.47 to 0.57, p < 0.01). The present findings confirm the concurrent validity of the FTSST when performed without hands for LEMS and functional mobility necessary for the ability of independence and safety of ambulatory individuals with SCI. However, the test using hands distort the ability of the outcomes to reflect LEMS and WISCI II that reflect lower limb functions. By contrast, the 10MWT, TUGT, and 6MWT allowed upper limb contribution in the tests. Therefore, outcomes of these tests showed a significant correlation to the outcomes of FTSST when assessed using hands. Consequently, the use of FTSST with or without hands needs to consider the clinical application of the outcomes, i.e., to reflect lower limb functions or mobility of the patients.

Keywords: mobility, lower limb muscle strength, clinical test, rehabilitation

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Authors: Iryna P. Dzieciuch, Michael D. Putman

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Humidity is known to degrade Navy ship electronic equipment, especially in hot moist environments. If left untreated, it can cause significant and permanent damage. Even rigorous inspection and frequent clean-up would not prevent further equipment contamination and degradation because of the constant presence of favorable growth conditions for many microorganisms. Generally, relative humidity levels of less than 60% will inhibit corrosion in electronic equipment, but because NAVY electronics often operate in hot and humid environments, prevention via dehumidification is not always possible. Currently, there is no defined research that fully describes key mechanisms which cause electronics and its coating degradation. The corrosive action of most bacteria is mainly developed through (i) mycelium adherence to the metal plates, (ii) facilitation the formation of pitting areas, (iii) production of organic acids such as citric, iso-citric, cis-aconitic, alpha-ketoglutaric, which are corrosive to electronic equipment and its components. Our approach studies corrosive action in electronic equipment: circuit-board, wires and connections that are exposed in the humid environment that gets worse during condensation. In our new approach the technical task is built on work with the bacterial communities in public areas, bacterial genetics, bioinformatics, biostatistics and Scanning Electron Microscopy (SEM) of corroded circuit boards. Based on these methods, we collect and examine environmental samples from biofilms of the corroded and non-corroded sites, where bacterial contamination of electronic equipment, such as machine racks and shore boats, is an ongoing concern. Sample collection and sample analysis is focused on addressing the key questions identified above through the following tasks: laboratory sample processing and evaluation under scanning electron microscopy, initial sequencing and data evaluation; bioinformatics and data analysis. Preliminary results from scanning electron microscopy (SEM) have revealed that metal particulates and alloys in corroded samples consists mostly of Tin ( < 40%), Silicon ( < 4%), Sulfur ( < 1%), Aluminum ( < 2%), Magnesium ( < 2%), Copper ( < 1%), Bromine ( < 2%), Barium ( <1%) and Iron ( < 2%) elements. We have also performed X 12000 magnification of the same sites and that proved existence of undisrupted biofilm organelles and crystal structures. Non-corrosion sites have revealed high presence of copper ( < 47%); other metals remain at the comparable level as on the samples with corrosion. We have performed X 1000 magnification on the non-corroded at the sites and have documented formation of copper crystals. The next step of this study, is to perform metagenomics sequencing at all sites and to compare bacterial composition present in the environment. While copper is nontoxic to the living organisms, the process of bacterial adhesion creates acidic environment by releasing citric, iso-citric, cis-aconitic, alpha-ketoglutaric acidics, which in turn release copper ions Cu++, which that are highly toxic to the bacteria and higher order living organisms. This phenomenon, might explain natural “antibiotic” properties that are lacking in elements such as tin. To prove or deny this hypothesis we will use next - generation sequencing (NGS) methods to investigate types and growth cycles of bacteria that from bacterial biofilm the on corrosive and non-corrosive samples.

Keywords: bacteria, biofilm, circuit board, copper, corrosion, electronic equipment, organic acids, tin

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Authors: Abdul Basit, Gildas Lhostis, Bernard Durand

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Shape memory polymers (SMPs) are replacing shape memory alloys (SMAs) in many applications as SMPs have certain superior properties than SMAs. However, SMAs possess some properties like recovery under stress that SMPs lack. SMPs cannot give complete recovery even under a small load. SMPs are initially heated close to their transition temperature (glass transition temperature or the melting temperature). Then force is applied to deform the heated SMP to a specific position. Subsequently, SMP is allowed to cool keeping it deformed. After cooling, SMP gets the temporary shape. This temporary shape can be recovered by heating it again at the same temperature that was given it while heating it initially. As a result, it will recover its original position. SMP can perform unconstrained recovery and constrained recovery, however; under the load, it only recovers partially. In this work, the recovery under the load of an asymmetrical shape memory composite called as CBCM-SMPC has been investigated. It is found that it has the ability to recover under different loads. Under different loads, it shows powerful complete recovery in reference to initial position. This property can be utilized in many applications.

Keywords: shape memory, polymer composite, thermo-mechanical testing, recovery under load

Procedia PDF Downloads 405

Authors: Hanbyul Kim, Hye-Jin Kin, Taehun Park, Woo Jun Sul, Susun An

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Skin is the largest organ of the human body and can provide the diverse habitat for various microorganisms. The ecology of the skin surface selects distinctive sets of microorganisms and is influenced by both endogenous intrinsic factors and exogenous environmental factors. The diversity of the bacterial community in the skin also depends on multiple host factors: gender, age, health status, location. Among them, age-related changes in skin structure and function are attributable to combinations of endogenous intrinsic factors and exogenous environmental factors. Skin aging is characterized by a decrease in sweat, sebum and the immune functions thus resulting in significant alterations in skin surface physiology including pH, lipid composition, and sebum secretion. The present study gives a comprehensive clue on the variation of skin microbiota and the correlations between ages by analyzing and comparing the metagenome of skin microbiome using Next Generation Sequencing method. Skin bacterial diversity and composition were characterized and compared between two different age groups: younger (20 – 30y) and older (60 - 70y) Xian, Chinese women. A total of 73 healthy women meet two conditions: (I) living in Xian, China; (II) maintaining healthy skin status during the period of this study. Based on Ribosomal Database Project (RDP) database, skin samples of 73 participants were enclosed with ten most abundant genera: Chryseobacterium, Propionibacterium, Enhydrobacter, Staphylococcus and so on. Although these genera are the most predominant genus overall, each genus showed different proportion in each group. The most dominant genus, Chryseobacterium was more present relatively in Young group than in an old group. Similarly, Propionibacterium and Enhydrobacter occupied a higher proportion of skin bacterial composition of the young group. Staphylococcus, in contrast, inhabited more in the old group. The beta diversity that represents the ratio between regional and local species diversity showed significantly different between two age groups. Likewise, The Principal Coordinate Analysis (PCoA) values representing each phylogenetic distance in the two-dimensional framework using the OTU (Operational taxonomic unit) values of the samples also showed differences between the two groups. Thus, our data suggested that the composition and diversification of skin microbiomes in adult women were largely affected by chronological and physiological skin aging.

Keywords: next generation sequencing, age, Xian, skin microbiome

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Authors: Siti Salbiah Samsudin, Hamzah Arof, Ainuddin Wahid Abdul Wahab, Mohd Yamani Idna Idris

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Standard X-ray spine images produced by conventional screen-film technique have a limited field of view. This limitation may obstruct a complete inspection of the spine unless images of different parts of the spine are placed next to each other contiguously to form a complete structure. Another solution to producing a whole spine image is by assembling the digitized x-ray images of its parts automatically using image stitching. This paper presents a new Medical Image Stitching (MIS) method that utilizes Minimum Average Correlation Energy (MACE) filters to identify and merge pairs of x-ray medical images. The effectiveness of the proposed method is demonstrated in two sets of experiments involving two databases which contain a total of 40 pairs of overlapping and non-overlapping spine images. The experimental results are compared to those produced by the Normalized Cross Correlation (NCC) and Phase Only Correlation (POC) methods for comparison. It is found that the proposed method outperforms those of the NCC and POC methods in identifying both the overlapping and non-overlapping medical images. The efficacy of the proposed method is further vindicated by its average execution time which is about two to five times shorter than those of the POC and NCC methods.

Keywords: image stitching, MACE filter, panorama image, scoliosis

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Authors: Betsy Hannam

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Background: Staff nurses felt overwhelmed to learn new skills or complete competencies during their shift. Med/Surg units need to provide dedicated, uninterrupted time to complete training and mandatory competencies and practice skills. Purpose: To improve nurse satisfaction and competence by creating a Skills Day with uninterrupted time to complete competencies, brush up on skills, and evaluate skills learned through pre- and post-tests. Methods: The USL and CNL interviewed nurses to obtain input regarding skills needing reinforcement and included mandatory competencies relevant to Med/Surg to create the Skills Day agenda. Content experts from multiple disciplines were invited to educate staff to help address knowledge gaps. To increase attendance, multiple class days were offered. Results: 2018 Skills Day was held for an inpatient unit with 95% participation (n=35 out of 37RNs). The average pretest score, comprised of content questions from topics discussed, was 57%, and post test scoresaveraged 80%. 94% of test scores improved or remained the same. RNs were given an evaluation at the end of the day, where100% of staff noted Skills Day as beneficial, and 97% requested to repeat next year. Another Med/Surg unit asked to join Skills Day in 2019. In 2019, with 89% participation (n=57 out 64 RNs), the average pretest score was 68%, and the average post test score was 85%. 97% of scores improved or remained the same. 98% reported the class as beneficial, and 96% requested to repeat next year. Skills Day 2020-2022 on hold due to COVID. Looking forward to Skills Day 2023. Conclusion: Skills Day allows nurses to maintain competencies and improve knowledge in areas of interest without the stress of a patient assignment. Having unit leaders organize Skills Day, with the involvement of content experts from multiple disciplines, showed to be a successful and innovative team approach to support professional development.

Keywords: education, competency, skills day, medical/surgical

Procedia PDF Downloads 78

Authors: Francesco Pantano, Marta Fogolari, Michele Iuliani, Sonia Simonetti, Silvia Cavaliere, Marco Russano, Fabrizio Citarella, Bruno Vincenzi, Silvia Angeletti, Giuseppe Tonini

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Background: Although immune checkpoint inhibitors (ICIs) have changed the treatment paradigm of non–small cell lung cancer (NSCLC), these drugs fail to elicit durable responses in the majority of NSCLC patients. The gut microbiota, able to regulate immune responsiveness, is emerging as a promising, modifiable target to improve ICIs response rates. Since the oral microbiome has been demonstrated to be the primary source of bacterial microbiota in the lungs, we investigated its composition as a potential predictive biomarker to identify and select patients who could benefit from immunotherapy. Methods: Thirty-five patients with stage IV squamous and non-squamous cell NSCLC eligible for an anti-PD-1/PD-L1 as monotherapy were enrolled. Saliva samples were collected from patients prior to the start of treatment, bacterial DNA was extracted using the QIAamp® DNA Microbiome Kit (QIAGEN) and the 16S rRNA gene was sequenced on a MiSeq sequencing instrument (Illumina). Results: NSCLC patients were dichotomized as “Responders” (partial or complete response) and “Non-Responders” (progressive disease), after 12 weeks of treatment, based on RECIST criteria. A prevalence of the phylum Candidatus Saccharibacteria was found in the 10 responders compared to non-responders (abundance 5% vs 1% respectively; p-value = 1.46 x 10-7; False Discovery Rate (FDR) = 1.02 x 10-6). Moreover, a higher prevalence of Saccharibacteria Genera Incertae Sedis genus (belonging to the Candidatus Saccharibacteria phylum) was observed in "responders" (p-value = 6.01 x 10-7 and FDR = 2.46 x 10-5). Finally, the patients who benefit from immunotherapy showed a significant abundance of TM7 Phylum Sp Oral Clone FR058 strain, member of Saccharibacteria Genera Incertae Sedis genus (p-value = 6.13 x 10-7 and FDR=7.66 x 10-5). Conclusions: These preliminary results showed a significant association between oral microbiota and ICIs response in NSCLC patients. In particular, the higher prevalence of Candidatus Saccharibacteria phylum and TM7 Phylum Sp Oral Clone FR058 strain in responders suggests their potential immunomodulatory role. The study is still ongoing and updated data will be presented at the congress.

Keywords: oral microbiota, immune checkpoint inhibitors, non-small cell lung cancer, predictive biomarker

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Authors: N. Songumpai, W. Sumranwanich, S. Chatmaneerungcharoen

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This research aims to study the understanding of 8 aspects of nature of science (NOS). The research participants were 39 General Science student teachers who were selected by purposive sampling. In 2015 academic year, they enrolled in the course of Science Education Learning Management. Qualitative research was used as research methodology to understand how the student teachers propose on NOS. The research instruments consisted of open-ended questionnaires and semi-structure interviews that were used to assess students’ understanding of NOS. Research data was collected by 8 items- questionnaire and was categorized into students’ understanding of NOS, which consisted of complete understanding (CU), partial understanding (PU), misunderstanding (MU) and no understanding (NU). The findings reveal the majority of students’ misunderstanding of NOS regarding the aspects of theory and law(89.7%), scientific method(61.5%) and empirical evidence(15.4%) respectively. From the interview data, the student teachers present their misconceptions of NOS that indicate about theory and law cannot change; science knowledge is gained through experiment only (step by step); science is the things that are around humans. These results suggest that for effective science teacher education, the composition of design of NOS course needs to be considered. Therefore, teachers’ understanding of NOS is necessary to integrate into professional development program/course for empowering student teachers to begin their careers as strong science teachers in schools.

Keywords: nature of science, student teacher, no understanding, misunderstanding, partial understanding, complete understanding

Procedia PDF Downloads 241