THE IMPLEMENTATION OF CONVERSATION IMPROVEMENT ON FISHBOWL METHOD TO IMPROVE THE SPEAKING ABILITY OF STUDENTS: A CASE STUDY OF TEACHING EFL AT SMAN 2 KUPANG

This research was conducted in Class X of SMAN 2 Kupang in the academic year 2018/2019. The subjects in this study were 36 students of class X IPA 1 of SMAN 2 Kupang. This study aimed to determine the increase in English speaking skills of students by applying the fishbowl method based on conversation improvement. This type of research was qualitative with descriptive design. Data collection techniques used in this study were tests, observations, and speaking assessment sheets. The researcher observed what students did while having a conversation in class. The researcher used 4 (four) conversation improvement strategies. In the pra research, there were 31 students (86%) failed to reach the minimum completion criteria. In the first cycle, there was an increasing of the results of students' speaking skills where 41% students reached the minimum completion criteria. At this stage, students had not shown significant improvement in linguistics aspects (such as stress, speech, tone and rhythm) and non-linguistics aspects (such as fluency and mastery of the topic). The results of the first cycle were followed up by the second cycle. The results showed that there was an increasing in the the minimum completion criteria for 88%. There were also significant improvements in linguistics aspects (such as stress, speech, tone and rhythm) and non-linguistics aspects (such as fluency and mastery of the topic)

ANALISIS PENGELOLAAN TENAGA KERJA DIFABEL BERDASARKAN PEDOMAN INTERNATIONAL LABOUR ORGANIZATION (ILO) PADA YAYASAN KELUARGA SEJAHTERA MANUNGGAL SLAWI

Semua manusia berhak mendapatkan kesempatan untuk bekerja sesuai dengan bidang yang mereka inginkan tanpa memandang fisik, suku, ras, dan agama yang dimilikinya. Para penyandang difabel adalah salah satu contoh masyarakat minoritas yang juga berhak untuk mendapatkan hak mereka untuk dapat bekerja sesuai dengan yang mereka inginkan. Namun pada kenyataannya masih sedikit organisasi yang mau menerima penyandang difabel. International Labor Organization (ILO) mendefinisikan MSDM penyandang difabel sebagai proses di organisasi yang dirancang untuk memberikan fasilitas berupa pekerjaan kepada para penyandang difabel melalui berbagai upaya yang terkoordinasi serta dengan memperhitungkan kebutuhan tiap individu, lingkungan kerja, kebutuhan organisasi serta tanggung jawab hukum. ILO juga memberikan beberapa pedoman untuk organisasi bagaimana mengelola tenaga kerja difabel yang bekerja bersamanya. Penelitian ini bertujuan untuk mengetahui bagaimana Yayasan Keluarga Sejahtera Slawi mengelola tenaga kerja difabel yang dimilikinya sesuai dengan pedoman yang diberikan oleh ILO. Penelitian ini menganalisis 4 aspek MSDM difabel yang didasarkan dari pedoman yang dibuat oleh ILO, yaitu perekrutan, promosi, mempertahankan pekerjaan, dan penyesuaian aksesibilitas dan adaptasi. Penilitan dilakukan menggunakan pendekatan deskriptif kualitatif, dengan wawancara, studi observasi, dan studi dokumentasi digunakan untuk mengumpulkan data. Data yang didapat kemudian diuji keabsahannya menggunakan triangulasi sumber dan kemudian menggunakan teknik analisis data interaktif Miles dan Huberman untuk menganalisis data tersebut. Hasil penelitian menyatakan bahwa Yayasan Keluarga Sejahtera Manunggal Slawi belum sepenuhnya sesuai dengan pedoman dari ILO dalam melakukan MSDM difabel

PRODUKSI REKOMBINAN SEFALOSPORIN ASILASE SEBAGAI BIOKATALIS UNTUK PRODUKSI ASAM 7-AMINOSEFALOSPORANAT

Production of Cephalosporin Acylase Recombinant as Biocatalyst for 7-Aminocephalosporanic Acid Production7-aminocephalosporanic acid (7-ACA) is a precursor for the production of semisynthetic cephalosporin derivatives. The enzymatic 7-ACA production can use two-stage and one-step enzymatic methods. Two-stage enzymatic method uses D-amino acid oxidase (DAAO) enzyme to produce glutaryl-7-aminocephalosporanic acid (GL-7-ACA) in the first stage and glutaryl-7-aminocephalosporanic acid acylase to produce 7-ACA in the second stage. The one-stage enzymatic method using cephalosporin acylase (CPC acylase) converts the CPC to 7-ACA directly. The aim of this research was to produce recombinant CPC acylase in Escherichia coli BL21(DE3). Transformantion culture E. coli BL21(DE3) was induced with concentrations of IPTG 0; 0.25; 0.5; 0.75; 1; 2 mM for 5 hours. The induction time of IPTG was determined at 0, 1, 2, 3, 4, and 5 hours. The results showed that CPC acylase produced by E. coli BL21(DE3) with optimum condition of CPC acylase production was 0.5 mM IPTG and optimal induction time of IPTG was 5 hours.Keywords: Cephalosporin, cephalosporin acylase, 7-ACA, protein expression, Escherichia coli BL21(DE3) ABSTRAKAsam 7-aminosefalosporanat (7-ACA) merupakan prekursor untuk produksi turunan sefalosporin semisintetik. Produksi 7-ACA secara enzimatik dapat menggunakan metode dua tahap dan satu tahap enzimatik. Metode enzimatik secara dua tahap menggunakan enzim asam D-amino oksidase (DAAO) untuk menghasilkan asam glutaril-7-aminosefalosporinat (GL-7-ACA) pada tahap pertama dan menggunakan asam glutaril-7-aminosefalosporinat asilase untuk menghasilkan 7-ACA pada tahap kedua. Metode enzimatik satu tahap dengan sefalosporin asilase (CPC asilase) mengubah CPC menjadi 7-ACA secara langsung. Tujuan penelitian adalah memproduksi rekombinan CPC asilase di dalam sel Escherichia coli BL21(DE3). Kultur Transforman E. coli BL21(DE3) diinduksi dengan konsentrasi IPTG 0; 0,25; 0,5; 0,75; 1; 2 mM selama 5 jam. Waktu induksi IPTG ditentukan pada 0, 1, 2, 3, 4 dan 5 jam. Hasil penelitian menunjukan bahwa CPC asilase diproduksi oleh E. coli BL21(DE3) dengan kondisi optimal produksi CPC asilase adalah konsentrasi IPTG 0,5 mM dan waktu induksi IPTG optimal adalah 5 jam

BIOKONVERSI SEFALOSPORIN C MENJADI ASAM 7-AMINOSEFALOSPORANAT DENGAN SEFALOSPORIN ASILASE

Cephalosporins are the most widely used class of β-lactam antibiotic in the world and clinically active against gram positive and gram negative bacteria. Cephalosporin C (CPC) is naturally produced by fungus Cephalosporiun acremonium. CPC has moderate antibacterial activity with minimum inhibitory concentration values of 25-100 µg/mL and 12-25 µg/mL for gram-positive and for gram-negative bacteria, respectively. CPC can be converted into 7-aminocephalosporonic acid (7-ACA) as intermediate compound for cephalosporin derivatives by two-steps or one-step enzymatic method. Two-step enzymatic method uses D-amino acid oxidase (DAAO) to produce glutaryl-7-amino cephalosporanic acid (GL 7-ACA) for the first step and GL-7-ACA acylase to produce 7-ACA for the second step. One-step enzymatic method uses CPC acylase to convert CPC into 7-ACA directly. Some microorganisms produce CPC acylase, such as Pseudomonas sp., Bacillus megaterium, Aeromonas sp., dan Arthrobacler. A natural CPC acylase has low activity and genetic engineering was used to increase its activity.Keywords: Cephalosporin, cephalosporin acylase, 7-ACA, genetic engineering, mutation ABSTRAKSefalosporin merupakan antibiotik golongan β-laktam yang paling banyak digunakan di dunia dan secara klinis aktif terhadap bakteri gram positif dan gram negatif. Sefalosporin C merupakan sefalosporin alami yang dihasilkan oleh kapang Cephalosporium acremonium. Sefalosporin C mempunyai aktivitas antibakteri moderat dengan nilai konsentrasi hambat minimum 25-100 µg/mL untuk bakteri gram positif dan 12-25 µg/mL untuk bakteri gram negatif. Sefalosporin C dapat diubah menjadi asam 7-aminosefalosporanat (7-ACA) sebagai senyawa antara untuk pembuatan turunan sefalosporin dengan metode enzimatik secara dua atau satu tahap. Produksi 7-ACA secara enzimatik dapat menggunakan metode dua tahap dan satu tahap enzimatik. Metode enzimatik secara dua tahap menggunakan enzim asam D-amino oksidase (DAAO) untuk menghasilkan asam glutaril-7-aminosefalosporinat (GL-7-ACA) pada tahap pertama dan menggunakan asam glutaril-7-aminosefalosporinat asilase untuk menghasilkan 7-ACA pada tahap kedua. Metode enzimatik secara satu tahap menggunakan sefalosporin asilase untuk mengubah CPC menjadi 7-ACA secara langsung. Beberapa mikroorganisme penghasil sefalosporin asilase yaitu Pseudomonas sp., Bacillus megaterium, Aeromonas sp., dan Arthrobacter. Aktivitas CPC asilase alami sangat rendah dan rekayasa genetik digunakan untuk meningkatkan aktivitasnya.Kata kunci : Sefalosporin, sefalosporin asilase, 7-ACA, rekayasa genetik, mutas

Systems-level host responses to highly and less virulent influenza A (H3N2) virus infections

Severe influenza infections have been associated with dysregulated innate immunity that involves macrophages and neutrophils. While the contributions of macrophages to the dysregulation have been broadly investigated, the contributions of neutrophils remain unclear. Hence, in this thesis, we uncovered systems-level neutrophil response to highly virulent influenza infection by employing MPRO neutrophils and highly virulent, mouse adapted H3N2 influenza virus (HVI). Firstly, we showed that HVI induced hypercytokinemia and increased antiviral (interferon) response in the infected lungs. Moreover, increased apoptotic activity and under-expression of genes associated with metabolic and developmental processes mirrored severe pathological changes in HVI-infected lungs. Following pathway analysis, we highlighted the significant roles of the TREM1 signaling pathway in enhancing cytokine expression, and linked the hypercytokinemia to metabolic defect through the activation of LPS/IL1-mediated inhibition of retinoid X receptor (RXR) function pathway. With regards to infection of MPRO neutrophils (optimally containing 20%-30% mature neutrophils, as inspected with differential counting of giemsa-stained cells and flow cytometry based on neutrophil markers), influenza virus could induce apoptosis even though its infection was abortive. Finally, we revealed that HVI mainly activated a rapid induction of type I interferon-inducible genes in MPRO neutrophils, an event that potentially contributes to the dysregulated innate immunity observed in vivo.DOCTOR OF PHILOSOPHY (SCE

Rule-based meta-analysis reveals the major role of PB2 in influencing influenza A virus virulence in mice

Background: Influenza A virus (IAV) poses threats to human health and life. Many individual studies have been carried out in mice to uncover the viral factors responsible for the virulence of IAV infections. Nonetheless, a single study may not provide enough confident about virulence factors, hence combining several studies for a meta-analysis is desired to provide better views. For this, we documented more than 500 records of IAV infections in mice, whose viral proteins could be retrieved and the mouse lethal dose 50 or alternatively, weight loss and/or survival data, was/were available for virulence classification. Results: IAV virulence models were learned from various datasets containing aligned IAV proteins and the corresponding two virulence classes (avirulent and virulent) or three virulence classes (low, intermediate and high virulence). Three proven rule-based learning approaches, i.e., OneR, JRip and PART, and additionally random forest were used for modelling. PART models achieved the best performance, with moderate average model accuracies ranged from 65.0 to 84.4% and from 54.0 to 66.6% for the two-class and three-class problems, respectively. PART models were comparable to or even better than random forest models and should be preferred based on the Occam’s razor principle. Interestingly, the average accuracy of the models was improved when host information was taken into account. For model interpretation, we observed that although many sites in HA were highly correlated with virulence, PART models based on sites in PB2 could compete against and were often better than PART models based on sites in HA. Moreover, PART had a high preference to include sites in PB2 when models were learned from datasets containing the concatenated alignments of all IAV proteins. Several sites with a known contribution to virulence were found as the top protein sites, and site pairs that may synergistically influence virulence were also uncovered. Conclusion: Modelling IAV virulence is a challenging problem. Rule-based models generated using viral proteins are useful for its advantage in interpretation, but only achieve moderate performance. Development of more advanced approaches that learn models from features extracted from both viral and host proteins shall be considered for future works.Agency for Science, Technology and Research (A*STAR)Ministry of Education (MOE)Published versionPublication of this supplement was funded by AcRF Tier 2 Grant MOE2014-T2–2-023, Ministry of Education, Singapore and A*STAR-NTU-SUTD AI Partnership Grant RGANS1905

Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches

The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain–Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine

Identification of potential critical virulent sites based on hemagglutinin of influenza A virus in past pandemic strains

The influenza pandemics have caused millions of deaths and enormous economic loss. Current circulating influenza viruses in human, avian, swine and other animals are potential to evolve into novel strains that may cause another pandemic in the future. Hence, recognizing the determinants of pandemic strains helps to raise the alarm of future pandemics. With increasingly huge biological data, computational modeling is a good technique for analyzing data, providing novel insight into significant patterns and rules. Here we define a binary classification problem of categorizing influenza strains into pandemic and non-pandemic classes based on amino acid sequences. Three rule-based algorithms are applied, namely OneR, JRip and PART, to extract rules, composed of potential critical virulent sites. The results present good performance in term of accuracy, specificity, sensitivity and F-measure (more than 0.9 on average for each). Fourteen out of the sixteen potential critical virulent sites detected in our experiments are overlapped with receptor binding sites or antigenic sites. In addition, some variations occurred in these sites are known to affect the pathogenicity of influenza viruses or to cause more severe symptom in the infected patients. The pandemic potential of uncovered sites in our study needs to be further experimentally validated.MOE (Min. of Education, S’pore)Accepted versio

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses

Abstract Background Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. Results The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. Conclusion The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses

The healthy airway mycobiome in individuals of Asian descent

Fungal infection in association with lung disease has emerged as a significant clinical problem. Owing to a ubiquitous environmental abundance, fungal spores, inhaled daily, can reach even the smallest airways. Although healthy individuals have effective immune mechanisms to clear this, individuals with anatomically abnormal airways and chronic respiratory disease (CRD) such as bronchiectasis are at higher risk of colonization and complications. Use of high-throughput sequencing has allowed insight into the pulmonary microbiome. This is well characterized for bacteria, in both healthy individuals and those with CRD; however, analysis of the fungal microbiome (the mycobiome) has lagged because of technical challenges. Despite the existence of fungi in healthy and diseased states, most published work to date has focused on CRD, in which judgments on fungal identity and burden may be confounded by use of inhaled corticosteroids and the underlying disease. This highlights a critical need to understand the airway mycobiome in healthy (nondiseased) individuals. Although the effect of aging on lung microbiomes remains to be established, our recent work illustrates that aging may potentially associate with specific microbes. Here, for the first time, we characterize the airway mycobiome in healthy subject pairs (first-degree relatives) of Asian descent.Nanyang Technological UniversityThis research is supported by the Ageing Research Institute for Society and Education (ARISE), Nanyang Technological University, Singapore [ARISE/2017/6; S.H.C]