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"Ebola adalah penyakit endemik yang telah terjadi selama tiga puluhan tahun setelah pertama kali ditemukan di daerah Afrika Barat pada tahun 1976. Penyakit ini disebabkan oleh virus ebola (EBOV) yang adalah salah satu bagian dari famili Filovoridae atau filovirus. Kasus ebola tidak dilaporkan secara intens, karena sifatnya yang endemik, namun tidak dapat dipungkiri, penyakit ini tetap memakan korban. Beberapa tahun terakhir, wabah ini merebak dan kembali menjadi pebincangan hangat. Penyebaran tersebut dikhawatirkan terjadi akibat adanya mutasi virus. Beberapa bagian lain mengkhawatirkan penggunaan virus tersebut dalam tindakan bioterorisme. Perkembangan virus dipengaruhi juga oleh proses replikasi, sehingga replikasi menjadi salah satu faktor penentu terjadinya penyakit. Pada ebola, replikasi dipengaruhi oleh protein VP35. Ilmu bioinformatika dianggap mampu menjadi salah satu cara menganalisis mutasi protein tersebut secara in silico, sehingga diharapkan para ilmuwan mampu menemukan desain inhibitor potensial untuk melawan ebola secara in vivo. Secara in silico telah diketahui perubahan yang terjadi pada VP35 virus ebola saat ini dibandingkan dengan yang ditemukan pertama kali pada tahun 1976. Perbedaan tersebut terjadi dalam hal susunan residu asam amino penyusun protein, terbukti dengan analisis pohon filogenetik, dan analisis lanjutan.

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Ebola is an endemic disease which has been happened about thirty years after its first discovered in West Africa at 1976. It caused by ebolavirus (EBOV), member of Filoviridae. The ebola cases were not intensely reported, because it’s endemic disease, but the it still causes many deaths. Lately, ebola has been the headline, since its outbreak in West Africa, March 2014, and caused more than 50% mortality. Replication is one of the virulence factor. In ebolavirus, VP35 plays role in replication system, so the in silico study of VP35 ebolavirus is required, before the in vivo. Using bioinformatics tools, the differences between the 1976’s ebolavirus and 2014’s ebolavirus has been discovered. The differences are analyzed using phylogenetic tree, and advanced analyzing."

"Demam berdarah ebola atau selanjutnya disebut dengan ebola mrupakan penyakit menular yang mematikan. Saat ini di kenal empat tipe virus penyebab ebola, tiga diantaranya dapat menyerang manusia. dengan mempertimbangkan satu dari ketiga tipe virus tersebut, dalam tugas akhir ini akan dilakukan proses pemodelan penyebaran"

"Although Ebola and similar hemorrhagic fevers have occurred in the past, both the numbers and geographic spread of the 2014-15 West African Ebola epidemic were unprecedented. Ebola and the associated risks drove an improvised, sometimes ineffective, response from political and medical authorities. Fear, rather than rational planning, drove many decisions made at population and leadership levels. Institutions, practices, economies, and governments were all deeply affected by the demands engendered by this emergency. Ultimately, the epidemic revealed serious fault lines at all levels in the theories and practices of global public health. Doctors Without Borders/Medecins sans Frontieres (MSF), as the major provider of medical care to the afflicted, was deeply entangled in many of these issues. From difficult choices made for the care of individual patients to the impact of Ebola on entire health systems, the common thread in each chapter is how fear influenced the political and medical response. Using materials from the MSF archives, this book explores this theme in ten chapters and four eyewitness vignettes. The book examines the epidemic from the perspectives of a wide range of actors from distinct sectors, including a bioethicist, a political scientist, a historian, clinical doctors, policymakers, and anthropologists."

"Virus Ebola adalah salah satu penyakit paling mematikan di dunia, dengan hampir 29.000 kasus melaporkan dan membunuh 11.000 dari mereka, tetapi tidak ada perawatan atau vaksin yang dapat melawan penyakit ini secara efektif. Penyakit ini disebabkan oleh virus ebola (EBOV), anggota utama dari keluarga Filoviridae. Siklus hidup virus ini telah dioperasikan oleh beberapa mayor protein, salah satunya adalah protein HSP70, yang telah dikenal penting peran dalam transkripsi dan replikasi EBOV. Karena itu, targetkan protein HSP70 dapat menjadi solusi untuk mengobati penyakit patogen ini. Dalam penelitian ini, skrining virtual Produk alami Indonesia dilakukan sebagai inhibitor HSP70 EBOV. Molekuler simulasi docking dilakukan untuk menguji interaksi dan afinitas ligan obligasi dengan protein HSP70 EBOV; simulasi ini dilakukan dengan menggunakan MOE 2014.09 perangkat lunak. Hasil yang diperoleh menunjukkan bahwa penghambatan HSP70 berkurang secara signifikan Replikasi EBOV dengan menggunakan ligan senyawa bahan alami Indonesia. Itu nilai bioavailabilitas diperoleh sebesar 0,56. Ini menunjukkan bahwa obat tersebut dapat digunakan secara oral.

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The Ebola virus is one of the deadliest diseases in the world, with nearly 29,000 cases reporting and killing 11,000 of them, but there is no treatment or vaccine that can fight this disease effectively. This disease is caused by the Ebola virus (EBOV), a major member of the Filoviridae family. The life cycle of this virus has been operated by several major proteins, one of which is the HSP70 protein, which has been recognized for an important role in the transcription and replication of EBOV. Therefore, targeting the HSP70 protein can be a solution to treat this pathogenic disease. In this study, virtual screening of Indonesian natural products was carried out as an EBP HSP70 inhibitor. Molecular docking simulation was carried out to test the interaction and affinity of bond ligands with the EBP HSP70 protein; This simulation was carried out using MOE 2014.09 software. The results obtained showed that HSP70 inhibition was significantly reduced by EBOV replication using ligands of Indonesian natural compounds. The bioavailability value was obtained at 0.56. This shows that the drug can be used orally."

"Ebola adalah virus penyebab fatal hemoragik pada manusia dan primata non-manusia. Virus ebola memiliki lima spesies dan yang paling mematikan ialah virus ebola Zaire. Genom virus ebola mengkodekan tujuh protein yang penting bagi siklus hidupnya dan penelitian ini dilakukan untuk menghambat VP24 virus ebola Zaire. VP24 memiliki potensi sebagai target obat karena memiliki peran penting dalam replikasi virus ebola dan penghambatan interferon sel inang. Dalam penelitian ini, senyawa terpenoid digunakan untuk menghambat VP24 Zaire secara komputasi dengan menggunakan fitur farmakofor. Terdapat 55.979 senyawa terpenoid diperoleh dari pangkalan data Pubchem kemudian ligan disaring berdasarkan sifat toksisitas melalui Osiris DataWarrior dan terdapat 3.353 ligan yang memiliki sifat toksisitas yang menguntungkan. Selanjutnya fitur farmakofor digunakan untuk menyaring ligan dan 1.375 ligan memiliki struktur yang sesuai dengan fitur farmakofor. Kemudian ligan dilakukan simulasi penambatan molekul dengan target protein dan terdapat 10 ligan terbaik berdasarkan sifat molekul dan interaksi molekuler. Selanjutnya, semua ligan dianalisa sifat farmakologisnya melalui Osiris DataWarrior, Toxtree, admetSAR, SwissADME, dan pkCSM. Akhirnya, terdapat tiga ligan terbaik yaitu Taxumairol V, Acrivastine, dan 3-O-acetyluncaric acid. Dalam penelitian ini, Taxumairol V adalah ligan terbaik untuk menghambat VP24 virus ebola Zaire karena ligan memiliki sifat molekul, interaksi molekuler, dan sifat farmakologis yang baik sebagai kandidat obat.

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Ebola is a pathogenic virus which causes fatal hemorrhagic fever in humans and non-human primates. Ebolavirus has five species, and there is the most pathogenic of ebolavirus namely Zaire ebolavirus. Ebola virus genome encodes seven protein which important for the ebolavirus life cycle and in this research was conducted to inhibit VP24 Zaire ebolavirus. VP24 has potential as a drug target because VP24 has an essential role in replication and interferon inhibition. In this research, 55,979 terpenoid compounds were obtained from PubChem database then the ligands were screened based on toxicity properties through Osiris DataWarrior, and there were 3,353 ligands which have beneficial toxicity properties. Afterward, the pharmacophore features were used to screen all ligands and 1,375 ligands have suitable structures according to the pharmacophore features. All ligands were docked with the protein target, and there were ten best ligands based on the molecular properties and interactions. Furthermore all ligands were investigated their pharmacological properties through Osiris DataWarrior, Toxtree, admetSAR, SwissADME, and pkCSM. Finally, there were three best ligands namely, Taxumairol V, Acrivastine, and 3-O-acetyluncaric acid. In this study, Taxumairol V was the best ligand to inhibit VP24 Zaire ebolavirus because the ligand has good molecular interactions, molecular and pharmacological properties."

"[Salah satu tujuan dalam studi ekpresi gen (DNA/Protein) adalah menemukan subbagianyang penting secara biologis dan kelompok-kelompok dari gen-gen. Pengelompokan gen tersebut dapat dilakukan dengan metode hirarki maupun metode partisi. Kedua metode pengelompokan dapat dikombinasikan, dimanadilakukan fase partisi dan hirarki secara bergantian, metode ini dikenal dengan metode Hopach. Tahap partisi dapat dilakukan dengan metode PAM, SOM, atau K-Means. Proses partisi dilanjutkan dengan proses Ordered, baru kemudian dikoreksi dengan proses agglomorative, sehingga hasil pengelompokan menjadi lebih akurat. Dalam menentukan kelompok utama digunakan ukuran MSS (Median Split Silhouette). MSS mengukur homogenitas hasil pengelompokan,dimana hasil pengelompokan yang dipilih adalah yang meminimumkan MSS. Pada pengelompokan 136 barisan DNA Virus Ebola dari GeneBank. Prosesawalnya dilakukan pensejajaran global, dan dilanjutkan dengan perhitungan jarak genetik dengan menggunakan koreksi Jukes-Cantor. Pada penelitian ini didapat jarak genetik maksimum adalah 0.6153407 sedangkan jarak genetik minimum adalah 0. Selanjutnya matriks jarak genetik dapat dijadikan dasar untuk mengelompokkan barisan-barisan tersebut dengan menggunakan metode Hopach. Pada hasil pengelompokan Hopach-PAM, diperoleh kelompok utama sebanyak 10 kelompok dengan nilai MSS sebesar 0,8873843. Kelompok-kelompok virus ebola dapat diidentifikasikan berdasarkan subspesies dan tahun pertama kali mewabah.Proses pensejajaran global dan pengelompokan Hopach-PAM menggunakan bantuan program open source R.

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One goal in the study of gene expression (DNA/Protein) is finding biologically important subsets and clusters of genes. Clustering these genes can be achieved by hierarchical and partitioning methods. Both clustering methods can be combined, where partition and hierarchy phases can be executed alternately, this method is known as a Hopach method. The partitioning step can be done by the PAM, SOM, or K-Means clustering method. The partition process continued with the process of Ordered, then corrected with agglomorative process, so that the clustminering results become more accurate. The main clusters determine by using MSS

(Median Split Silhouette). MSS is used to measure homogeneity of the clustering result, in which the clustering is selected to minimize its MSS. The clustering procceses of 136 DNA sequences of Ebola virus, are started by performing a global alignment, and continued with the genetic distance calculations using

Jukes-Cantor correction. In this research we found the maximum genetic distance is 0.6153407, meanwhile the minimum genetic distance is 0. Furthermore, the genetic distance matrix can be used as a basis for clustering sequences in Hopach-PAM clustering method. Based on, the clustering results, we obtained 10 major clusters with MSS value of 0.8873843. Ebola virus clusters can be identified by subspecies and the first occoring year of their outbreak. We implemented the global alignment process and Hopach-PAM clustering algorithm using the open source program R.;One goal in the study of gene expression (DNA/Protein) is finding biologically important subsets and clusters of genes. Clustering these genes can be achieved by hierarchical and partitioning methods. Both clustering methods can be combined, where partition and hierarchy phases can be executed alternately, this method is known as a Hopach method. The partitioning step can be done by the PAM, SOM, K-Means clustering method. The partition process continued with the process

of Ordered, then corrected with agglomorative process, so that the clustmineringresults become more accurate. The main clusters determine by using MSS (Median Split Silhouette). MSS is used to measure homogeneity of the clustering result, in which the clustering is selected to minimize its MSS. The clustering procceses of 136 DNA sequences of Ebola virus, are started by performing a global alignment, and continued with the genetic distance calculations using Jukes-Cantor correction. In this research we found the maximum genetic distance is 0.6153407, meanwhile the minimum genetic distance is 0. Furthermore, the genetic distance matrix can be used as a basis for clustering sequences in Hopach-PAM clustering method. Based on, the clustering results, we obtained 10 major clusters with MSS value of 0.8873843. Ebola virus clusters can be identified by subspecies and the first occoring year of their outbreak. We implemented the global alignment process and Hopach-PAM clustering algorithm using the open

source program R., One goal in the study of gene expression (DNA/Protein) is finding biologically

important subsets and clusters of genes. Clustering these genes can be achieved by

hierarchical and partitioning methods. Both clustering methods can be combined,

where partition and hierarchy phases can be executed alternately, this method is

known as a Hopach method. The partitioning step can be done by the PAM, SOM,

or K-Means clustering method. The partition process continued with the process

of Ordered, then corrected with agglomorative process, so that the clustminering

results become more accurate. The main clusters determine by using MSS

(Median Split Silhouette). MSS is used to measure homogeneity of the clustering

result, in which the clustering is selected to minimize its MSS. The clustering

procceses of 136 DNA sequences of Ebola virus, are started by performing a

global alignment, and continued with the genetic distance calculations using

Jukes-Cantor correction. In this research we found the maximum genetic distance

is 0.6153407, meanwhile the minimum genetic distance is 0. Furthermore, the

genetic distance matrix can be used as a basis for clustering sequences in Hopach-

PAM clustering method. Based on, the clustering results, we obtained 10 major

clusters with MSS value of 0.8873843. Ebola virus clusters can be identified by

subspecies and the first occoring year of their outbreak. We implemented the

global alignment process and Hopach-PAM clustering algorithm using the open

source program R.]"

"ABSTRAKWabah penyakit Ebola di Afrika Barat yang meledak pada tahun 2014 menyebabkan dampakkerugian yang besar pada bidang ekonomi, politik dan sosial sehingga mendorong PBBmengeluarkan Resolusi 2177. Disusul pada tahun 2015, terjadi peningkatan penularan penyakitMERS dari Timur Tengah sampai ke wilayah Korea Selatan dan ASEAN. Ebola dan MERSmerupakan jenis penyakit Zoonosis, yaitu penyakit (infeksi) yang dapat menular dari hewan kemanusia dan sebaliknya. Untuk mencegah masuknya penyakit Zonosis dari luar negeri ke Indonesiadiperlukan kondisi Biosecurity disertai dengan Sistem Kesehatan Nasional yang kuat. Hal tesebutdisebabkan karena perang Asimetrik (Asymetric Warfare) dewasa ini tidak hanya melibatkan senjatakonvensional, namun juga wabah penyakit dan penguasaan ekonomi.Kebarhasilan penanganan penyakit Zoonosis juga dipengaruhi oleh kemampuan industrivaksin nasional suatu negara. Indonesia merupakan salah satu negara dengan potensi penyakitzoonosis (terutama tropical disease) yang besar. Kemandirian suatu negara untuk membuat vaksinsendiri dari penyakit-penyakit zoonosis yang mewabah akan meningkatkan kemampuan Biosecuritynegara tersebut, sehingga tidak terlalu bergantung dan dapat ?disetir? oleh industri vaksin global.Tesis ini membahas mengenai penilaian terhadap ancaman dan peluang Biosecurity di Indonesia,yang salah satunya melibatkan kemampuan industri vaksin nasional. Melalui faktor-faktor yangberpengaruh terhadap obyek penelitian, penelitian ini memberikan penjelasan (eksplanasi) terhadapkondisi kemampuan Biosecurity Nasional. Penilaian terhadap kondisi Biosecurity Nasional inidiharapkan dapat digunakan sebagai rekomendasi bagi stakeholder terkait untuk melihat danmengevaluasi bagaimana peluang dan ancaman pengembangan industri vaksin di masa mendatang

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ABSTRACTEbola Virus Disease (EVD) outbreaks in West Africa that was exploded in 2014 causinghuge impact on economic, political and social. The spread of Ebola and this impact encouraged theUnited Nations to adopt Resolution 2177. One year after Ebola outbreak, in 2015, the case numberof another zoonotic disease like Middle East Respiratory Syndrome (MERS) have increased, andtransmitted to South Korea and also to ASEAN region. Ebola and MERS are zoonotic disease thatcan be transmitted from animals to human. Indonesia needs strong Biosecurity to prevent zoonoticdisease from another country or region. Biosecurity condition is accompanied by a strong NationalHealth System. Asymmetric warfare involves not only conventional weapons, but also the uses ofdiseases and control of the economy.The ability of handling zoonotic diseases in a country is also affected by the condition oftheir national vaccine industry. Indonesia is one country with the potential for zoonotic diseases(called tropical disease country). The independence of a country to make its own vaccine willincrease the ability of Biosecurity of the country, so it is not too dependent and can be "driven" bythe global vaccine industry. This thesis discusses the assessment of the threats and opportunities forBiosecurity in Indonesia, one of which involves the ability of national vaccine industry. This researchalso provides an explanation of the condition of the ability of the National Biosecurity. Anassessment of the condition of the National Biosecurity is expected to be used as recommendations tothe relevant stakeholders to see and evaluate how the opportunities and threats in IndonesianBiosecurity in the future."

"ABSTRAKPenyakit Ebola disebabkan oleh virus Ebola yang termasuk dalam keluarga virus floviridae. Penyakit ini menyebar melalui kontak langsung dengan cairan tubuh individu terinfeksi. Dalam penelitian ini, dibahas mengenai model matematika transmisi penyakit ebola dengan relapse dan reinfeksi. Penyakit tersebut dimodelkan dengan menggunakan sistem persamaan diferensial biasa berdimensi tujuh. Model ini menunjukkan adanya fenomena backwards bifurcation yang dianalisa dengan memperhatikan perubahan arah pada titik keseimbangan endemik. Eksistensi backward bifurcation pada model penyakit Ebola dikarenakan adanya relapse dan reinfeksi sehingga terdapat titik keseimbangan endemik saat basic reproduction number R0 kurang dari satu. Jumlah total kasus baru individu terinfeksi Ebola meningkat dengan meningkatnya nilai parameter relapse dan reinfeksi.

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ABSTRACTEbola disease is caused by the Ebola virus which belongs to the floviridae virus family.This disease spreads through direct contact with the body fluids of infected individuals.In this undergraduate thesis, we discussed the mathematical model of Ebola diseasetransmission with relapse and reinfection. This infection is modeled using systemof seven dimensions ordinary differential equation. This model shows the backwardbifurcation phenomenon that is analyzed by considering the direction change in theendemic equilibrium point. The existence of backward bifurcation in the Ebola diseasemodel is due to relapse and reinfection so there is an endemic equilibrium point whenbasic reproduction number R0 is less than one. The total number of new cases ofindividuals infected with Ebola increases with increasing values of the parameters relapseand reinfection."

"Virus Ebola (EBOV) adalah salah satu virus paling mematikan di dunia yang memiliki virus wabah pada tahun 2014 di Afrika Barat. Ada lima jenis virus Ebola, Zaire (ZEBOV), Sudan (SEBOV), Pantai Gading (CEBOV), dan Bundibugyo (BEBOV). Virus ini sudah terbunuh sekitar 11.310 hidup dari 28.616 kasus, dan sampai sekarang tidak ada antivirus untuk EBOV. Salah satunya protein potensial yang bisa dihambat adalah Nucleoprotein (NP). EBOV NP ini memiliki fungsi sebagai replikasi virus dan perancah untuk protein virus tambahan. Dengan menghambat virus ini, itu dapat memotong replikasi RNA dan mengakhiri siklus hidup virus EBOV. Dari sebelumnya penelitian, Fu et al, menyatakan bahwa EBOV NP dapat disisipkan dengan asam 18β-glycyrrhetinic dan licochalcone A. Dalam penelitian ini, kami menggunakan modifikasi asam 18β-glycyrrhetinic dan licochalcone A menggunakan metode farmakofor untuk menghambat EBOV NP dan membandingkan yang terbaik ADMET mencetak skor untuk mendapatkan ligan baru sebagai penghambat nukleoprotein. Penelitian ini menggunakan MOE (Lingkungan Operasi Molekuler) 2014.09 dan DataWarrior v4.7.3. Ini dimodifikasi ligan ingin memiliki hasil yang lebih baik daripada ligan standar. Dalam penelitian ini, dimodifikasi senyawa 541 dari asam 18β-glycyrrhetinic dan senyawa termodifikasi 207 dari licochalcone A dipilih sebagai antivirus EBOV.

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The Ebola Virus (EBOV) is one of the deadliest viruses in the world that had an outbreak virus in 2014 in West Africa. There are five types of Ebola viruses, Zaire (ZEBOV), Sudan (SEBOV), Ivory Coast (CEBOV), and Bundibugyo (BEBOV). This virus has been killed around 11,310 lives out of 28,616 cases, and until now there is no antivirus for EBOV. One of the potential proteins that can be inhibited is Nucleoprotein (NP). This EBOV NP has a function as a viral replication and scaffold for additional viral proteins. By inhibiting this virus, that can cut RNA replication and end the life cycle of the EBOV virus. From previous studies, Fu et al. Stated that EBOV NP can be inserted with 18β-glycyrrhetinic acid andlicochalcone A. In this study, we used a modification of 18β-glycyrrhetinic acid and licochalcone A used a pharmacophore method to inhibit EBOV NP and compared the best ADMET score to get a new ligand as a nucleoprotein inhibitor. This research uses MOE (Molecular Operating Environment) 2014.09 and DataWarrior v4.7.3. This modified ligand wants to have better results than standard ligands. In this study, it was modified compound 541 from 18β-glycyrrhetinic acid and 207 modified compound from licochalcone A selected as an EBOV antivirus."

"The outbreak of Ebola virus disease in West Africa shocked the world as the disease spread rapidly from its origin to neighboring countries, Europe, and North America while the systems in place to handle such an epidemic failed. The United Nations, the World Health Organization, and major international humanitarian organizations scrambled to respond as thousands died and infections spiraled out of control. All are now contemplating: What went wrong, and how do we stop it from happening again? Global Management of Infectious Disease After Ebola is the first and most comprehensive volume to address these questions. It brings together the analyses and retrospectives of diplomats, scholars, and advocates studying from afar, as well as those of physicians and front-line responders who witnessed the epidemic sweep through already poor, devastated countries as their nascent health systems collapsed. The volume assesses not only the global response to Ebola but also current and emerging infectious disease threats, changes in the global system to handle them, and the critical ethics and human rights issues that will shape the next episode in the perpetual struggle against infectious disease."