Hasil Pencarian  ::  Simpan CSV :: Kembali

Abstrak :
MERS merupakan penyakit menular yang disebabkan oleh Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Masalah kontrol optimal dari pengontrolan epidemi penyakit MERS dengan intervensi masker kesehatan (u1), kampanye kesehatan mengenai pentingnya masker kesehatan (u2) dan pengobatan (u3) bertujuan untuk meminimalkan jumlah individu yang terinfeksi MERS sembari meminimalkan biaya intervensi. Sistem optimalitas diperoleh dengan menggunakan prinsip Pontryagin dan diselesaikan secara numerik berdasarkan metode gradient descent. Hasil simulasi numerik menunjukkan bahwa intervensi masker kesehatan, kampanye kesehatan, dan pengobatan yang bergantung terhadap waktu dapat mengurangi jumlah infeksi MERS secara signifikan. Strategi dalam mengontrol penyebaran penyakit MERS lebih baik jika mendahulukan strategi pencegahan endemik dari pada strategi penanggulangan. Hal ini ditunjukkan melalui nilai fungsi biaya pada strategi pencegahan hanya mencapai kurang lebih 10% dari biaya strategi penanggulangan. Selain itu, jika terdapat keterbatasan biaya sedemikian sehingga jenis intervensi hanya diperbolehkan satu jenis (masker saja atau pengobatan saja), maka intervensi masker jauh lebih baik untuk diimplementasikan. Namun apabila endemik telah terjadi, intervensi masker harus tetap di implementasikan bersama dengan intervensi pengobatan agar endemik segera menurun. ...... MERS is an infectious disease caused by Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Optimal control problem of controlling epidemics of MERS disease with interventions of medical mask (u1), medical campaigns about importance of medical mask (u2) and supportive care (u3) aiming to minimize the number of individual infected MERS while minimizing the cost of intervention. The optimality system is derived using Pontryagin principle and then solved numerically using the gradient descent method. The results from numerical simulation show that the intervention of medical mask, medical campaigns and supportive care depend on time will be suppressed number of MERS infection significantly. Strategy of controlling epidemics of MERS disease is better if prioritizing prevention strategy than reduction strategy. This is shown through the value of the cost function on prevention strategy only achieve approximately 10% of the cost reduction strategy. In addition, if there are cost limitations such kind of intervention is allowed only one type (only mask or only supportive care), then intervention with medical mask is much better to be implemented. However, if the endemic has occurred, intervention of medical mask should be implemented with intervention of supportive care to make endemic immediately decline.

Abstrak :
[ABSTRAK
Hierarchical clustering merupakan metode yang efektif dalam membentuk pohon filogenetik dengan mengetahui matriks jarak antar barisan DNA. Salah satu cara untuk membuat matriks jarak yaitu dengan cara menggunakan metode -mer. Kelebihan dari metode -mer yaitu lebih efisien dalam segi waktu. Langkahlangkah dalam membuat matriks jarak dengan metode -mer dimulai dengan membentuk -mer sparse matrix dari masing barisan DNA. Selanjutnya, membentuk -mer singular value vector. Pada tahap akhir yaitu menghitung jarak antar vektor. Pada tesis ini akan dilakukan analisis terhadap barisan DNA MERSCoV dengan mengimplementasi Hierarchical clustering menggunakan -mers sparse matrix sehingga dapat diketahui leluhur dari masing-masing barisan DNA MERS-CoV.

---

ABSTRACT
Hierarchical clustering is an effective method in creating phylogenetic by knowing the distance matrix between DNA sequence. One of methods to make the distance matrix use -mer method. -mer is more efficient than others. The steps to make distance matrix using -mer method starts from creating -mer sparse matrix. Then, creating -mer singular value vector. The last steps is counting distance each vectors. This thesis will analyze the sequence of DNA MERS-CoV by implementing Hierarchical clustering using k-mers sparse matrix so that will be known the ancestor of each sequence of DNA MERS-CoV., Hierarchical clustering is an effective method in creating phylogenetic by knowing the distance matrix between DNA sequence. One of methods to make the distance matrix use -mer method. -mer is more efficient than others. The steps to make distance matrix using -mer method starts from creating -mer sparse matrix. Then, creating -mer singular value vector. The last steps is counting distance each vectors. This thesis will analyze the sequence of DNA MERS-CoV by implementing Hierarchical clustering using k-mers sparse matrix so that will be known the ancestor of each sequence of DNA MERS-CoV.]

Abstrak :
Model penyebaran penyakit MERS dengan intervensi masker kesehatan, kampanye kesehatan mengenai pentingnya menggunakan masker, dan pengobatan dibahas pada skripsi ini. Model deterministik dibuat dengan menggunakan sistem persamaan diferensial biasa berdimensi lima yang merepresentasikan lima kelompok individu yaitu individu rentan (S1), individu rentan dengan masker kesehatan (S2), individu terinfeksi (I1), individu terinfeksi dengan masker kesehatan (I2), dan individu pulih (R). Kajian analitik dan numerik digunakan untuk menjelaskan keberadaan titik keseimbangan dan basic reproduction number (R0) pada model. Dari kajian analitik dan numerik, didapatkan bahwa titik kesetimbangan bebas penyakit stabil asimtotik lokal jika R0<1 dan tidak stabil jika R0>1. Dari analisis sensitivitas terhadap R0 dan simulasi numerik, dapat ditunjukkan bahwa intervensi masker kesahatan jauh lebih baik dalam mengontrol penyebaran penyakit MERS dibandingkan dengan intervensi pengobatan. ...... A mathematical model for the spread of MERS with various interventions such as medical mask, medical campaign about importance of medical mask, and supportive care is discussed in this thesis. The deterministic model is constructed using SIR model in five dimensional system which interpreted as five different human subpopulations such as susceptible human (S1), susceptible human with medical mask (S2), infected human (I1), infected human with medical mask (I2), and recovered human (R). Analytical and numerical analysis are used to explain the existence of equilibrium points and basic reproduction number R0 of the model. We find that the disease free equilibrium point is locally asymptotic stable if R0<1 and unstable if R0>1. According to the sensitivity analysis of R0, we find that the intervention of medical mask along with campaign about its importance is much better rather than medical treatment intervention to control the spread of MERS.

Abstrak :
Respiratory Syndrome (MERS) telah menyebar ke Korea Selatan sejak bulan Mei sampai Juli 2015 dan terdapat 185 kasus infeksi dengan 36 kasus kematian, menjadikan Korea Selatan sebagai negara dengan kasus MERS tertinggi di luar Semenanjung Arab.Korea Disease Control and Prevention Agency (KDCA), sebagai instansi pencegahan dan pengendalian bencana dinilai gagal dalam melakukan pengawasan, pengendalian penyebaran dari rumah sakit ke rumah sakit, dan komunikasi risiko. Kegagalan ini mendorong KDCA untuk mengevaluasi perencanaan kesiapsiagaan menghadapi wabah penyakit yang akan datang. Dengan menerapkan metode deskriptif-analisis, penelitian ini menjelaskan bentuk refleksi KCDA pasca MERS sampai menghadapi pandemi Covid-19 tahun 2020. Hasil penelitian menunjukkan bahwa refleksi perencanaan kesiapsiagaan KCDA menghadapi wabah penyakit dinilai cukup efektif dengan terciptanya strategi penanganan Covid-19 di Korea Selatan bernama 3T (test, trace, treatment). ......Middle East Respiratory Syndrome (MERS) has spread to South Korea from May to July 2015 and there have been 185 cases of infection with 36 deaths, making South Korea the country with the highest MERS cases outside the Arabian Peninsula. The Korea Disease Control and Prevention Agency (KDCA), considered to have failed in carrying out supervision, controlling hospital-to-hospital transmission, and risk communication. This failure prompted KDCA to evaluate its preparedness plans for the upcoming disease outbreak. By applying the descriptive-analytical method, this study explains the form of reflection of KCDA after MERS to face the Covid-19 pandemic in 2020. The results show that the reflection of KCDA's preparedness planning to face disease outbreaks is considered quite effective with the creation of a Covid-19 handling strategy in South Korea called 3T. (test, trace, treatment).

Abstrak :
[ABSTRAK
Berdasarkan data WHO tahun 2014, diperkirakan sekitar 15 juta orang di dunia yang terinfeksi hepatitis B (HBsAg+) juga terinfeksi hepatitis D. Infeksi hepatitis D dapat terjadi bersamaan (koinfeksi) atau setelah seseorang terkena hepatitis B kronis (superinfeksi). Penyakit hepatitis B disebabkan oleh virus HBV dan penyakit hepatitis D disebabkan oleh virus HDV. HDV tidak dapat hidup tanpa HBV. Hepatitis D erat hubungannya dengan infeksi virus HBV, sehingga sangat realistis bila setiap usaha pencegahan terhadap hepatitis B, maka secara tidak langsung mencegah hepatitis D. Pada tesis ini akan dibahas bagaimana hasil pengelompokan barisan DNA HBV menggunakan algoritma k-means clustering dengan menggunakan perangkat lunak R. Dimulai dengan mengumpulkan barisan DNA HBV yang diambil dari GenBank, kemudian dilakukan ekstraksi ciri menggunakan n-mers frequency, dan hasil ekstraksi ciri barisan DNA tersebut dikumpulkan dalam sebuah matriks dan dilakukan normalisasi menggunakan normalisasi min-max dengan interval [0, 1] yang akan digunakan sebagai data masukan. Jumlah cluster yang dipilih dalam penelitian ini adalah dua dan penentuan centroid awal dilakukan secara acak. Pada setiap iterasi dihitung jarak masing-masing objek ke masing-masing centroid dengan menggunakan Euclidean distance dan dipilih jarak terpendek untuk menentukan keanggotaan objek di suatu cluster sampai akhirnya terbentuk dua cluster yang konvergen. Hasil yang diperoleh adalah virus HBV yang berada pada cluster pertama lebih ganas dibanding virus HBV yang berada pada cluster kedua, sehingga virus HBV pada cluster pertama berpotensi berevolusi dengan virus HDV menjadi penyebab penyakit hepatitis D.

---

ABSTRACT
Based on WHO data, an estimated of 15 millions people worldwide who are infected by hepatitis B (HBsAg+) are also infected by hepatitis D. Hepatitis D infection can occur simultaneously with hepatitis B (co infection) or after a person is exposed to chronic hepatitis B (super infection). Hepatitis B is caused by the HBV virus and hepatitis D is caused by HDV virus. HDV can not live without HBV. Hepatitis D virus is closely related to HBV infection, hence it is really realistic that every effort of prevention against hepatitis B can indirectly prevent hepatitis D. This thesis discussed the clustering of HBV DNA sequences by using k-means clustering algorithm and R programming. Clustering processes is started with collecting HBV DNA sequences that are taken from GenBank, then performing extraction HBV DNA sequences using n-mers frequency and furthermore the extraction results are collected as a matrix and normalized using the min-max normalization with interval [0, 1] which will later be used as an input data. The number of clusters is two and the initial centroid selected of cluster is choosed randomly. In each iteration, the distance of every object to each centroid are calculated using the Euclidean distance and the minimum distance are selected to determine the membership in a cluster until two convergent clusters are created. As the result, the HBV viruses in the first cluster is more virulent than the HBV viruses in the second cluster, so the HBV viruses in the first cluster can potentially evolve with HDV viruses that cause hepatitis D., Based on WHO data, an estimated of 15 millions people worldwide who are infected by hepatitis B (HBsAg+) are also infected by hepatitis D. Hepatitis D infection can occur simultaneously with hepatitis B (co infection) or after a person is exposed to chronic hepatitis B (super infection). Hepatitis B is caused by the HBV virus and hepatitis D is caused by HDV virus. HDV can not live without HBV. Hepatitis D virus is closely related to HBV infection, hence it is really realistic that every effort of prevention against hepatitis B can indirectly prevent hepatitis D. This thesis discussed the clustering of HBV DNA sequences by using k-means clustering algorithm and R programming. Clustering processes is started with collecting HBV DNA sequences that are taken from GenBank, then performing extraction HBV DNA sequences using n-mers frequency and furthermore the extraction results are collected as a matrix and normalized using the min-max normalization with interval [0, 1] which will later be used as an input data. The number of clusters is two and the initial centroid selected of cluster is choosed randomly. In each iteration, the distance of every object to each centroid are calculated using the Euclidean distance and the minimum distance are selected to determine the membership in a cluster until two convergent clusters are created. As the result, the HBV viruses in the first cluster is more virulent than the HBV viruses in the second cluster, so the HBV viruses in the first cluster can potentially evolve with HDV viruses that cause hepatitis D.]

Abstrak :
Model deterministik penyebaran penyakit Middle East Respiratory Syndrome MERS pada skripsi ini melibatkan interaksi antara populasi manusia dan populasi unta di daerah peternakan. Model matematika pada penyebaran penyakit MERS disajikan dengan intervensi rawat inap pada populasi manusia dan vaksinasi pada populasi unta. Proporsi konstan akan diberikan kepada kelompok manusia yang memiliki pekerjaan di area rumah sakit, kawasan peternakan dan tidak di kedua tempat tersebut. Ada lima titik kesetimbangan yang diperoleh pada model, yaitu titik kesetimbangan bebas penyakit pada kedua populasi, titik keseimbangan bebas penyakit pada populasi manusia saja, titik keseimbangan bebas penyakit pada populasi unta saja, titik keseimbangan endemik tanpa dan dengan intervensi. Eksistensi titik-titik kesetimbangan dan kriteria kestabilitan lokal diberikan de- ngan pendekatan analitik dan numerik. Basic reproduction number R0 sebagai ambang batas endemik diberikan secara analitik dengan pendekatan next-generation matrix. Dari analisis sensitivitas R0 dan simulasi numerik terhadap parameter intervensi, ditemukan bahwa intervensi rawat inap dapat menekan penyebaran penyakit MERS pada populasi terinfeksi manusia dan intervensi vaksinasi pada unta dapat membuat penyakit MERS dapat punah dari populasi unta pada suatu waktu. ...... A deterministic model of Middle East Respiratory Syndrome MERS spread involving mass interaction between human and camel in a ranch area will be introduced in this thesis. This mathematical model for the spread of MERS with Intervention of medical treatment to human population and vaccination in camel population included in to the model. Constant proportions will be given to separate group of human who has a daily activity in a hospital area, ranch area and not in these both place. There are four equilibrium points respect to the introduced model, i.e. completely disease free equilibrium, disease free equilibrium in human population only, disease free equilibrium in camel population only, and endemic equilibrium. Existence and local stability criteria of equilibrium points are given from analytic and numerical approach. Basic reproduction number as an endemic threshold given analytically with next generation matrix approach. From sensitivity analysis of basic reproduction number and numerical simulation to the parameters of the intervention we find that inpatient intervention could suppress the spread of MERS disease in human infected populations and vaccination intervention in camels could make MERS disease extinct from camel populations at some time.

Abstrak :
Middle East Respiratory Syndrome (MERS) adalah penyakit sistem pernafasan yang baru-baru ini terjadi telah dikenali pada manusia. Sejak kasus ini pertama kali diterbitkan di Arab Saudi pada 2012, penyakit ini telah menyebar ke beberapa negara lain seperti Uni Emirat Arab, Irak, dan Korea Selatan. MERS disebabkan oleh virus bernama Middle East Respiratory Syndrome Coronavirus (MERS-CoV) yang juga ditemukan di unta. Dari beberapa laporan, dinyatakan bahwa manusia yang bekerja di area peternakan memiliki risiko lebih besar untuk terinfeksi oleh MERS. Di sini dalam presentasi ini, model matematika dari penyebaran penyakit MERS dengan intervensi, yang vaksinasi pada unta di daerah peternakan, dan rawat inap di manusia yang terinfeksi dipertimbangkan. Sepele, dengan memberikan sebanyak mungkin intervensi kepada individu mungkin bisa mengurangi penyebaran penyakit MERS lebih optimal, tetapi biaya tambahan yang terjadi sangat tinggi. Oleh karena itu, diperlukan strategi intervensi yang optimal. Strategi ini dapat dimodelkan menjadi masalah kontrol yang optimal dengan tujuan untuk mengatur angka individu yang harus disembuhkan dengan biaya minimum. Prinsip Maksimum Pontryagin digunakan untuk membangun karakteristik dari masalah kontrol optimal yang sesuai. Simulasi numerik dilakukan untuk memodelkan beberapa skenario yang mungkin di lapangan, termasuk perbedaan dalam biaya intervensi, preferensi untuk intervensi kontrol tunggal, dan potensi interaksi lingkungan yang bersifat endemik dan non-endemik. Dari tiga simulasi di atas, disimpulkan bahwa rawat inap dan vaksinasi berhasil dalam mengurangi jumlah kasus MERS. Tetapi jika biayanya terbatas, disarankan untuk memilih rawat inap saja, karena jauh lebih efektif daripada vaksinasi.

---

Middle East Respiratory Syndrome (MERS) is a respiratory system disease that has recently been recognized in humans. Since the case was first published in Saudi Arabia in 2012, the disease has spread to several other countries such as the United Arab Emirates, Iraq and South Korea. MERS is caused by a virus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV) which is also found in camels. From a number of reports, it was stated that humans who work in livestock areas have a greater risk of being infected by MERS. Here in this presentation, a mathematical model of the spread of MERS disease by intervention, the vaccination of camels in farm areas, and hospitalization in infected humans is considered. Trivial, by giving as many interventions as possible to individuals might reduce the spread of MERS disease more optimally, but the additional costs incurred are very high. Therefore, an optimal intervention strategy is needed. This strategy can be modeled into optimal control problems with the aim of organizing numbers individuals who must be cured at a minimum cost. Pontryagin's Maximum Principle is used to build the characteristics of the optimal optimal control problem. Numerical simulations are carried out to model a number of possible scenarios in the field, including differences in intervention costs, preferences for single control interventions, and potential environmental interactions that are endemic and non-endemic. From the three simulations above, it was concluded that hospitalization and vaccination were successful in reducing the number of MERS cases. But if the costs are limited, it is advisable to choose hospitalization, because it is far more effective than vaccination.

Abstrak :
The global widespread mortality after the emergence of SARS-CoV-2 infection in China, has become a critical concern all around the world. Convalescent plasma (CP) therapy is one of the methods elevating the survival rate for COVID-19 infection cases. This technique, as a practicable therapy, was used in previous viral outbreaks including influenza, SARS and MERS. In CP therapy, the blood plasma is collected from persons rehabilitated from that specific infection in order to develop a passive immunity in other patients. Therefore, this review aimed to point out the role of CP therapy in aforementioned viral infections and illustrate different factors influencing the efficacy of CP therapy.

Abstrak :
ABSTRAK
Pada Juni 2012, suatu virus korona, yang selanjutnya dikenal dengan Mers-CoV, terdeteksi pada seorang pria di Arab Saudi. Sejak saat itu, virus tersebut menyebar dengan cepat ke kawasan lain di Timur Tengah dan berbagai negara lain. Oleh karena itu, pada tesis ini diajukan suatu model penyebaran penyakit Mers yang melibatkan populasi manusia dan unta untuk kemudian dianalisa besaran basic reproduction numbernya (R0) sebagai indikator keendemikan pada populasi, dianalisa kecepatan minimum penyebarannya, serta dianalisa pengaruh pergerakan difusi dari individu terinfeksi terhadap kecepatan minimum penyebarannya. Keberadaan titik keseimbangan dan kestabilannya dipengaruhi oleh R0 yang diperoleh dari spektral radius dari matriks Next Generation-nya. Dari analisa terhadap model spasial, ditemukan kecepatan minimum dari penyebaran Mers yang menghubungkan titik keseimbangan bebas penyakit dengan titik keseimbangan endemik. Hasil tersebut ditampilkan sebagai solusi traveling wave dengan simulasi numerik melalui pendekatan finite difference. Dari kajian analisis terhadap R0, diperoleh kesimpulan bahwa meningkatkan laju intervensi (tindakan rawat inap di rumah sakit) terhadap pederita Mers dan membatasi pergerakan individu yang terinfeksi Mers, dapat meminimalkan penyebaran penyakit Mers dengan efektif. Sebagai catatan, tindakan yang dilakukan terhadap pasien penderita Mers di rumah sakit adalah berupa supportive care. Kata kunci

---

ABSTRACT
In June 2012, a kind of coronavirus, which latter is known as MERS-CoV, was identified from a man in Saudi Arabia. Since then, that kind of virus spread quickly to the countries in and neighboring the Arabian Peninsula and to several other countries in the world. In this thesis, a model of MERS disease spreading which involves camel and human population is proposed to analyze the magnitude of basic reproduction number (R0) as an indicator of epidemic, analyze the speed of MERS propagation and analyze the effect of diffusion movements in infected people with respect to the speed of MERS propagation spatially. The existence of equilibrium point and their local stability are affected by R0 which is obtained from spectral radius of the next-generation matrix. By analyzing the spatial model, we find the minimum speed of MERS propagation connecting the disease free equilibrium to endemic equilibrium point. That result is performed as a traveling wave solution by numerical simulation with finite difference approach. Analyzing R0, we find that MERS propagation can be minimized effectively by increasing the intervention rate through medical support and restricting the movement of infected people.

Abstrak :
Middle east respiratory syndrome coronavirus (MERS-CoV) telah menjadi wabah saat ini, infeksi MERS-CoV menyebabkan gangguan pada sistem pernapasan, pencernaan, bahkan menyebabkan kematian dengan rata-rata kematian yang disebabkan infeksi MERS-CoV mencapai 50%. Sampai saat ini belum ditemukannya vaksin atau obat yang efektif untuk mengurangi infeksi MERS-CoV. papain-like protease (PLpro) bertanggung jawab untuk melepaskan potein nonstruktual yang berperan penting dalam proses pematangan virus. Dengan menginhibisi papain-like protease (PLpro) dengan suatu ligan, akan menghambat proses pelepasan protein nonstruktural, sehingga mengurangi infeksi yang diakibatkan oleh virus MERS-CoV. Melalui studi bioinformatika dengan metode molecular docking dan melalui analisis drug scan, didapatkan inhibitor berbasiskan senyawa peptida siklis komersial yang dapat berikatan dengan PLpro dan mengurangi proses infeksi yaitu Aldosterone Secretion Inhibiting Factor (1-35) (bovine). Melalui analisis molecular dynamics, inhibitor ini stabil dalam tubuh baik dalam keadaan normal (310 K) dan keadaan demam (312 K), sehingga senyawa Aldosterone Secretion Inhibiting Factor (1-35) (bovine) berpotensi untuk dikembangkan menjadi obat terbarukan MERS-CoV.

---

Middle east respiratory syndrome (MERS-CoV) has become the current outbreak, MERS-CoV infection results in illness in respiratory system, digestive, and even lad to death with an average mortality caused by MERS-CoV infection reaches 50%. Until now no effective vaccine or drug to ward off MERS-CoV infection. Papain-like protease (PLpro), is responsible for cleavage of nonstructural potein that is important for viral maturation. Inhibition the papain-like protease (PLpro) with a ligand will block the cleavage process of nonstructural protein, thus reduce the infection of MERS-CoV. Through of bionformatics study with molecular docking, molecular dynamics and drug scan analysis, Aldosterone Secretion Inhibiting Factor (1-35) (bovine) was obtained as a inhibitor of commercial cyclic peptide, it can inhibit the papain-like protease (PLpro) and reduce infection process. With molecular dynamics analysis, this inhibitor was stable at normal body temperature (310 K) and fever temperature (312 K), with the result that Aldosterone Secretion Inhibiting Factor (1-35) (bovine) has a potential as novel candidate drug.