Joint Estimation of DNA Copy Number From Multiple Platforms

DNA copy number variants (CNV) are gains and losses of segments of chromosomes, and comprise an important class of genetic variation. Recently, various microarray hybridization based techniques have been developed for high throughput measurement of DNA copy number. In many studies, multiple technical platforms or different versions of the same platform were used to interrogate the same samples; and it became necessary to pool information across these multiple sources to derive a consensus molecular profile for each sample. An integrated analysis is expected to maximize resolution and accuracy, yet currently there is no well formulated statistical method to address the between-platform differences in probe design, assay methods, sensitivity, and analytical complexity. The conventional approach is to apply one of the CNV detection (a.k.a. “segmentation”) algorithms to search for DNA segments of altered signal intensity. The results from three platforms are combined after segmentation. Here we propose a new method, Multi-Platform Circular Binary Segmentation (MPCBS), which pools statistical evidence across platforms during segmentation, and does not require pre-standardization of different data sources. It involves a weighted sum of t-statistics, which arises naturally from the generalized log-likelihood ratio of a multi-platform model. We show by comparing the integrated analysis of Affymetrix and Illumina SNP array data with fosmid clone end-sequencing results on 8 HapMap samples that MPCBS achieves improved spatial resolution, detection power, and provide a natural consensus across platforms. We also apply the new method to analyze the multi-platform data from TCGA. The R package for MPCBS is registered on R-Forge under project name MPCB

Power loss estimation due to difference transformer tap changer position at interface

No Abstract

Fragmentation Method of Coral (Caulastrea Furcata) for Growth Measured at Controlling Condition

The objective of the research are: (1) to analyze the water quality condition of water circulation system at laboratory and (2) to measure the growth (length and height) and survival rate of Caulastrea furcata which was fragmented at the laboratory. The water quality condition at the laboratory showed that every parameter has normal value in which organism can live and grow. Natural feed such as Copepoda and Nannoclhoropsis were also cultured at the laboratory as food for the coral. Transplantation was done by cutting the colony of coral or by breaking the branch of coral into pieces from every kind of coral spesies and placed those on artificial substrate made from ceramic bricks. Cutting process was done after the acclimatization process. Fragmentation treatment of C. furcata become 1 polyp, 2 polyp, 3 polyp and 4 polyp that was reared on circulation system did not give significant impact on height and length growth after 160 days. Mean of growth length of C. furcata on treatment 1, 2, 3 and 4 polyps in every month after 160 days was 1.64 mm, 1.55 mm, 1.42 mm and 1.08 mm, respectively, whereas mean of growth broad was 0.71 mm, 0.82 mm, 0.51 mm and 0.62 mm, respectively. Fragmentation treatment of C. furcata become 1 polyp was best length if compare other treatment.Tujuan penelitian ini adalah: (1) menganalisis kondisi kualitas air pada system sirkulasi air di laboratorium dan (2) mengukur pertumbuhan (panjang dan tinggi) dan tingkat kelulushidupan Caulastrea furcate yang telah difrakmentasi di laboratorium. Nilai kualitas air menunjukkan bahwa setiap parameter adalah normal dan dapat mendukung kehidupan dan pertumbuhan organisme. Pakan alami seperti Copepoda dan Nannoclhoropsis yang juga dikultur di laboratorium sebagai pakan karang. Tansplantasi dilakukan melalui pemotongan koloni karang pada bagian cabang karang kedalam bagian kecil dari setiap spesies karang dan ditempatkan pada subtrak buatan yang dibuat dari keramik. Proses pemotongan dilakukan setelah proses aklimatisasi dilakukan. Perlakuan frakmentasi C. furcate menjadi 1 polip, 2 polip, 3 polip dan 4 polip kemudian didedahkan dalam air berskirkulasi tidak memberikan efek yang signifikan terhadap pertumbuhan tinggi dan panjang setelah 160 hari. Rata-rata pertambahan lebar pada perlakuan 1, 2, 3 dan 4 polip pada setiap bulan setelah 160 hari adalah 1.64 mm, 1.55 mm, 1.42 mm dan 1.08 mm. dimana rata-rata pertumbuhan tinggi secara berurutan adalah 0.71 mm, 0.82 mm, 0.51 mm dan 0.62 mm. Perlakuan frakmentasi 1 polip pada C. furcate menghasilkan panjang terbaik dibandingkan perlakuan lainnya

Coral Recruitment Before and After Bleaching Event 2010 in Pulau Weh, Aceh, Indonesia

A monitoring study was conducted at Pulau Weh, which is located in Sabang Province Aceh, Indonesia in the northern part of Sumatera from April 2010 to April 2013. This study aims to monitor and evaluate the current status of coral reef, compotition and abundance of juvenile corals on natural substrates and recruits in the chosen sampling sites. Six sampling stations were chosen to determine the changes in coral reef after bleaching event and two stations were chosen to study coral recruitment. The survey was conducted using 5x5m permanent quadrate, placed at two different depths: 4m and 8m. Photo Quadrate method was applied to monitor the coral changes and the recovery of coral reefs in Pulau weh. Where at each sampling location within the quadrate, a series of photographs was taken with a digital camera with wide angle lens and analyzed in the laboratory. A digital probe was placed at each site, where by the temperature was recorded every 2 hours starting from April 2010 to September 2011. An increasing and extreme temperature shock was recorded in May 2010, where the highest temperature recorded was as high as 32 °C for a long duration. From the series of observation, 85% of the coral coverage in the study area in the six sampling site was found bleached and dead during the bleaching phenomena in May to July 2010. The overall number and density of juvenile corals were higher in the upper reef than the lower reef. Low coral recruitment occurred during the sampling periods interfered with disturbances (bleaching event and storm) compared to normal sampling period without disturbance.Penelitian ini dilakukan di Pulau Weh, yang terletak di Provinsi Aceh, Indonesia mulai dari bulan April 2010 sampai dengan April 2013. Penelitian ini bertujuan untuk memantau dan mengevaluasi status terumbu karang, komposisi dan kelimpahan juvenil karang pada substrat alami dan rekrutmen di lokasi yang sudah ditentukan. Enam stasiun pengambilan dipilih untuk melihat Perubahan terumbu karang setelah peristiwa pemutihan berlangsung dan dua stasiun dipilih untuk melihat rekrutmen karang baru. Survei ini dilakukan dengan menggunakan kuadrat permanen yang berukuran 5x5m yang ditempatkan pada dua kedalaman yang berbeda yaitu: 4m dan 8m. MetodeFoto Kuadrat diaplikasikan untuk memantau Perubahan karang dan pemulihan terumbu karang di Pulau weh setelah peristiwa pemutihan. Foto hasil pengambilan gambar dengan kamera bawah air selanjutnya dianalisis di laboratorium. Alat perekam suhu dan cahaya digital ditempatkan di setiap lokasi penelitian, dimana suhu akan direkam setiap 2 jam sekali mulai dari April 2010 sampai September 2011. Peningkatan suhu secara ekstrim telah dicatat pada bulan Mei 2010 yaitu setinggi 32 °C dalam jangka waktu yang lama. Dari serangkaian pengamatan 85% dari tutupan karang di daerah penelitian ditemukan mati disebabkan fenomena bleaching bulan Mei-Juli 2010. Jumlah keseluruhan dan kepadatan juvenile karang lebih tinggi pada terumbu bagian atas daripada karang yang lebih rendah. Rekrutmen karang yang rendah terjadi selama periode bleaching berlangsung dibandingkan dengan periode sampling normal tanpa gangguan

Pembentukan Pohon Klasifikasi Biner Dengan Algoritma Cart (Classification and Regression Trees) (Studi Kasus: Kredit Macet Di Pd. Bpr-bkk Purwokerto Utara)

Modernization and globalization of the world today has entered into various lines of Indonesian society. One consequence is people's lifestyles are more consumptive. This lifestyle causes people take out a loan at a bank or other financial institution to fulfill his wish. Some people pay the loan on credit. But in implementation, there is a variety of things causes the credit not running properly or called with problem loan. As a service provider of credit institutions, PD. BPR-BKK Purwokerto Utara is also not free from this problem. Therefore, it is necessary to classify customers based on demographic variables using Classification and Regression Trees (CART) to minimize the chances of problem loans. Based on analysis of customer credit status data PD. BPR-BKK Purwokerto Utara, optimal classification tree formed by the number of terminal nodes as much as 6 nodes. This means there are 6 characteristics of customers PD. BPR-BKK Purwokerto Utara. And level of accuracy of the classification tree in classifying credit status of customers is 81.0 %

Effectiveness of Antiemetic Treatment Among Breast Cancer Patients in Inpatient Unit Sardjito General Hospital

Nausea and vomiting are chemotherapy adverse events that influence breast cancer patient’s quality of life. Antiemetic regimen as premedication was given to prevent those adverse events and need to be evaluated. This study aimed to present the effectiveness of antiemetic treatment among breast cancer patients in the inpatient unit, Rumah Sakit Umum Pusat Dr. Sardjito [Central Public Hospital Dr. Sardjito] Yogyakarta, Indonesia.A cohort study was used in this study during July 2008 to January 2009. Thirty-one breast cancer patients, who are receiving antiemetic therapy and having no disease that induced nausea and vomiting were involved, signed informed consent and had been followed by before-post chemotherapy. The data was gained from chemotherapy and antiemetic regimens, medical records, patient’s interviews, and finally analyzedusing descriptive, evaluative approach. This study presented that antiemetic treatment among breast cancer patient in the inpatient unit was 61.40 % ineffective reducing incidence of nausea vomiting events. The majority of cases of nausea and vomiting onset among patients were acute-delayed (56.2 %; 52.0 %), severity of nausea and vomiting laid mostly in the second level (54.54 %; 52.00 %), and appropriateness antiemetic treatment complied to NCCN guideline 2007 and ASCO guideline 2006 was only applied in low emetic risk of chemotherapy-induced nausea and vomiting. Antiemetic regimens that had been implemented need to be evaluated because of majority cases of nausea and vomiting were the acute-delayed type, level two of severity and inappropriateness of international guideline. This study should be followed with the future study of the evaluation of the effectiveness of another medication supported the patient in receiving chemotherapy. Keywords: Antiemetic, Breast cancer, Effectiveness, Nausea, Vomiting

Impact Resisting Concrete

Different percentages of polymers have been added to concrete, to evaluate its  impact resistance. Mixes have been made for plain concrete with crushed stone, also plain concrete mixes with round gravel, Concrete mixes with (0.2, 0.85, 1.5 and 2.0) % of Melment to 100 Kg of binder, Concrete mixes with (0.2, 0.5, 0.75 and 1.5) liter of Glenium to 100 Kg of cement and concrete mixes with three sheets of polystyrene and concrete mixes made using polystyrene sheets with 0.85% by weight of Melment. Concrete with polystyrene sheets and Melment gives average compressive strength of 59.3Mpa, tensile strength of 5.8 Mpa and impact strength when the first crack appears was 1486 blows at 28 days. Using 0.85 % of Melment per 100Kg of binder enhance the concrete resistance to Impact. Using 0.5 Liter of Glenium per 100Kg of cement shows good performance of concrete to Impact. Using three layers of Polystyrene sheets with 0.85% of Melment gives high compressive strength and improve the Impact capacity of concrete. Polystyrene sheets increases the adhesive forces between materials in the mix and superplasticizers increases the workability so as to produce self compacting concrete. Keywords: Polystyrene, Melment, Glenium, Impact Strength. Self Compacting Concrete