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"ABSTRACTTo overcome the disadvantages of open pond and cement tube as an outdoor algal cultured system, a simple inclined algal culture system was developed. the system composed of an 18.9 L polyethylene terephthalate (PET)bottle placed on a degree adjustable stand using an air pump to generate water mixing and circulation. The system was tested by culturing 45 mL Oscillatoria sp. in 13 L Blue-Green-11 (BG-11)medium supplemented with 3 g L-1 NaNO3 in plastic bottle, which was placed on different angles of inclination, viz. 45°, 60° and 90°. The system was operated outdoor under natural daylight and temperature. After 11 days, 11.5 L culture medium was poured out and 11.5 L fresh medium was refilled. Algal cell was precipitated to measure algal yield. Then, cell harvesting was done every 7 days for 6 batches. This system could culture algae continuously for 5 batches. The highest productivity was 32.23 gram wet (gw) ×m-2×d-1, which was recorded from a second and fifth round of 45° angular system and also from third round of 60° angular system. The result showed that this simple inclined algal culture system can be done continuously for one and a half month with high productivity by 45° inclination, which was proved as a good mixing and circulation. Showing advantages over open-pond, this system was moveable and could reduce possibility of contamination."

"Telah dilakukan penelitian mengenai sebaran spasial spesies Harmful Algal Bloom (HAB) di lokasi budidaya kerang hijau (Perna viridis) Kalibaru, Cilincing, Jakarta Utara pada bulan Mei 2012. Sampel diambil secara vertikal dari kedalaman 3 meter dan pencacahan dilakukan dengan metode sub sampel. Hasil pencacahan menemukan 9 spesies penyebab HAB yang berpotensi red tide maker dan toxin producer. Berdasarkan peta sebaran, kepadatan tertinggi spesies penyebab HAB terdapat di stasiun yang dekat dengan garis pantai (Stasiun 1). Berdasarkan hasil Analisis Faktorial Koresponden (AFK) dan Analisis Komponen Utama (AKU) diketahui bahwa Stasiun 1 dicirikan oleh Thalassiosira mala yang dipengaruhi oleh kecepatan arus dan intensitas cahaya.

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Research on the spatial distribution of Harmful Algal Bloom (HAB) species at green mussel (Perna viridis) aquaculture area, Kalibaru, Cilincing, North Jakarta has been held in May 2012. Samples from 3 meter depth were taken vertically and then identified using sub sample method.

The results showed 9 HAB phytoplankton species which potentially red tide maker and toxin producer. Based on the distribution map, the highest density of HAB species is at station close to the shoreline (Station 1). Based on Correspondent Analysis (CA) and Principle Component Analysis (PCA), Station 1 is characterized by Thalassiosira mala and are affected by current velocity and light intensity."

"Fenomena Harmful Algal Blooms (HABs) di Teluk Lampung, khususnya di Teluk Hurun, telah banyak dibahas oleh beberapa peneliti. Fenomena HABs diduga akibat peningkatan unsur hara (N dan P) dari limbah pertambakan, pembenihan (hatchery) dan budidaya ikan dalam karamba jaring apung. Masukan N dan P ke perairan akan menyebabkan eutrofikasi perairan yang selanjutnya dapat memicu terjadinya ledakan populasi fitoplankton yang dapat berbahaya bagi organisme perairan. Penelitian ini bertujuan menganalisis hubungan kadar nutrient N dan P dengan kemunculan fitoplankton berbahaya, akibat limbah budidaya perikanan yang berbeda pada lokasi penelitian. Secara deskristif hubungan unsur hara N dan P terhadap kelimpahan fitoplankton dapat dilihat dengan adanya kecenderungan peningkatan unsur hara tertentu yang diikuti oleh peningkatan kelimpahan total fitoplankton atau kelimpahan salah satu jenis fitoplankton. Beberapa fitoplankton berbahaya yang ditemukan dengan kelimpahan tinggi pada penelitian ini adalah Ceratium furca dengan kepadatan tertinggi mencapai 5.314 x 10 sel/l, Trichodesmium erithraeum dengan kelimpahan mencapai 1.05 x 10 sel/l and Noctiluca scintilans dengan kelimpahan mencapai 5.99 x 10 sel/l. Hubungan unsur hara N dan P dengan HABs juga ditunjukkan dengan analisis regresi berganda dan canonical corelation analysis (CCA) yang menunjukkan adanya korelasi positif yang kuat antara konsentrasi unsur hara N dan P dengan potensi kemunculan HABs pada berbagai lokasi budidaya perikanan di Teluk Lampung.

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The phenomenon of harmful algal blooms (HABs) in the Lampung Bay has been reported by many researchers. The occurrence of HABs may be due to the increase of nutrient (N and P) as results of waste water of aquaculture (shrimp farms, hatcheries and fish cage farms). This study aim to determine the relationship between N and P concentrations in some aquaculture sites with harmful algal blooms. The analysis revealed the differences concentration of N and P at each different shrimp farms and fish cage farms sites (Hurun, Sidodadi, Ringgung, and Cikunyinyi Bay). The result showed that the increase of N and P concentration were followed by the increase of harmful phytoplankton populations. High density HABs were found in this study, such as: Ceratium furca with the highest density at 5.314 x 10 cells l -1, Trichodesmium erithraeum 1.05 x 10 cells l-1 and Noctiluca scintilans 5.99 x 10 cells l-1. The Multiple regression and canonical corelation analysis (CCA) also indicated a strong positive relationship between N and P with the HABs at the shrimp farms and fish cage farms sites in the Lampung Bay."

"ABSTRAK Latar belakang: Fibroadenoma dan tumor filodes jinak merupakan tumorfibroepitelial dengan gambaran histopatologik yang tumpang tindih. Saat inibanyak pengambilan jaringan tumor payudara secara core biopsy, termasuk padatumor fibroepitelial. Jumlah jaringan yang sedikit dan gambaran histopatologikyang tumpang tindih sering menyulitkan Dokter Spesialis Patologi Anatomikdalam menentukan diagnosis fibroadenoma dan tumor filodes jinak. Penelitian inibertujuan untuk mengetahui gambaran histopatologik apa saja yang bermaknauntuk mendiagnosis fibroadenoma dan tumor filodes jinak dan untuk mengujiapakah diagnosis fibroadenoma dan tumor filodes jinak pada core biopsy denganmenggunakan sistem skoring lebih baik dibandingan tanpa skoring.Bahan dan cara: Penelitian ini merupakan suatu uji diagnostik. 57 kasusfibroadenoma dan tumor filodes jinak yang memiliki slaid core biopsy danmastektomi/lumpektomi/eksisi dinilai ulang tanpa sistem skoring danmenggunakan skoring. Gambaran histopatologik yang dinilai pada sistem skoringadalah selularitas stroma, atipia inti, fragmentasi jaringan, infiltrasi lemak, mitosisdan heterogenitas stroma. Kemudian dilakukan analisis statistik, uji diagnostikdan uji kappa.Hasil: Selularitas stroma, heterogenitas stroma dan fragmentasi jaringan lebihsering ditemukan pada tumor filodes jinak dan berbeda bermakna (p=0,001;p=0,000; p=0,021). Spesifisitas pada sistem skoring meningkat sebesar 17,9%.Nilai duga positif dan nilai duga negatif pada sistem skoring meningkat sebesar11,9% dan 5,1%. Area under curve (AUC) meningkat 8,9%. Uji Cohen?s kappaantara diagnosis core biopsy tanpa dan dengan skoring bernilai rendah (0,545).Kesimpulan: Adanya peningkatan spesifisitas, nilai duga positif dan AUCmenunjukkan bahwa penilaian core biopsy sistem skoring lebih baikdibandingkan tanpa skoring dan dapat menjadi acuan untuk diagnosis fibroadenoma dan tumor filodes jinak.ABSTRACT Background: Fibroadenoma and benign phyllodes tumor are kinds of fibroepithelial tumor which have overlapping histopathological features. Recently, core biopsy is commonly performed to determine breast tumor, including fibroepithelial tumor. Small amount of tissue and overlapped histopathological features often complicate the Pathologist in diagnosing both. This study aims to describe the histopathological appearance which needed to diagnose fibroadenoma and benign phyllodes tumor and to verify if the diagnosis of fibroadenoma and benign phyllodes tumor in core biopsy using scoring system is more accurate than without scoring system.Method: This study was a diagnostic test, in which 57 cases of fibroadenoma and benign phyllodes tumor which had undergone core biopsy and mastectomy/excision were re-assessed using and without using scoring system. Histopathologic features which assessed using scoring system were stromal cellularity, nuclear atypia, tissue fragmentation, fat infiltration, mitotic figure, stromal heterogeneity. Analytical statistic, diagnostic test, accuracy test and Kappa test were done.Results: Stromal cellularity, stromal heterogeneity and tissue fragmentation mostly found in benign phyllodes tumor and significantly different (p=0,001; p=0,000; p=0,021).There were significant differences between stromal cellularity (p=0,001), stromal heterogeneity (p=0,000), and tissue fragmentation (p=0,021) in diagnosis of benign phyllodes tumor. Specificity in scoring system increased by17,9 %. Positive predictive value, negative predictive value and accuracy increased in scoring system (11,9% and 5,1%). Area under curve (AUC) increased by 8,9%. Cohen's Kappa test between core biopsy diagnosis without using and using scoring system had low result(0,545). Conclusion: The increasing of specificity, positive predictive value, accuracy and AUC proved that core biopsy with scoring system is more accurate than without scoring. This can be used as reference to diagnose fibroadenoma and benign phyllodes tumor.;Background: Fibroadenoma and benign phyllodes tumor are kinds of fibroepithelial tumor which have overlapping histopathological features. Recently, core biopsy is commonly performed to determine breast tumor, including fibroepithelial tumor. Small amount of tissue and overlapped histopathological features often complicate the Pathologist in diagnosing both. This study aims to describe the histopathological appearance which needed to diagnose fibroadenoma and benign phyllodes tumor and to verify if the diagnosis of fibroadenoma and benign phyllodes tumor in core biopsy using scoring system is more accurate than without scoring system.Method: This study was a diagnostic test, in which 57 cases of fibroadenoma and benign phyllodes tumor which had undergone core biopsy and mastectomy/excision were re-assessed using and without using scoring system. Histopathologic features which assessed using scoring system were stromal cellularity, nuclear atypia, tissue fragmentation, fat infiltration, mitotic figure, stromal heterogeneity. Analytical statistic, diagnostic test, accuracy test and Kappa test were done.Results: Stromal cellularity, stromal heterogeneity and tissue fragmentation mostly found in benign phyllodes tumor and significantly different (p=0,001; p=0,000; p=0,021).There were significant differences between stromal cellularity (p=0,001), stromal heterogeneity (p=0,000), and tissue fragmentation (p=0,021) in diagnosis of benign phyllodes tumor. Specificity in scoring system increased by17,9 %. Positive predictive value, negative predictive value and accuracy increased in scoring system (11,9% and 5,1%). Area under curve (AUC) increased by 8,9%. Cohen's Kappa test between core biopsy diagnosis without using and using scoring system had low result(0,545). Conclusion: The increasing of specificity, positive predictive value, accuracy and AUC proved that core biopsy with scoring system is more accurate than without scoring. This can be used as reference to diagnose fibroadenoma and benign phyllodes tumor.;Background: Fibroadenoma and benign phyllodes tumor are kinds of fibroepithelial tumor which have overlapping histopathological features. Recently, core biopsy is commonly performed to determine breast tumor, including fibroepithelial tumor. Small amount of tissue and overlapped histopathological features often complicate the Pathologist in diagnosing both. This study aims to describe the histopathological appearance which needed to diagnose fibroadenoma and benign phyllodes tumor and to verify if the diagnosis of fibroadenoma and benign phyllodes tumor in core biopsy using scoring system is more accurate than without scoring system.Method: This study was a diagnostic test, in which 57 cases of fibroadenoma and benign phyllodes tumor which had undergone core biopsy and mastectomy/excision were re-assessed using and without using scoring system. Histopathologic features which assessed using scoring system were stromal cellularity, nuclear atypia, tissue fragmentation, fat infiltration, mitotic figure, stromal heterogeneity. Analytical statistic, diagnostic test, accuracy test and Kappa test were done.Results: Stromal cellularity, stromal heterogeneity and tissue fragmentation mostly found in benign phyllodes tumor and significantly different (p=0,001; p=0,000; p=0,021).There were significant differences between stromal cellularity (p=0,001), stromal heterogeneity (p=0,000), and tissue fragmentation (p=0,021) in diagnosis of benign phyllodes tumor. Specificity in scoring system increased by17,9 %. Positive predictive value, negative predictive value and accuracy increased in scoring system (11,9% and 5,1%). Area under curve (AUC) increased by 8,9%. Cohen's Kappa test between core biopsy diagnosis without using and using scoring system had low result(0,545). Conclusion: The increasing of specificity, positive predictive value, accuracy and AUC proved that core biopsy with scoring system is more accurate than without scoring. This can be used as reference to diagnose fibroadenoma and benign phyllodes tumor.;Background: Fibroadenoma and benign phyllodes tumor are kinds of fibroepithelial tumor which have overlapping histopathological features. Recently, core biopsy is commonly performed to determine breast tumor, including fibroepithelial tumor. Small amount of tissue and overlapped histopathological features often complicate the Pathologist in diagnosing both. This study aims to describe the histopathological appearance which needed to diagnose fibroadenoma and benign phyllodes tumor and to verify if the diagnosis of fibroadenoma and benign phyllodes tumor in core biopsy using scoring system is more accurate than without scoring system.Method: This study was a diagnostic test, in which 57 cases of fibroadenoma and benign phyllodes tumor which had undergone core biopsy and mastectomy/excision were re-assessed using and without using scoring system. Histopathologic features which assessed using scoring system were stromal cellularity, nuclear atypia, tissue fragmentation, fat infiltration, mitotic figure, stromal heterogeneity. Analytical statistic, diagnostic test, accuracy test and Kappa test were done.Results: Stromal cellularity, stromal heterogeneity and tissue fragmentation mostly found in benign phyllodes tumor and significantly different (p=0,001; p=0,000; p=0,021).There were significant differences between stromal cellularity (p=0,001), stromal heterogeneity (p=0,000), and tissue fragmentation (p=0,021) in diagnosis of benign phyllodes tumor. Specificity in scoring system increased by17,9 %. Positive predictive value, negative predictive value and accuracy increased in scoring system (11,9% and 5,1%). Area under curve (AUC) increased by 8,9%. Cohen's Kappa test between core biopsy diagnosis without using and using scoring system had low result(0,545). Conclusion: The increasing of specificity, positive predictive value, accuracy and AUC proved that core biopsy with scoring system is more accurate than without scoring. This can be used as reference to diagnose fibroadenoma and benign phyllodes tumor."

"The concept of periphyton growth is globally regarded as a functional unit, without considering the dynamics of various components as have been reported by earlier scholars, and is used as references to the algal periphyton growth modelling conducted in this study. Experimental data on the growth of periphyton biomass versus time was used to test two basic hypotheses to account for feedback effects on periphyton growth."

"ABSTRACTSel tumor adalah sel yang terbentuk akibat kegagalan beberapa protein dalam mengatur siklus sel. Protein TP53 berperan penting dalam mengatur siklus sel, khususnya dalam menekan perkembangan sel tumor. Perubahan pada gen TP53 ditemukan dalam lebih dari setengah kasus tumor pada manusia. Protein lain yang berhubungan dengan protein TP53 juga ditemukan terlibat dalam proses pembentukan kanker. Analisis interaksi protein TP53 dengan melakukan clustering jaringan interaksi protein (PPI) TP53 adalah hal penting dalam membantu mengatasi sel tumor. Jaringan PPI dinyatakan sebagai graf dengan protein dan interaksinya masing-masing sebagai simpul dan busur pada graf. Spectral clustering adalah metode graph clustering yang menggunakan eigenvector dari matriks Laplacian.

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ABSTRACTFuzzy random walk adalah metode fuzzy clustering yang menggunakan probabilitas transisi dari random walk pada data. Dua metode tersebut akan digabungkan dan diimplementasikan pada penelitian ini. Menggunakan data PPI protein TP53 dari STRING database, didapat gabungan kedua metode tersebut mampu menghasilkan cluster yang fuzzy dan robust di mana setiap cluster dapat menjelaskan bagian tertentu dari fungsi protein TP53. Tumor cell is formed as a result of malfunctioning of some proteins that regulates the cell cycle. TP53 protein plays an important role in managing cell cycle, especially in tumor cell suppression. An alteration of TP53 gene is found in more than half cases of human tumor. Moreover, TP53-related proteins are also found involved in the carcinogenesis process. Therefore, it is important to analyze the interactions of TP53 protein by clustering protein-protein interactions (PPI) network of TP53. PPI networks are usually represented as a graph network with proteins and interactions as vertices and edges respectively. Spectral Clustering is a graph clustering algorithm based on eigenvector of the graph Laplacian. Fuzzy Random Walk is a fuzzy clustering method based on transition probability from a random walk on a dataset. In this paper, we combine both Spectral Clustering and Fuzzy Random Walk. Using PPI datasets of TP53 obtained from the STRING database, we found the combined algorithm is proven to produce both robust and fuzzy clusters with each cluster explains one of TP53 proteins functionality."

"ABSTRAK Latar belakang: Sarkoma Ewing merupakan suatu small round cell tumor yang ditandai dengan fusi gen EWSR1/FLI1 pada 85 kasus. Diagnosis akurat diperlukan karena memiliki respon baik terhadap protokol kemoterapi spesifik. Baku emas diagnosis sarkoma Ewing adalah deteksi translokasi spesifik dengan RT-PCR atau FISH, namun pemeriksaan tersebut belum tersedia di institusi kami, sehingga dilakukan upaya lain untuk mempertajam diagnosis. Secara morfologi, sarkoma Ewing sering overlapping dengan small round cell tumor lainnya. Pulasan CD99 merupakan penanda yang sangat sensitif untuk mendiagnosis sarkoma Ewing, namun juga sering overlapping dengan small round cell tumor lainnya. Beberapa penelitian mengemukakan FLI1 dapat digunakan sebagai penanda diagnosis sarkoma Ewing. Tujuan penelitian ini adalah menilai ekspresi FLI1 untuk membantu menegakkan diagnosis sarkoma Ewing pada small round cell tumor yang memberikan hasil positif terhadap CD99, terutama pada kasus biopsi.Bahan dan cara: Penelitian ini menggunakan desain potong lintang. Sampel terdiri atas 36 kasus sarkoma Ewing dan 18 kasus small round cell tumor yang sudah dilakukan pulasan imunohistokimia CD99 di RSCM dari Januari 2011 sampai Mei 2018. Dilakukan pulasan FLI1 dan penilaian menggunakan H-score.Hasil: Titik potong H-score pada ekspresi FLI1 didapatkan 226.1 75 dengan sensitivitas 81.6 dan spesifisitas 94.4 . Ekspresi FLI1 tinggi didapatkan pada 31 kasus sarkoma Ewing, sedangkan pada 18 kasus small round cell tumor umumnya memiliki ekspresi FLI1 yang rendah ABSTRACT Background: Ewing 39;s sarcoma is a small round cell tumor characterized by EWSR1 / FLI1 gene fusion in 85 of cases. Accurate diagnosis is necessary because it has a good response to a specific chemotherapy protocol. The gold standard of Ewing 39;s sarcoma diagnosis is the detection of specific translocation with RT-PCR or FISH, but the examination is not yet available at our institution, so another attempt is made to sharpen the diagnosis. Morphologically, Ewing 39;s sarcoma is often overlapping with other small round cell tumor. CD99 is a very sensitive marker for diagnosing Ewing 39;s sarcoma, but also often overlapping with other small round cell tumors. Several studies have suggested that FLI1 can be used as a marker of Ewing rsquo;s sarcoma. The purpose of this study was to assess the FLI1 expression to help establish the diagnosis of Ewing rsquo;s sarcoma in small round cell tumors that gave CD99 positive results, especially in the biopsy cases. Materials and methods: This was a cross-sectional study with 36 cases of Ewing rsquo;s sarcoma and 18 cases of other small round cell tumor that had been performed CD99 immunohistochemistry at RSCM from January 2011 to May 2018. All cases stained by FLI1 antibody and evaluated using H-score. Results: The H-score cut-off point on FLI1 expression was obtained at 226.1 75 with 81.6 sensitivity and 94.4 specificity. The high FLI1 expression was obtained in 31 cases of Ewing rsquo;s sarcoma, while in 18 cases of small round cell tumor were generally had low expression of FLI1 p"

"Eutrofikasi merupakan fenomena pengkayaan nutrient khususnya fosfat yang dapat menyebabkan terjadinya peledakan pertumbuhan alga algae blooming) dan menimbulkan efek samping yaitu penurunan konsentrasi oksigen dalam badan air yang menyebabkan kematian biota. Sedimen di perairan merupakan kompartemen dan sumber lepasnya fosfat ke badan air. Oleh karena itu, untuk memonitor dan mengkontrol eutrofikasi di badan air perlu dikaji interaksi antara sedimen dan badan air dengan mengetahui dan mengkarakterisasi spesi senyawa fosfat di sedimen yang berpotensi menjadi sumber fosfat bagi alga di badan air. Identifikasi spesi senyawa fosfat di sedimen dilakukan dengan proses ekstraksi bertahap. Dalam penelitian ini empat metode ekstraksi bertahap dibandingkan, yaitu metode yang diusulkan oleh Bowman Cole, Hedley et al., Ivanoff et al., dan metode standard-Baoqing, et al. Berdasarkan percobaan yang dilakukan, metode ekstraksi yang paling efektif adalah metode yang diusulkan oleh Ivanoff et al dengan waktu ekstraksi yang lebih efisien dan dapat mengekstrak kadar P 99.83 dari kadar P total dengan memperoleh 6 tipe spesi fosfat dari 7 fraksi menggunakan metode ekstraksi bertahap. Tipe fosfat yang berada dalam sedimen yaitu fosfat organik fosfat labile, P-mikrobal, dan fosfat yang bersifat cukup resisten dan resisten dan fosfat anorganik fosfat labile, fosfat cukup labile, dan Ca-P dengan senyawa fosfat yang paling banyak ditemukan di sedimen yaitu tipe fosfor anorganik pada fraksi P Labile. Faktor yang mempengaruhi proses ekstraksi bertahap spesi fosfat pada sedimen yaitu 1 pH, 2 ekstraktan, 3 waktu ekstraksi, dan 4 tahapan prosedur pada metode ekstraksi bertahap.

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Eutrophication is a phenomenon of nutrient enrichment especially phosphates that can cause the explosion of algal growth alga bloom and side effects is the decrease of oxygen concentration in porewater that causing the death of biota. Aquatic sediments are the compartment and the source of the phosphate release to the porewater. Therefore, to monitor and control eutrophication in the porewater, it is necessary to examine the interactions between sediments and porewater by knowing and characterizing phosphate specifications in the sediments that are the source of phosphates for algae in the porewater. Identification of the species phosphate in the sediment was carried out by a sequential extraction process. In this study several sequential extraction methods used namely as follow the method of Bowman Cole, Hedley et al., Ivanoff et al., and standard methods Baoqing, et al. The most effective sequential extraction method is the method devised by Ivanoff et al. With the more efficient extraction time which has extracted 99.83 of P from total P content with 6 species of phosphate. It is found that phosphate species in sediment were organic phosphate labile P, P microbal, and moderately resistant P and resistant P and inorganic phosphate labile P, moderately labile P, and Ca P with the most widely found species of phosphate were inorganic phosphorus in P Labile fraction. Factors affecting the gradual extraction process is 1 pH, 2 extractants, 3 extraction times, and 4 the procedure stage of the method."