Visualization for exploratory analysis of spatio-temporal data

Analysis of spatio-temporal data has become critical with the emerge of ubiquitous location sensor technologies and applications keeping track of such data. Especially with the widespread availability of low cost GPS devices, it is possible to record data about the location of people and objects at a large scale. Data visualization plays a key role in the successful analysis of these kind of data. Due to the complex nature of this analysis process, current approaches and analytical tools fail to help spatio-temporal thinking and they are not effective when solving large range of problems. In this work, we propose an interactive visualization tool to support human analyst understand user behaviors by analyzing location patterns and anomalies in massive collections of spatio-temporal data. The tool that we developed within this work combines a geovisualization framework with 3D visualizations and histograms. Tool's effectiveness in exploratory analysis is tested by trend analysis and anomaly detection in a real mobile service dataset with almost 1.5 million rows

Automatic path generation for terrain navigation

Navigation in 3D terrain is considered to be a challenging task and requires virtual camera control skills such as zooming, panning and tilting. Novice users can easily get distracted and disorientated which may result in being lost in space. Solutions for the virtual environment exploration problems are still being researched in order to assist users during their journey inside virtual environments. Among these solutions, assisted camera control techniques require viewpoint computation and path planning. This paper introduces a novel approach to navigate over a 3D terrain using best viewpoints. We exploit the concept of Viewpoint Entropy for best view determination and use Greedy N-Best View Selection for visibility calculations. We integrate road network data to extract regions for detailed visibility analysis in subsections of the terrain. In order to connect the calculated viewpoints, we use an evolutionary programming approach for the Traveling Salesman problem. We present the generated tour using a Google Earth framework. The computed and planned viewpoints in our solution reduce human effort when used as starting points for scene exploration or to generate the representative images of the terrain dataset. The proposed framework can be integrated into 3D game engines or urban visualization systems. This integration gives quickly a glimpse or tour of the environment for novice users without the help of prior planning. Furthermore, terrain visibility used together with road network data and an optimization method for final path construction allows the computed path to be used for large urban area reconnaissance and surveillance tasks with aerial vehicles

Tannik asidin tavşan karaciğerinde flavin monooksijenaz, sitokrom p450 ve antioksidan enzim aktiviteleri üzerine in vitro etkileri

Giriş: Bu çalışmada bitki fenolik bileşiklerinden tannik asidin ilaçlar ve çeşitli kimyasal bileşiklerin metabolizmasında rol alan enzimler ile antioksidan enzim sistemleri üzerine in vitro etkileri incelenmiştir. Gereç ve Yöntem: Tavşan karaciğerleri homojenize edildikten sonra mikrozomal ve sitozolik fraksiyonlar diferansiyel santrifügasyon yöntemiyle elde edilmiştir. Tavşan karaciğer mikrozomal anilin 4-hidroksilaz (CYP2E1), benzfetamin N-demetilaz (CYP2B4), eritromisin N-demetilaz (CYP3A4), flavin monooksijenaz (FMO) ile sitozolik süperoksit dismutaz (SOD), glutatyon peroksidaz (GPx), glutatyon S-trasferaz (GST) ve NAD(P)H:kuinon oksidoredüktaz 1 (NQO1) enzim aktiviteleri üzerine tannik asidin etkileri her bir enzim için optimize edilen reaksiyon ortamları kullanılarak spektrofotometrik olarak incelenmiştir. Tannik asidin her bir enzim için önce IC50 değerleri bulunmuş, sonra da Km, Vmax ve KI değerleri hesaplanarak inhibisyon tipleri belirlenmiştir. Bulgular: Anilin 4-hidroksilaz, benzfetamin N-demetilaz, eritromisin N-demetilaz, FMO, GST, NQO1, SOD ve GPx için IC50 değerleri sırasıyla 60.3 µM, 50 µM, 16.9 µM, 169 µM, 0.33 µM, 7.25 µM, 17.4 ve 3.81 olarak bulunmuştur. Elde edilen Lineweaver-Burk ve Dixon grafiklerinden, tannik asitin anilin 4-hidroksilaz, benfetamin N-demetilaz, GST ve NQO1 enzim aktivitelerini nonkompetitif tarzda inhibe ettiği bulunmuş (Km sabit kalırken Vmax azalmıştır) ve KI değerleri sırasıyla 54.7 µM, 65.7 µM, 0.3 µM ve 41 µM olarak hesaplanmıştır. Sonuç: Bu sonuçlar ile tannik asidin ksenobiyotik aktivasyon/detoksifikasyon yolaklarında rol alan enzimleri etkileyerek ilaçların ve birçok kimyasalın metabolizmasını değiştirebileceği gösterilmiştir.Bu çalışma Devlet Planlama Teşkilatı (DPT) tarafından desteklenmiştir (Proje No: ODTÜ-BAP-08-11-DPT2002 K120510)

In vitro effects of mercury and silver on rat liver nad(p)h:quinone oxidoreductase 1

Kirlenmiş toprak ve sularda bulunan ağır metallerin sağlığa zararlı olduğu bilinmektedir. Bu çalışmada, civa ve gümüşün ksenobiyotik kuinonların detoksifikasyonunda rol alan ve antioksidan olarak da görev yapabilen NAD(P)H:Kuinon Oksidoredüktaz 1 (NQO1) enzimi üzerine in vitro etkileri incelenmiştir. Sıçan karaciğerleri homojenize edildikten sonra sitozolik fraksiyonlar diferansiyel santrifügasyon yöntemiyle elde edildi. NQO1 substratı olarak 2,6-diklorofenolindofenol (DCPIP) kullanıldı ve 600 nanometrede azalan absorbans spektrofotometrik olarak gözlemlendi. Civa ve gümüşün NQO1 üzerine etkisi, bu metallerin 10 µM ile 150 µM arasında değişen konsantrasyonları kullanılarak incelendi. Elde edilen data ile önce her iki metalin de IC50 değerleri bulundu, sonra çizilen Lineweaver-Burk ve Dixon grafiklerinden Km, Vmax ve KI değerleri hesaplanarak inhibisyon tipleri belirlendi. Civanın NQO1 enzimi için IC50 değeri 60.7 µM; gümüşün NQO1 enzimi için IC50 değeri 30.36 µM olarak bulundu. Lineweaver-Burk grafiklerinden belirlendiği üzere civa NQO1 enzimini nonkompetitif tarzda inhibe ederken (Vmax azalırken Km sabit kaldı) gümüş bu enzimi kompetitif tarzda inhibe etmiştir (Vmax sabit kalırken Km arttı). KI değerleri ise civa için 87 µM gümüş için 19.2 µM olarak hesaplandı. Sonuç olarak, kirlenmiş sulardaki ağır metallerin başında gelen civa ve gümüşün NQO1 enzimi üzerindeki inhibe ediciliği, enzimin ksenobiyotik kuinonların detoksifikasyonunda önemli ölçüde azalmaya sebebiyet vereceğinden ksenobiyotik kuinonların zararları daha fazla görülebilecektir

Alteration of rat liver flavin-containing monooxygenase (fmo) activity and protein expression by ellagic acid

Flavin monooksijenazlar (FMO) FAD içeren endoplazmik retikuluma ve de çekirdek zarına yapışık bulunan ve ksenobiyotik metabolizmasında rol alan Faz I enzimleridir. FMO’lar NADPH’ı kofaktör olarak kullanarak çok çeşitli nükleofilik azot, sülfür, fosfor ve selenyum içeren tamoxifen, imipramin, metimazol gibi ilaçların ve diğer kimyasalların oksidasyonundan sorumludurlar. Elajik asit birçok bitki türünde, özellikle meyvelerde doğal olarak bulunan bir çeşit polifenoldür. Elajik asidin antimutajenik, antioksidan, antiinflamatuvar ve potansiyel antikarsinojenik aktivitelere sahip olduğu düşünülmektedir. Bu çalışmada elajik asidin FMO aktivitesi ve protein ekspresyonu üzerine in vivo etkileri araştırıldı. Bunun için, erkek sıçanlara kilo başına günlük 10 mg DMSO’da çözülmüş elajik asit 9 gün boyunca periton içine enjekte edildi. Bunun yanı sıra bir grup sıçana da sadece DMSO çözeltisi enjekte edildi ve bunlar da kontrol olarak kullanıldı. Sıçan karaciğerlerinden mikrozomal fraksiyonlar elde edilip, metimazol substratı kullanılarak FMO aktivitesi ve “Western blot” tekniği kullanılarak da FMO3 protein ekspresyonu tayini yapıldı. Deneyler sonucunda, elajik asidin FMO aktivitesini %57 ve FMO3 protein ekspresyonunu da %40 artırdığı bulunmuştur. Bu sonuçlar göstermektedir ki bitkilerde bulunan ve diyetle birlikte alınan elajik asit, ilaçları ve diğer ksenobiyotikleri metabolize eden FMO enzimini modüle ederek bu çeşit moleküllerin detoksifikasyonunu artırabilir.Flavin-containing monooxygenases (FMOs) are flavoproteins which contain FAD molecule. They are phase I xenobiotic-metabolizing enzymes bound to smooth endoplasmic reticulum and nuclear envelope. FMOs are responsible for oxidation of wide-range of nucleophilic nitrogen, sulfur, phosphorus, and selenium heteroatom-containing drugs such as tamoxifen, imipramine,methimazole and other chemicals by using NADPH as cofactor. Ellagic acid is a polyphenolic compound that exists naturally in the plant species, and considered as anti-mutagenic, antioxidant, anti-inflammatory, and potent anti-carcinogenic agent in mammalian cells. The aim of the present study was to determine the in vivo effect of ellagic acid on FMO activity and FMO3 protein expression in rat liver. 10 mg of ellagic acid in DMSO/kg body weight was injected intraperitoneally to Wistar albino rats for nine consecutive days. On the other hand, a group of rats was injected only with DMSO solution and used as control. Following the decapitation of the animals, the livers were removed and microsomal fractions were prepared by differential centrifugation. FMO activities by using methimazole as substrate and FMO3 protein expressions by Western blot were determined. The results showed that ellagic acid significantly increased the mean FMO activity, 57%, and mean FMO3 protein expression, 40% with respect to control group. In conclusion, FMO dependent metabolism of drugs and other xenobiotics may be altered due to the changes in activity and protein expressions of FMO enzyme by the ellagic acid found in the die

Alteration of enzyme activities and kinetic properties of GST and NQO1 with naturally occurring phenolic compounds

Objective: Glutathione S-transferase (GST) and NAD(P)H:quinine oxidoreductase 1 (NQO1) are the enzymes important in cytoprotection and bioactivation of chemicals. This study has addressed effects of polyphenolic compounds; ellagic acid, quercetin, naringenin, resveratrol, rutin and hesperidin on rabbit liver GST and NQO1 enzyme activities

Alteration of enzyme activities and kinetic properties of GST and NQO1 with naturally occurring phenolic compounds

Objective: Glutathione S-transferase (GST) and NAD(P)H:quinine oxidoreductase 1 (NQO1) are the enzymes important in cytoprotection and bioactivation of chemicals. This study has addressed effects of polyphenolic compounds; ellagic acid, quercetin, naringenin, resveratrol, rutin and hesperidin on rabbit liver GST and NQO1 enzyme activities

Effects of medicinal plant viscum album l. on rat liver flavin-containing monooxygenase activity and expression

Viscum album L., a species of mistletoe, contains lectins, polypeptides, mucilage, sugar alcohols, flavonoids, lignans, triterpenes, and phenylallyl alcohols1. The leaves and twigs of Viscum album L., taken as tea, have been traditionally used for hypertension, stomachache, diarrhea, dysuria and also as analgesic and cardiotonic agent in Anatolia, Turkey2. In addition, in Europe, sterile extracts of Viscum album L. are among the most common herbal extracts applied in cancer treatment and have been used as prescription drugs, while in US, considered as dietary supplement3. Flavin-containing monooxygenases (FMOs, EC 1.14.13.8) are FAD-containing phase I enzymes and responsible for the oxidation of wide-range of nucleophilic nitrogen, sulfur, phosphorus, and selenium heteroatom-containing drugs such as tamoxifen, methimazole and imipramine, pesticides, neurotoxins, and other chemicals by using NADPH as cofactor4. The aim of this study was to determine the in vivo effects of Viscum album L. on FMO activity, mRNA and protein expression in rat liver. The water extract of Viscum album was injected intraperitonally (i.p) into 15 wistar albino rats as 10 mg/kg of body weight for 9 consecutive days, while 11 rats were used as control. Then, following the decapitation, the livers were removed and microsomal fractions were prepared. FMO activity using methimazole as substrate, mRNA expression by quantitative Real-Time PCR, and protein expression by Western Blot were determined. The results showed that extract of Viscum album L. decreased mRNA, and protein expressions as well as enzyme activity of FMO with respect to controls. Liver microsomal FMO activity was decreased from 5.1±0.9 to 4.1±1.1 nmol/min/mg (p<0.05). mRNA expression of FMO in extract injected animals was found to be 2.6 fold lower compared to controls (p<0.0001). In addition, the plant extract decreased the FMO protein level 28% with respect to controls (p<0.05). In conclusion, the metabolism of xenobiotics by FMO-catalyzed reactions may be altered due to the changes in FMO expression and activity by Viscum album L. extract

In vivo effects of o-coumaric acid on rat liver flavin-containing monooxygenase (fmo) activity and expression

Phenolic compounds are biologically active molecules and suggested to have some disease-preventive properties such as cardiovascular and certain types of cancer. Coumaric acid has been known as a phenolic compound and found in a wide variety of plants such as peanuts, tomatoes, carrots, and garlic and form the part of human diet; function as antioxidant and chemopreventive agents. 1-2 Flavin-containing monooxygenases (FMOs, EC 1.14.13.8) are phase I enzymes, responsible for oxygenation of a wide range of nucleophilic heteroatom-containing xenobiotics such as drugs, pesticides, neurotoxins, and other chemicals. They contain FAD in their structure and use NADPH as cofactor and molecular oxygen for their reactions. FMOs can be affected by hormonal and dietary components.3 The aim of this study was to determine the in vivo effects of o-coumaric acid on rat liver FMO activity, protein and mRNA expressions. 30 mg/kg of body weight of o-coumaric acid was intraperitonally injected to 14 albino Wistar rats, while 8 rats were used as control. After 9 days of injection, the rats were decapitated and microsomal fractions of livers were prepared using homogenization and differential centrifugation. FMO enzyme activity of microsomal samples was assayed by using methimazole as substrate. Protein and mRNA expressions were carried out by Western Blot and quantitative Real-Time PCR techniques respectively. The results showed that FMO activity and protein expression were increased 48% and 34%, respectively, by o-coumaric acid injection compared to controls (p<0.05). In addition, o-coumaric acid injection increased the mRNA expression of FMO as 2.1-fold compared to controls (p<0.05). In conclusion, our data suggest that o-coumaric acid found in diet may induce FMO expression and FMO activity enhanced metabolism of drugs, pesticides, and other xenobiotics