PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 20Citation - Scopus: 23Estimation of Suspended Sediment Concentration in Rivers Using Acoustic Methods(Springer Verlag, 2009) Elçi, Şebnem; Aydın, Ramazan; Work, Paul A.Acoustic Doppler current meters (ADV, ADCP, and ADP) are widely used in water systems to measure flow velocities and velocity profiles. Although these meters are designed for flow velocity measurements, they can also provide information defining the quantity of particulate matter in the water, after appropriate calibration. When an acoustic instrument is calibrated for a water system, no additional sensor is needed to measure suspended sediment concentration (SSC). This provides the simultaneous measurements of velocity and concentration required for most sediment transport studies. The performance of acoustic Doppler current meters for measuring SSC was investigated in different studies where signal-to-noise ratio (SNR) and suspended sediment concentration were related using different formulations. However, these studies were each limited to a single study site where neither the effect of particle size nor the effect of temperature was investigated. In this study, different parameters that affect the performance of an ADV for the prediction of SSC are investigated. In order to investigate the reliability of an ADV for SSC measurements in different environments, flow and SSC measurements were made in different streams located in the Aegean region of Turkey having different soil types. Soil samples were collected from all measuring stations and particle size analysis was conducted by mechanical means. Multivariate analysis was utilized to investigate the effect of soil type and water temperature on the measurements. Statistical analysis indicates that SNR readings ob tained from the ADV are affected by water temperature and particle size distribution of the soil, as expected, and a prediction model is presented relating SNR readings to SSC mea surements where both water temperature and sediment characteristics type are incorporated into the model. The coefficients of the suggested model were obtained using the multivariate anal ysis. Effect of high turbidity conditions on ADV performance was also investigated during and after rain events.Article Citation - WoS: 8Citation - Scopus: 9Modeling of Polygalacturonase Enzyme Activity and Biomass Production by Aspergillus Sojae Atcc 20235(Springer Verlag, 2009) Tokatlı, Figen; Tarı, Canan; Ünlütürk, Mehmet; Göğüş, NihanAspergillus sojae, which is used in the making of koji, a characteristic Japanese food, is a potential candidate for the production of polygalacturonase (PG) enzyme, which of a major industrial significance. In this study, fermentation data of an A. sojae system were modeled by multiple linear regression (MLR) and artificial neural network (ANN) approaches to estimate PG activity and biomass. Nutrient concentrations, agitation speed, inoculum ratio and final pH of the fermentation medium were used as the inputs of the system. In addition to nutrient conditions, the final pH of the fermentation medium was also shown to be an effective parameter in the estimation of biomass concentration. The ANN parameters, such as number of hidden neurons, epochs and learning rate, were determined using a statistical approach. In the determination of network architecture, a cross-validation technique was used to test the ANN models. Goodness-of-fit of the regression and ANN models was measured by the R 2 of cross-validated data and squared error of prediction. The PG activity and biomass were modeled with a 5-2-1 and 5-9-1 network topology, respectively. The models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 value of 0.83, whereas the regression models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 of 0.69.Article Citation - WoS: 26Citation - Scopus: 31Groundwater Quality and Hydrogeochemical Properties of Torbali Region, Izmir, Turkey(Springer Verlag, 2008) Tayfur, Gökmen; Kırer, Tuğba; Baba, AlperThe large demand for drinking, irrigation and industrial water in the region of Torbalö (Izmir, Turkey) is supplied from groundwater sources. Almost every factory and farm has private wells that are drilled without permission. These cause the depletion of groundwater and limiting the usage of groundwater. This study investigates spatial and temporal change in groundwater quality, relationships between quality parameters, and sources of contamination in Torbali region. For this purpose, samples were collected from 10 different sampling points chosen according to their geological and hydrogeological properties and location relative to factories, between October 2001 and July 2002. Various physical (pH, temperature, EC), chemical (calcium, magnesium, potassium, sodium, chloride, alkalinity, copper, chromium, cadmium, lead, zinc) and organic (nitrate, nitrite, ammonia, COD and cyanide) parameters were monitored. It was observed that the groundwater has bicarbonate alkalinity. Agricultural contamination was determined in the region, especially during the summer. Nitrite and ammonia concentrations were found to be above drinking water standard. Organic matter contamination was also investigated in the study area. COD concentrations were higher than the permissible limits during the summer months of the monitoring period.Article Citation - WoS: 8Citation - Scopus: 8The Effects of Urease Immobilization on the Transport Characteristics and Protein Adsorption Capacity of Cellulose Acetate Based Hemodialysis Membranes(Springer Verlag, 2009) Yaşar Mahlıçlı, Filiz; Alsoy Altınkaya, SacideIn this study, cellulose acetate (CA) based hemodialysis membranes were prepared by a dry phase inversion method and the influences of urease immobilization on the clearing performance and protein adsorption capacity of the membranes were investigated. Permeation experiments have shown that modification of CA membranes with urease immobilization not only enhanced the transport rate of urea but also increased the permeation coefficients of uric acid and creatinine by changing the structure of the membrane. Furthermore, the protein adsorption capacity of the CA membranes decreased. On the other hand, the mechanical strength of the modified CA membrane did not change significantly compared with that of the unmodified one. A mathematical model was derived to determine the rate of mass transfer of urea through modified CA membranes. Model predictions along with the experimental data suggest that urease immobilization can be used as an alternative method in preparing CA based hemodialysis membranes with improved transport characteristics and biocompatibility through reduced protein adsorption capacities.Article Citation - WoS: 36Citation - Scopus: 46Expression of Vitreoscilla Hemoglobin in Gordonia Amarae Enhances Biosurfactant Production(Springer Verlag, 2006) Doğan, İlhan; Pagilla, Krishna R.; Webster, Dale A.; Stark, Benjamin C.The gene (vgb) encoding Vitreoscilla (bacterial) hemoglobin (VHb) was electroporated into Gordonia amarae, where it was stably maintained, and expressed at about 4 nmol VHb g -1 of cells. The maximum cell mass (OD 600) of vgb-bearing G. amarae was greater than that of untransformed G. amarae for a variety of media and aeration conditions (2.8-fold under normal aeration and 3.4-fold under limited aeration in rich medium, and 3.5-fold under normal aeration and 3.2-fold under limited aeration in mineral salts medium). The maximum level of trehalose lipid from cultures grown in rich medium plus hexadecane was also increased for the recombinant strain, by 4.0-fold in broth and 1.8-fold in cells under normal aeration and 2.1-fold in broth and 1.4-fold in cells under limited aeration. Maximum overall biosurfactant production was also increased in the engineered strain, by 1.4-fold and 2.4-fold for limited and normal aeration, respectively. The engineered strain may be an improved source for producing purified biosurfactant or an aid to microorganisms bioremediating sparingly soluble contaminants in situ.Article Citation - WoS: 115Citation - Scopus: 142Development of a Set of Pcr-Based Anchor Markers Encompassing the Tomato Genome and Evaluation of Their Usefulness for Genetics and Breeding Experiments(Springer Verlag, 2005) Farry, Anne; Xu, Yimin; Liu, Jiping; Mitchell, Sharon E.; Tedeschi, Eloisa; Tanksley, Steven D.Tomato and potato expressed sequence tag (EST) sequences contained in the solanaceae genomics network (SGN) database were screened for simple sequence repeat (SSR) motifs. A total of 609 SSRs were identified and assayed on Solanum lycopersicum LA925 (formerly Lycopersicon esculentum) and S. pennellii LA716 (formerly L. pennellii). The SSRs that did not amplify, gave multiple band products, or did not exhibit a polymorphism that could be readily detected on standard agarose gels in either of these species were eliminated. A set of 76 SSRs meeting these criteria was then placed on the S. lycopersicum (LA925) × S. pennellii (LA716) high-density map. A set of 76 selected cleaved amplified polymorphism (CAP) markers was also developed and mapped onto the same population. These 152 PCR-based anchor markers are uniformly distributed and encompass 95% of the genome with an average spacing of 10.0 cM. These PCR-based markers were further used to characterize S. pennellii introgression lines (Eshed and Zamir, Genetics 141:1147-1162, 1995) and should prove helpful in utilizing these stocks for high-resolution mapping experiments. The majority of these anchor markers also exhibit polymorphism between S. lycopersicum and two wild species commonly used as parents for mapping experiments, S. pimpinellifolium (formerly L. pimpinellifolium) and S. habrochaites (formerly L. hirsutum), indicating that they will be useful for mapping in other interspecific populations. Sixty of the mapped SSRs plus another 49 microsatellites were tested for polymorphism in seven tomato cultivars, four S. lycopersicum var. cerasiforme accessions and eight accessions of five different wild tomato species. Polymorphism information content values were highest among the wild accessions, with as many as 13 alleles detected per locus over all accessions. Most of the SSRs (90%) had accession-specific alleles, with the most unique alleles and heterozygotes usually found in accessions of self-incompatible species. The markers should be a useful resource for qualitative and quantitative trait mapping, marker-assisted selection, germplasm identification, and genetic diversity studies in tomato. The genetic map and marker information can be found on SGN ( http://www.sgn.cornell.edu ).Article Citation - WoS: 64Citation - Scopus: 82Advanced Backcross Qtl Analysis of a Lycopersicon Esculentum X L. Pennellii Cross and Identification of Possible Orthologs in the Solanaceae(Springer Verlag, 2004) Frary, Anne; Fulton, Theresa M.; Zamir, Dani; Tanksley, Steven D.In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC2 plants were genotyped with 150 molecular markers and BC2F1 plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs (fs2b.1, fw3.1/fsz3.1 andfs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.Article Citation - WoS: 50Citation - Scopus: 53Organization of Carboxysome Genes in the Thiobacilli(Springer Verlag, 2003) Cannon, Gordon C.; Baker, Stefanie H.; Soyer Dönmez, Ferda; Johnson, Diana R.; Bradburne, Christopher E.; Mehlman, Jennifer L.; Davies, Paige S.; Jiang, Qinli; Heinhorst, Sabine; Shively, Jessup M.The order of genes in the carboxysome gene clusters of four thiobacilli was examined and the possibility of the cluster forming an operon evaluated. Furthermore, carboxysome peptide homologs were compared with respect to similarities in primary sequence, and the unique structural features of the shell protein CsoS2 were described.Article Citation - WoS: 67Citation - Scopus: 81Qtl Analysis of Morphological Traits in Eggplant and Implications for Conservation of Gene Function During Evolution of Solanaceous Species(Springer Verlag, 2003) Frary, Anne; Doğanlar, Sami; Daunay, Marie-Christine; Tanksley, Steven D.An interspecific F2 population from a cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, was analyzed for quantitative trait loci (QTL) affecting leaf, flower, fruit and plant traits. A total of 58 plants were genotyped for 207 restriction fragment length polymorphism (RFLP) markers and phenotyped for 18 characters. One to eight loci were detected for each trait with a total of 63 QTL identified. Overall, 46% of the QTL had allelic effects that were the reverse of those predicted from the parental phenotypes. Wild alleles that were agronomically superior to the cultivated alleles were identified for 42% of the QTL identified for flowering time, flower and fruit number, fruit set, calyx size and fruit glossiness. Comparison of the map positions of eggplant loci with those for similar traits in tomato, potato and pepper revealed that 12 of the QTL have putative orthologs in at least one of these other species and that putative orthology was most often observed between eggplant and tomato. Traits showing potential orthology were: leaf length, shape and lobing; days to flowering; number of flowers per inflorescence; plant height and apex, leaf and stem hairiness. The functionally conserved loci included a major leaf lobing QTL (llob6.1) that is putatively orthologous to the potato leaf (c) and/or Petroselinum (Pts) mutants of tomato, two flowering time QTL (dtf1.1, dtf2.1) that also have putative counterparts in tomato and four QTL for trichomes that have potential orthologs in tomato and potato. These results support the mounting evidence of conservation of gene function during the evolution of eggplant and its relatives from their last common ancestor and indicate that this conservation was not limited to domestication traitsArticle Citation - WoS: 11Citation - Scopus: 16Influence of Menthol on Caffeine Disposition and Pharmacodynamics in Healthy Female Volunteers(Springer Verlag, 2003) Gelal, Ayşe; Güven, Hülya; Balkan, Dilara; Artok, Levent; Benowitz, Neal L.Objectives: The present study was undertaken to determine whether a single oral dose of menthol affects the metabolism of caffeine, a cytochrome P 450 1A2 (CYP1A2) substrate, and pharmacological responses to caffeine in people. Methods: Eleven healthy female subjects participated in a randomized, double-blind, two-way crossover study, comparing the kinetics and effects of a single oral dose of caffeine (200 mg) in coffee taken together with a single oral dose of menthol (100 mg) or placebo capsules. Serum caffeine concentrations and cardiovascular and subjective parameters were measured throughout the study. Results: Co-administration of menthol resulted in an increase of caffeine tmax values from 43.6 ± 20.6 min (mean ± SD) to 76.4 ± 28.0 min (P<0.05). The Cmax values of caffeine were lower in the menthol phase than in the placebo phase, but this effect was not statistically significant (P=0.06). (AUG)0-24, (AUC)0-∞, terminal half-life and oral clearance were not affected by menthol. Only nine subjects' cardiovascular data were included in the analysis because of technical problems during the measurements. After caffeine, heart rate decreased in both treatment phases. The maximum decrease in heart rate was less in the menthol phase (-8.9 ± 3.9 beats/min) than in the placebo phase (-13.1 ± 2.1 beats/min) (P = 0.024). There were no statistically significant differences in systolic and diastolic blood pressures between the two treatments. Conclusions: We conclude that a single oral dose of pure menthol (100 mg) delays caffeine absorption and blunts the heart-rate slowing effect of caffeine, but does not affect caffeine metabolism. The possibility that menthol slows the absorption of other drugs should be considered.