45 research outputs found
Transformation-Invariant Dictionary Learning for Classification with 1-Sparse Representations
Sparse representations of images in well-designed dictionaries can be used for effective classification. Meanwhile, training data available in most realistic settings are likely to be exposed to geometric transformations, which poses a challenge for the design of good dictionaries. In this work, we study the problem of learning class-representative dictionaries from geometrically transformed image sets. In order to efficiently take account of arbitrary geometric transformations in the learning, we adopt a representation of the dictionaries in an analytic basis. Then, the proposed algorithm learns atoms that are attracted to the samples of their own class while being repelled from the samples of other classes so that the discrimination between different classes is promoted. The dictionary learning objective is formulated such that it enhances the class-discrimination capabilities of individual atoms rather than the ones of the subspaces they generate, which renders the designed dictionaries especially suitable for fast classification of query images with very sparse approximations. Experimental results demonstrate the performance of the proposed method in handwritten digit recognition applications
Intraoral premalign ve malign lezyonlu hastaların doku örneklerindeki candida türlerinin DNA analiziyle belirlenmesi ve sağlıklı doku ile karşılaştırılması
Amaç: Bu retrospektif çalışmada premalign ve malign lezyonlu ile sağlıklı
bireylere ait doku örneklerindeki Candida albicans, Candida kruseii,
Candida parapsilosis, Candida tropicalis ve Candida
glabrata türlerinin belirlenmesi amaçlanmıştır. Gereç ve Yöntem: Çalışmaya oral premalign veya malign lezyon şüphesi nedeniyle biyopsi
uygulanmış doku örnekleri dahil edildi. Örnekler histolojik özelliklerine göre
sağlıklı (n=20), displazi (n=20), karsinoma in-situ (n=20) ve skuamoz hücreli
karsinom (SHK) (n=20) olmak üzere 4 gruba ayrıldı. DNA izolasyonunun
ardından Candida türlerine ait DNA örneklerinin miktar ve
saflık kontrolleri gerçekleştirildi. Kantitatif ölçümler için Real-Time PCR
(LightCycler 96, Almanya) kullanıldı ve standart eğriler hesaplandı. Veriler
Mann-Whitney ve Wilcoxon Signed Ranks testleri ile değerlendirildi (P<0.05).Bulgular: Sağlıklı ve displazik örneklerin yer aldığı gruplarda C.
parapsilosis (104DNA/50 mg) en sık görülen Candida türüydü.
Karsinoma in-situ grubunda C. tropicalis ve C.
kruseii (103DNA/50 mg), SHK grubunda ise C.
kruseii (104DNA/50 mg) seviyelerinin daha yüksek olduğu
belirlendi. Örneklerin hiçbirinde C. albicans varlığı
gösterilemedi. Gruplar arasında farklı Candida türlerinin
sayısına göre anlamlı bir fark gözlenmedi (P>0.05). Farklı Candida türlerinin
gruplar içerisindeki seviyeleri incelendiğinde; sağlıklı örneklerde C.
glabrata (103DNA/50 mg), displazi grubunda C.
parapsilosis (104DNA/50 mg), karsinoma in-situ
grubunda C. tropicalis-C. kruseii (103DNA/50
mg), SHK grubunda ise C. kruseii’nin (103DNA/50 mg) en
fazla sayıda gözlenen Candida türü olduğu belirlendi. Candida türlerinin
gruplar içerisindeki dağılımı anlamlı değildi (P>0.05).Sonuç: Sağlıklı, displazik, karsinoma in situ ve skuamöz hücreli karsinoma doku
örneklerinde Real-Time PCR yöntemiyle yapılan kantitatif değerlendirmede Candida türlerinin
tüm gruplarda benzer oranda mevcut oldukları belirlendi.ANAHTAR
KELİMELER
Oral Candida, C. albicans,
ağız kanseri, Real-Time PCR, moleküler analiz  
Farklı periodontal hastalıklara sahip bireylerden alınan mikrobiyal dental plak örneklerinden elde edilen patojen mikroorganizmaların real-time PCR ile kalitatif ve kantitatif analizi
Periodontal hastalıklara mikrobiyoloji penceresinden bakıldığında, ağız florasına dahil mikroorganizmaların birbirleriyle ve çevreleriyle olan etkileşimlerden söz edilebilir. Bu etkileşimler oldukça geniş, kapsamlı ve dinamiktir. Hastalığa sebep olan mikroorganizmaların ise belirli bazı dental patojen bakterilerin olduğu bilinmektedir. Birçok çevresel faktörlerle birlikte bu bakterilerin davranışları da değişebilmektedir. Beslenme, sigara kullanımı, genetik yatkınlık gibi faktörler bakterilerin hastalıktaki şiddetini etkilemektedir Periodontal hastalıklara sebep olan bakterilerin nitel ve nicel olarak belirlenmesi, hastalığın seyrinin gözlenmesi ve periodontal tedavinin şekillenmesi açısından oldukça faydalı olacağı düşünülmektedir. Bu tez çalışmasında periodontal açıdan öneme sahip Porpyhromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Fusobacterium nucleatum ve Prevotella intermedia bakterilerinin Real-time PCR ile SYBR Green 1 boyası kullanılarak nitel ve nicel analizleri gerçekleştirilmiş, kronik ve agresif periodontitis durumlarındaki toplam bakteri miktarına göre oranları saptanmıştır. Bu amaçla kağıt kona (paperpoint) emdirilmiş olan 28 subgingival dental plak örneklerinden genomik DNA izolasyonu yapıldı. Daha önceden miktarları ve saflık derecesi bilinen, analiz edilecek olan her bir bakteri DNA’sı belirli oranlarda seyreltilerek uygun primerler ile birlikte standart eğri oluşturulmak üzere Real-time PCR’da reaksiyona tabi tutulmuştur. Reaksiyon sonunda oluşan ürünlerin verileri kullanılarak standart eğriler çıkarılmıştır. Her bir bakteriye özgü oluşturulan bu standart eğriler vasıtasıyla analiz sonuçları yorumlanmış ve sayısal veriler elde edilmiştir. Bunda sonra erime eğrisi analizleri yapılarak reaksiyon sonuçları doğrulanmıştır. Yapılan analizler sonucunda, tedavi başlangıcında kronik periodontitisli cepteki P. gingivalis oranı %72 iken bunu sırasıyla %21 ile T. forsythia, %6 ile F. nucleatum ve %1 ile P. intermedia olduğu görülmüştür. Her iki durumda da A. actinomycetemcomitans saptanamamıştır. Agresif periodontitis de ise P. gingivalis %39, F. nucleatum %24, A. actinomycetemcomitans %15, T. forsythia %14 ve P. intermedia %8 oranında görülmüştür. Tedavi sonrasında ise yine kronik periodontitisli cepte P. gingivalis %50, T. forsythia %28, F. nucleatum %20 ve P. intermedia %2 oranları görülürken, agresif periodontitisli ceplerde ise F. nucleatum %57, P. gingivalis %36 ve T. forsythia %7 olarak bulunmuştur. Kronik periodontitiste başlangıç toplam bakteri miktarı 5,53x106, agresifte ise 1,04x107, tedavi sonundaki miktarları ise sırasıyla 3,05x106 ve 1,14x106’dır. Tedavi öncesi ve sonrasında periodontal ceplerdeki toplam bakteri miktarının ortalama 106 civarında olduğu saptanmıştır. Agresif periodontitiste toplam bakteri yükü açısından ciddi bir düşüş gözlenmiştir. Her iki hastalık durumunda da F.nucleatum yüzdelerinde ciddi bir artış gözlenmektedir. Ayrıca tedavi sonunda A. actinomycetemcomitans yüzdeleri saptanamamıştır. Kronik periodontitis tedavi sonunda P.gingivalis yüzdelerinde önemli bir azalma göstermiştir. Her iki bakteri sayısındaki bu azalmalar tedavinin olumlu sonuç verdiğini göstermektedir
An Investigation on the Removal of High Concentrations of PAHs Using Two-Liquid Phase System
Two-liquid phase systems consisting of two insoluble liquids can be effective in removing high concentrations of hydrocarbons from aqueous environments. In this study, the removal efficiencies of Naphthalene (Nap), Acenaphthene (Acn), Fluorene (Flu), Fluoranthene (Flr), Anthracene (Ant), and Pyrene (Pyr) at high concentrations in the two-liquid phase system were investigated. Two-liquid phase systems were constituted using Bis (2-Ethylhexyl) sebacate (BES) and aqueous fermentation media. Nutrient Broth (NB) and Bushnell Haas Yeast (BHY) medium were used as aqueous fermentation media. Acn, Flu, Flr, Ant, Pyr, and Nap were degraded at a rate of 93.1%, 80.8%, 57.6%, 68.5%, 63.8%, and 100%, respectively with BES/NB system. In the BES/BHY system, Acn, Flu, Flr, Ant, Pyr, and Nap, were degraded at a rate of 29.6%, 44.3%, 22.8%, 68.1%, and 19.7%, 45.4%, respectively. When both systems are compared, it has been shown that the BES/NB system can be effective under specified conditions
Monitoring of the degradation of aromatic hydrocarbons by bioaugmented activated sludge
BACKGROUND the petrochemical industry wastewater contains many organic compounds that are difficult to degrade. the activated sludge system reinforced by bioaugmentation technology represents a more effective alternative to treat industrial wastewater. in this study, bioaugmented activated sludge water demonstrated high efficiency in removing five tested hydrocarbons. RESULTS Optimized degradation rates were obtained upon inoculation of a continuous bioreactor system with degradative bacteria (Acinetobacter sp., Aeromonas sp., Arthrobacter nicotianae, Burkholderia cepacia, Chryseobacterium sp., Pseudomonas fluorescens, Micrococcus luteus and Raoultella planticola). the addition of a hydrocarbon mixture (terephthalic acid, acenaphthene, fluorene, anthracene, and pyrene) into the bioaugmented sludge resulted in degradation rates equivalent to 97.90%, 99.87%, 98.89%, 97.28%, and 94.55% respectively after 24-48 h incubation. Molecular biomonitoring was performed with real-time quantitative polymerase chain reaction (qPCR). According to the obtained results, the numbers of copy DNA of the degradative bacteria increased by 0.36-1.13 log at the end of the degradation process. the presence of some oxygenase genes (Nah, NidA, Pah Rhd Gr(+), Pah Rhd Gr(-) and C23O), that catabolize aromatic hydrocarbons in activated sludge, were detected by specific primers. CONCLUSION Bioaugmentation represents a potent and eco-friendly approach that can effectively remove the drastic increase in the concentrations of aromatic hydrocarbons in industrial wastewaters. Molecular biomonitoring during degradation can be considered a rapid and an effective in situ method that quantifies the active microbial population in wastewater. the method provides beneficial information about the composition of microbial community and sustainability of the degradation process. (c) 2019 Society of Chemical IndustryMinistry of Science, Industry, and Technology of Republic of TurkeyMinistry of Science, Industry & Technology - Turkey [639 STZ 2010-2]; Ege UniversityEge University [11 Fen 007]This study was performed within the scope of works supported by the Ministry of Science, Industry, and Technology of Republic of Turkey (Santez Project No: 639 STZ 2010-2), and Ege University Scientific Research Project No: 11 Fen 007. the authors would also like to thank B. Karabey and D. Aksu for helping with the isolation of some degradative bacteria from previous works
Biodegradation of phthalic acid and terephthalic acid by Comamonas testosteroni strains
Phthalic acid isomers are the monomers of phthalate molecules, also known as phthalic acid esters, widely employed in the plastics industry. This study aims to investigate the biodegradation of phthalic acid (PA) and terephthalic acid (TPA) by five industry-borne Comamonas testosteroni strains: 3APTOL, 3ABBK, 2B, 3A1, and C8. To assess the ability of C. testosteroni strains to biodegrade phthalic acid isomers in fermentation media, an analytical method was employed, consisting of high-performance liquid chromatography (HPLC) analyses. Subsequently, molecular screening of the genomic and plasmid DNA was conducted to identify the degradative genes responsible for the breakdown of these chemicals. The genes of interest, including ophA2, tphA2, tphA3, pmdA, and pmdB, were screened by real-time PCR. The five C. testosteroni strains effectively degraded 100% of 100 mg/L PA (p = 0.033) and TPA (p = 0.0114). Molecular analyses indicated that all C. testosteroni strains contained the pertinent genes at different levels within their genomes and plasmids, as reflected in the threshold cycle (Ct) values. Additionally, DNA temperature of melting (Tm) analyses uncovered minor differences between groups of genes in genomic and plasmid DNA. C. testosteroni strains could be excellent candidates for the removal of phthalic acid isomers from environmental systems.Ege University Scientific Research Projects Coordination Unit [16-Fen-023]The authors would like to thank Prof. Dr. Gueven OEzdemir for allowing the use of his laboratory infrastructure and bacterial strains. This work was supported by the Ege University Scientific Research Projects Coordination Unit (Project No.: 16-Fen-023)
Current global status of Candida auris an emerging multidrug-resistant fungal pathogen: bibliometric analysis and network visualization
Background Candida auris is an emerging multidrug-resistant fungal pathogen associated with nosocomial infections and hospital outbreaks worldwide, presenting a serious global health threat. There has been a rapid emergence of scientific research publications focusing on therapeutic compounds, diagnostic techniques, control strategies, prevention, and understanding the epidemiology related to C. auris.Objective This study aims to provide the most up-to-date comprehensive and integrated examination of C. auris research subject and demonstrate that C. auris is indeed a topic of increasing interest.MethodsThe search query candida-auris was used as a topic term to find and retrieve relevant data published between 2009 and 15 June 2023, from the Web of Science Core Collection (WoSCC) database. In this work, the bibliometric analysis and network visualization were conducted using VOSviewer software, and Biblioshiny interface accessible through the Bibliometrix R-package on RStudio software.Results The yearly growth rate percentage (37.91%), along with the strong positive correlations between publications and citations (r = 0.981; p 0.001), suggests heightened scholarly engagement in this topic. The USA, India, China, and the UK have emerged as pivotal contributors, with the Centers for Disease Control and Prevention (CDC) in the USA being the most productive institution. Current research hotspots in this field mainly focused on identifying and limiting transmission of the clonal strains, epidemiology, antifungal resistance, and in vitro antifungal susceptibility testing.Conclusion This detailed bibliometric analysis in C. auris topic shows that this fungal pathogen has garnered growing attention and attracted progressively more scholars. This paper will help researchers to find without difficulty the relevant articles, research hotspots, influential authors, institutions, and countries related to the topic