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  1. Article ; Online: Solar ultraviolet radiation sensitivity of SARS-CoV-2.

    Seyer, Ayse / Sanlidag, Tamer

    The Lancet. Microbe

    2020  Volume 1, Issue 1, Page(s) e8–e9

    MeSH term(s) COVID-19 ; Humans ; Photosensitivity Disorders ; RNA, Viral ; SARS-CoV-2 ; Ultraviolet Rays/adverse effects
    Chemical Substances RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-05-11
    Publishing country England
    Document type Journal Article
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(20)30013-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Solar ultraviolet radiation sensitivity of SARS-CoV-2

    Ayse Seyer / Tamer Sanlidag

    The Lancet Microbe, Vol 1, Iss 1, Pp e8-e

    2020  Volume 9

    Keywords Medicine (General) ; R5-920 ; Microbiology ; QR1-502
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Solar ultraviolet radiation sensitivity of SARS-CoV-2

    Seyer, Ayse / Sanlidag, Tamer

    The Lancet Microbe

    2020  Volume 1, Issue 1, Page(s) e8–e9

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ISSN 2666-5247
    DOI 10.1016/s2666-5247(20)30013-6
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: An Alternative Diagnostic Method for C. neoformans

    Ayse Seyer Cagatan / Mubarak Taiwo Mustapha / Cemile Bagkur / Tamer Sanlidag / Dilber Uzun Ozsahin

    Diagnostics, Vol 13, Iss 1, p

    Preliminary Results of Deep-Learning Based Detection Model

    2022  Volume 81

    Abstract: Cryptococcus neoformans is an opportunistic fungal pathogen with significant medical importance, especially in immunosuppressed patients. It is the causative agent of cryptococcosis. An estimated 220,000 annual cases of cryptococcal meningitis (CM) occur ...

    Abstract Cryptococcus neoformans is an opportunistic fungal pathogen with significant medical importance, especially in immunosuppressed patients. It is the causative agent of cryptococcosis. An estimated 220,000 annual cases of cryptococcal meningitis (CM) occur among people with HIV/AIDS globally, resulting in nearly 181,000 deaths. The gold standards for the diagnosis are either direct microscopic identification or fungal cultures. However, these diagnostic methods need special types of equipment and clinical expertise, and relatively low sensitivities have also been reported. This study aims to produce and implement a deep-learning approach to detect C. neoformans in patient samples. Therefore, we adopted the state-of-the-art VGG16 model, which determines the output information from a single image. Images that contain C. neoformans are designated positive, while others are designated negative throughout this section. Model training, validation, testing, and evaluation were conducted using frameworks and libraries. The state-of-the-art VGG16 model produced an accuracy and loss of 86.88% and 0.36203, respectively. Results prove that the deep learning framework VGG16 can be helpful as an alternative diagnostic method for the rapid and accurate identification of the C. neoformans , leading to early diagnosis and subsequent treatment. Further studies should include more and higher quality images to eliminate the limitations of the adopted deep learning model.
    Keywords artificial intelligence ; C. neoformans ; cryptococcosis ; deep learning ; diagnosis ; Medicine (General) ; R5-920
    Subject code 006
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Epidemiology and Prevalence of

    Seyer, Ayse / Karasartova, Djursun / Ruh, Emrah / Güreser, Ayse Semra / Turgal, Ebru / Imir, Turgut / Taylan-Ozkan, Aysegul

    The American journal of tropical medicine and hygiene

    2017  Volume 96, Issue 5, Page(s) 1164–1170

    Abstract: AbstractThis study was conducted to investigate the prevalence ... ...

    Abstract AbstractThis study was conducted to investigate the prevalence of
    MeSH term(s) Adolescent ; Adult ; Blastocystis/classification ; Blastocystis/genetics ; Blastocystis/isolation & purification ; Blastocystis Infections/diagnosis ; Blastocystis Infections/epidemiology ; Blastocystis Infections/parasitology ; Child ; Cyprus/epidemiology ; DNA, Protozoan/genetics ; Feces/parasitology ; Female ; Genetic Variation ; Humans ; Male ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Prevalence ; Sequence Analysis, DNA ; Serotyping
    Chemical Substances DNA, Protozoan
    Language English
    Publishing date 2017-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2942-7
    ISSN 1476-1645 ; 0002-9637
    ISSN (online) 1476-1645
    ISSN 0002-9637
    DOI 10.4269/ajtmh.16-0706
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.61: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Is "dried stool spots on filter paper method (DSSFP)" more sensitive and effective for detecting Blastocystis spp. and their subtypes by PCR and sequencing?

    Seyer, Ayse / Karasartova, Djursun / Ruh, Emrah / Güreser, Ayse Semra / Imir, Turgut / Taylan-Ozkan, Aysegul

    Parasitology research

    2016  Volume 115, Issue 12, Page(s) 4449–4455

    Abstract: PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of ... ...

    Abstract PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of PCR inhibitors. Filter paper technology may provide a solution to these issues. The aim of the present study was to detect Blastocystis spp. and their subtypes by employing two different preservation methods: conventional frozen stool (FS) and dried stool spots on filter paper (DSSFP). Concentration and purity of DNA, sensitivity of PCR, and DNA sequencing results obtained from the two methods were also compared. A total of 230 fecal samples were included and separated into two parts: one part of the fecal samples were directly frozen and stored at -20 °C. The remaining portion of the specimens were homogenized with saline and spread onto the filter papers as thin layer with a diameter of approximately 3 cm. After air-dried, the filter papers were stored at room temperature. DSSFP samples were collected by scraping from the filter papers. DNA were extracted by EURx Stool DNA Extraction Kit from both samples. Concentration and purity were measured with Nano-Drop, then PCR and sequencing were conducted for detection of Blastocystis spp. and its genotypes. Pure DNA was obtained with a A260/A280 ratio of 1.7-2.2 in both methods. DNA yield from FS was 25-405 ng/μl and average DNA concentration was 151 ng/μl, while these were 7-339 and 122 ng/μl for DSSFP, respectively. No PCR inhibition was observed in two methods. DNA from DSSFP were found to be stable and PCR were reproducible for at least 1 year. FS-PCR- and DSSFP-PCR-positive samples were 49 (21.3 %) and 58 (25.3 %), respectively (p = 0.078). The 43 specimens were concordantly positive by both FS-PCR and DSSFP-PCR. When the microscopy was taken as the gold standard, sensitivity of DSSFP-PCR and FS-PCR was 95.5 and 86.4 %, while specificity of both tests was 99.4 and 98.3 %, respectively. DNA sequencing results of 19 microscopically confirmed cases were strictly identical (concordance 100 %) in both methods, and ST2:6, ST3:8, ST4:3, and ST6:2 were the detected subtypes. Among the 230 fecal samples, the most predominant subtypes were ST3, ST2, ST4, and ST1 by both FS and DSSFP methods. Concordance of DNA sequencing results obtained from the two methods was noted to be 90.7 %. To our knowledge, this is the first study that demonstrates DNA extraction from DSSFP is more sensitive and effective than the FS method for diagnosis of Blastocystis spp. and their subtypes by PCR and DNA sequencing.
    MeSH term(s) Analytic Sample Preparation Methods/instrumentation ; Analytic Sample Preparation Methods/methods ; Blastocystis/classification ; Blastocystis/genetics ; Blastocystis/isolation & purification ; Blastocystis Infections/diagnosis ; Blastocystis Infections/parasitology ; Feces/chemistry ; Feces/parasitology ; Filtration/instrumentation ; Filtration/methods ; Genotype ; Humans ; Paper ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Sequence Analysis, DNA
    Language English
    Publishing date 2016-12
    Publishing country Germany
    Document type Evaluation Studies ; Journal Article
    ZDB-ID 284966-5
    ISSN 1432-1955 ; 0932-0113 ; 0044-3255
    ISSN (online) 1432-1955
    ISSN 0932-0113 ; 0044-3255
    DOI 10.1007/s00436-016-5231-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uh II Zs.124: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: Is “dried stool spots on filter paper method (DSSFP)” more sensitive and effective for detecting Blastocystis spp. and their subtypes by PCR and sequencing?

    Seyer, Ayse / Ayse Semra Güreser / Aysegul Taylan-Ozkan / Djursun Karasartova / Emrah Ruh / Turgut Imir

    Parasitology research. 2016 Dec., v. 115, no. 12

    2016  

    Abstract: PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of ... ...

    Abstract PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of PCR inhibitors. Filter paper technology may provide a solution to these issues. The aim of the present study was to detect Blastocystis spp. and their subtypes by employing two different preservation methods: conventional frozen stool (FS) and dried stool spots on filter paper (DSSFP). Concentration and purity of DNA, sensitivity of PCR, and DNA sequencing results obtained from the two methods were also compared. A total of 230 fecal samples were included and separated into two parts: one part of the fecal samples were directly frozen and stored at −20 °C. The remaining portion of the specimens were homogenized with saline and spread onto the filter papers as thin layer with a diameter of approximately 3 cm. After air-dried, the filter papers were stored at room temperature. DSSFP samples were collected by scraping from the filter papers. DNA were extracted by EURx Stool DNA Extraction Kit from both samples. Concentration and purity were measured with Nano-Drop, then PCR and sequencing were conducted for detection of Blastocystis spp. and its genotypes. Pure DNA was obtained with a A260/A280 ratio of 1.7–2.2 in both methods. DNA yield from FS was 25–405 ng/μl and average DNA concentration was 151 ng/μl, while these were 7–339 and 122 ng/μl for DSSFP, respectively. No PCR inhibition was observed in two methods. DNA from DSSFP were found to be stable and PCR were reproducible for at least 1 year. FS-PCR- and DSSFP-PCR-positive samples were 49 (21.3 %) and 58 (25.3 %), respectively (p = 0.078). The 43 specimens were concordantly positive by both FS-PCR and DSSFP-PCR. When the microscopy was taken as the gold standard, sensitivity of DSSFP-PCR and FS-PCR was 95.5 and 86.4 %, while specificity of both tests was 99.4 and 98.3 %, respectively. DNA sequencing results of 19 microscopically confirmed cases were strictly identical (concordance 100 %) in both methods, and ST2:6, ST3:8, ST4:3, and ST6:2 were the detected subtypes. Among the 230 fecal samples, the most predominant subtypes were ST3, ST2, ST4, and ST1 by both FS and DSSFP methods. Concordance of DNA sequencing results obtained from the two methods was noted to be 90.7 %. To our knowledge, this is the first study that demonstrates DNA extraction from DSSFP is more sensitive and effective than the FS method for diagnosis of Blastocystis spp. and their subtypes by PCR and DNA sequencing.
    Keywords air drying ; ambient temperature ; Blastocystis ; diagnostic techniques ; DNA ; feces ; genotype ; microscopy ; polymerase chain reaction ; sequence analysis ; transportation
    Language English
    Dates of publication 2016-12
    Size p. 4449-4455.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 284966-5
    ISSN 1432-1955 ; 0932-0113 ; 0044-3255
    ISSN (online) 1432-1955
    ISSN 0932-0113 ; 0044-3255
    DOI 10.1007/s00436-016-5231-y
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 75/710: Show issues

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