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  1. Article ; Online: Exploring invasiveness and versatility of used microhabitats of the globally invasive Gambusia holbrooki.

    Kurtul, Irmak / Tarkan, Ali Serhan / Sarı, Hasan Musa / Haubrock, Phillip J / Soto, Ismael / Aksu, Sadi / Britton, J Robert

    The Science of the total environment

    2024  Volume 925, Page(s) 171718

    Abstract: Non-native species can lead to severe impacts on invaded ecosystems, including the decline of ecosystem function through deleterious impacts on species diversity. The successful establishment of non-native species in new environments is the first barrier ...

    Abstract Non-native species can lead to severe impacts on invaded ecosystems, including the decline of ecosystem function through deleterious impacts on species diversity. The successful establishment of non-native species in new environments is the first barrier a species must overcome, ultimately depending on its ability to either cope with or adapt to local site-specific conditions. Despite the widespread distribution and ecological consequences of many freshwater invaders, site-specific and climatic preferences are often unknown. This is also the case of the Eastern mosquitofish Gambusia holbrooki, a global invader considered as a pervasive threat to endemic species. Here, we determined the ecological features and preferred site-specific conditions of G. holbrooki in Türkiye, which spans a wide range of diverse biogeographically distinct ecosystems by surveying populations from 130 localities in 2016 and 2017. Gambusia holbrooki were detected by hand-net in 48 of these sites (19 lotic, 29 lentic). It showed a preference for shallow waters with medium sized rocks, and abundances differed spatially across a latitudinal gradient and was influenced predominantly by variations in pH. The only other factors predicting its presence were low current velocities and gravel substrate, highlighting its ecological versatility in utilising a wide range of microhabitats. Bioclimatic models suggest that G. holbrooki is found in areas with a wide average annual temperature ranging from 10 to 20 °C, but with temperature not being a limiting factor to its invasion. Gambusia holbrooki shows a preference for xeric freshwater ecosystems and endorheic basins, as well as temperate coastal rivers, temperate upland rivers, temperate floodplain rivers and wetlands, and tropical and subtropical coastal rivers. These results, particularly the wide occurrence with only few limiting factors, emphasise the invasion potential of mosquitofish and should substantiate the need for localised invasive species management and conservation efforts, particularly in smaller or insular areas where mosquitofish and endemic fish species co-exist.
    MeSH term(s) Animals ; Ecosystem ; Introduced Species ; Rivers ; Fresh Water ; Cyprinodontiformes
    Language English
    Publishing date 2024-03-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2024.171718
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: BolT: Fused window transformers for fMRI time series analysis.

    Bedel, Hasan A / Sivgin, Irmak / Dalmaz, Onat / Dar, Salman U H / Çukur, Tolga

    Medical image analysis

    2023  Volume 88, Page(s) 102841

    Abstract: Deep-learning models have enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) data. Yet, many previous methods are suboptimally sensitive for contextual representations across diverse time scales. Here, we present BolT, a ... ...

    Abstract Deep-learning models have enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) data. Yet, many previous methods are suboptimally sensitive for contextual representations across diverse time scales. Here, we present BolT, a blood-oxygen-level-dependent transformer model, for analyzing multi-variate fMRI time series. BolT leverages a cascade of transformer encoders equipped with a novel fused window attention mechanism. Encoding is performed on temporally-overlapped windows within the time series to capture local representations. To integrate information temporally, cross-window attention is computed between base tokens in each window and fringe tokens from neighboring windows. To gradually transition from local to global representations, the extent of window overlap and thereby number of fringe tokens are progressively increased across the cascade. Finally, a novel cross-window regularization is employed to align high-level classification features across the time series. Comprehensive experiments on large-scale public datasets demonstrate the superior performance of BolT against state-of-the-art methods. Furthermore, explanatory analyses to identify landmark time points and regions that contribute most significantly to model decisions corroborate prominent neuroscientific findings in the literature.
    MeSH term(s) Humans ; Magnetic Resonance Imaging ; Time Factors
    Language English
    Publishing date 2023-05-18
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2023.102841
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Bakırçay Nehri (Kuzey Ege, Türkiye) Balık Faunası

    Irmak Kurtul / Ali İlhan / Hasan Sarı

    Su Ürünleri Dergisi, Vol 37, Iss 3, Pp 309-

    2020  Volume 312

    Abstract: Bakırçay Nehri’nin güncel balık faunasının belirlenmesi amacıyla yapılan bu çalışma, 2017 ve 2018 yılları içerisinde mevsimlik periyotlarda gerçekleştirilmiştir. Nehrin kaynağını oluşturan küçük derelerden mansap bölgesine kadar 11 lotik ve 4 lentik ... ...

    Abstract Bakırçay Nehri’nin güncel balık faunasının belirlenmesi amacıyla yapılan bu çalışma, 2017 ve 2018 yılları içerisinde mevsimlik periyotlarda gerçekleştirilmiştir. Nehrin kaynağını oluşturan küçük derelerden mansap bölgesine kadar 11 lotik ve 4 lentik olmak üzere 15 farklı lokasyonda örnekleme yapılmıştır. Örneklemeler, lotik habitatlarda “Samus 725 G” model elektroşoker, lentik habitatlarda ise “TS EN 14757 Su Kalitesi” kriterine uygun standart ağlar ile gerçekleştirilmiştir. Çalışma sonucunda, Anguillidae, Atherinidae, Cobitidae, Cyprinidae, Nemacheilidae, Poecilidae ve Gobiidae olmak üzere 7 familyadan 17 taksonun varlığı belirlenmiştir. Akarsu bünyesinde daha önce bildirimi yapılmış olan Mugilidae familyası türleri ile Salaria pavo türü çalışmamızda elde edilememiştir. Ancak, önceki çalışmalarda yer almayan Atherina boyeri, Cyprinus carpio, Carassius gibelio, Oxynemacheilus teophili, Gambusia holbrooki ve Knipowitschia caucasica olmak üzere 6 türün varlığı ilk kez bu çalışmada tespit edilmiştir. Nehir havzasında, tür çeşitliliği açısından Cyprinidae familyası 11 takson ile ilk sırada yer almaktadır. Anguillidae, Atherinidae, Cobitidae, Nemacheilidae, Poecilidae ve Gobiidae familyaları ise 1’er takson ile temsil edilmektedir. Nehrin biyoçeşitliliğinin korunması ve balıkçılık faaliyetlerinin etkin şekilde sürdürülebilmesi bakımından öncelikle, kirlilik kaynaklarının kontrol altına alınması gerekmektedir.
    Keywords bakırçay stream ; ichthyofauna ; distribution ; alien species ; bakırçay ; ihtiyofauna ; dağılım ; biyoçeşitlilik ; Aquaculture. Fisheries. Angling ; SH1-691 ; Ecology ; QH540-549.5
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Ege University
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Bakırçay Nehri (Kuzey Ege, Türkiye) Balık Faunası

    Ali İlhan / Hasan Sarı / Irmak Kurtul

    Su Ürünleri Dergisi, Vol 37, Iss 3, Pp 309-

    2020  Volume 312

    Abstract: Bakırçay Nehri’nin güncel balık faunasının belirlenmesi amacıyla yapılan bu çalışma, 2017 ve 2018 yılları içerisinde mevsimlik periyotlarda gerçekleştirilmiştir. Nehrin kaynağını oluşturan küçük derelerden mansap bölgesine kadar 11 lotik ve 4 lentik ... ...

    Abstract Bakırçay Nehri’nin güncel balık faunasının belirlenmesi amacıyla yapılan bu çalışma, 2017 ve 2018 yılları içerisinde mevsimlik periyotlarda gerçekleştirilmiştir. Nehrin kaynağını oluşturan küçük derelerden mansap bölgesine kadar 11 lotik ve 4 lentik olmak üzere 15 farklı lokasyonda örnekleme yapılmıştır. Örneklemeler, lotik habitatlarda “Samus 725 G” model elektroşoker, lentik habitatlarda ise “TS EN 14757 Su Kalitesi” kriterine uygun standart ağlar ile gerçekleştirilmiştir. Çalışma sonucunda, Anguillidae, Atherinidae, Cobitidae, Cyprinidae, Nemacheilidae, Poecilidae ve Gobiidae olmak üzere 7 familyadan 17 taksonun varlığı belirlenmiştir. Akarsu bünyesinde daha önce bildirimi yapılmış olan Mugilidae familyası türleri ile Salaria pavo türü çalışmamızda elde edilememiştir. Ancak, önceki çalışmalarda yer almayan Atherina boyeri, Cyprinus carpio, Carassius gibelio, Oxynemacheilus teophili, Gambusia holbrooki ve Knipowitschia caucasica olmak üzere 6 türün varlığı ilk kez bu çalışmada tespit edilmiştir. Nehir havzasında, tür çeşitliliği açısından Cyprinidae familyası 11 takson ile ilk sırada yer almaktadır. Anguillidae, Atherinidae, Cobitidae, Nemacheilidae, Poecilidae ve Gobiidae familyaları ise 1’er takson ile temsil edilmektedir. Nehrin biyoçeşitliliğinin korunması ve balıkçılık faaliyetlerinin etkin şekilde sürdürülebilmesi bakımından öncelikle, kirlilik kaynaklarının kontrol altına alınması gerekmektedir.
    Keywords bakırçay stream ; ichthyofauna ; distribution ; alien species ; bakırçay ; ihtiyofauna ; dağılım ; biyoçeşitlilik ; Aquaculture. Fisheries. Angling ; SH1-691 ; Ecology ; QH540-549.5
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Ege University
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: A plug-in graph neural network to boost temporal sensitivity in fMRI analysis

    Sivgin, Irmak / Bedel, Hasan A. / Öztürk, Şaban / Çukur, Tolga

    2023  

    Abstract: Learning-based methods have recently enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) time series. Deep learning models that receive as input functional connectivity (FC) features among brain regions have been commonly ... ...

    Abstract Learning-based methods have recently enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) time series. Deep learning models that receive as input functional connectivity (FC) features among brain regions have been commonly adopted in the literature. However, many models focus on temporally static FC features across a scan, reducing sensitivity to dynamic features of brain activity. Here, we describe a plug-in graph neural network that can be flexibly integrated into a main learning-based fMRI model to boost its temporal sensitivity. Receiving brain regions as nodes and blood-oxygen-level-dependent (BOLD) signals as node inputs, the proposed GraphCorr method leverages a node embedder module based on a transformer encoder to capture temporally-windowed latent representations of BOLD signals. GraphCorr also leverages a lag filter module to account for delayed interactions across nodes by computing cross-correlation of windowed BOLD signals across a range of time lags. Information captured by the two modules is fused via a message passing algorithm executed on the graph, and enhanced node features are then computed at the output. These enhanced features are used to drive a subsequent learning-based model to analyze fMRI time series with elevated sensitivity. Comprehensive demonstrations on two public datasets indicate improved classification performance and interpretability for several state-of-the-art graphical and convolutional methods that employ GraphCorr-derived feature representations of fMRI time series as their input.
    Keywords Electrical Engineering and Systems Science - Signal Processing
    Subject code 006
    Publishing date 2023-01-01
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Climatic and geographic variation as a driver of phenotypic divergence in reproductive characters and body sizes of invasive Gambusia holbrooki

    Kurtul, Irmak / Tarkan, Ali Serhan / Sarı, Hasan Musa / Britton, J. Robert

    Aquatic sciences. 2022 Apr., v. 84, no. 2

    2022  

    Abstract: Understanding the invasion success of alien species includes developing knowledge on how the biological traits of their populations respond to spatial differences in environmental conditions. For invasive fishes, while the influence of latitudinal and ... ...

    Abstract Understanding the invasion success of alien species includes developing knowledge on how the biological traits of their populations respond to spatial differences in environmental conditions. For invasive fishes, while the influence of latitudinal and climatic gradients on their biological traits over large spatial scales is well established, there is less certainty in how these vary over smaller scales. Here, we tested the influence of a climatic and geographic gradient on the reproductive traits and body sizes of the invasive mosquitofish Gambusia holbrooki across five climatic regions in Turkey. The results revealed that the environmental conditions across eight sites provided two gradients: a latitudinal gradient (where northern sites were cooler with less rainfall) and a coastal–inland gradient (where changes were apparent from coastal areas and into inland areas). These gradients had marked effects on the traits of both sexes. In sites in coastal and southern areas, males had significantly larger gonopodia and females had greater fecundity than in inland and warmer areas, and with both sexes having body sizes that were smaller. The spatial differences in the male traits were suggested as being driven by differences in selection pressures at the sites that related to differences in their population abundances. The results revealed that environmental conditions across a relatively small spatial scale had some strong influences on the expression of specific biological traits of these mosquitofish populations, but with further work needed to test how these influences affect their invasion success.
    Keywords Gambusia holbrooki ; colonizing ability ; fecundity ; geographical variation ; introduced species ; males ; phenotypic variation ; rain
    Language English
    Dates of publication 2022-04
    Size p. 29.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 1464021-1
    ISSN 1420-9055 ; 1015-1621
    ISSN (online) 1420-9055
    ISSN 1015-1621
    DOI 10.1007/s00027-022-00862-7
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Molecular characterization of goose parvovirus in geese of Turkey

    Oya Bulut / Irmak Dik / Hatice P. Aslim / Cagri Avci / Hasan S. Palanci / Sezer Akbaba / Varol Çivril / Hasan H. Hadimli

    Pesquisa Veterinária Brasileira, Vol

    2021  Volume 41

    Abstract: ABSTRACT: Goose parvovirus (GPV), also called Derzsy’s disease, is a viral pathogen that causes high morbidity and mortality in goslings and ducklings. In this study, we perform the molecular characterization of the GPV in Turkey. The definition of ... ...

    Abstract ABSTRACT: Goose parvovirus (GPV), also called Derzsy’s disease, is a viral pathogen that causes high morbidity and mortality in goslings and ducklings. In this study, we perform the molecular characterization of the GPV in Turkey. The definition of similarity to the world of GPV isolates in Turkey and construction of a phylogenetic tree was aimed. For this purpose, the presence of GPV in the liver, spleen, and intestine tissues of nine goslings with symptoms such as dysphagia, bilateral ocular swelling, eye discharge, diarrhea, and fatigue were investigated by real-time PCR method and all samples were detected as positive. According to the data obtained by molecular characterization, phylogenetic analysis of GPV has been presented in Turkey. As a result of this study, it was determined that the GPVs available in Turkey are virulent strains.
    Keywords Goose parvovirus ; real-time pcr ; phylogenetic analysis ; Turkey ; geese ; Veterinary medicine ; SF600-1100
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Colégio Brasileiro de Patologia Animal (CBPA)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: A MAP-Based Approach for Hyperspectral Imagery Super-resolution.

    Irmak, Hasan / Akar, Gozde Bozdagi / Yuksel, Seniha Esen

    IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

    2018  

    Abstract: In this study, we propose a novel single image Bayesian super-resolution (SR) algorithm where the hyperspectral image (HSI) is the only source of information. The main contribution of the proposed approach is to convert the ill-posed SR reconstruction ( ... ...

    Abstract In this study, we propose a novel single image Bayesian super-resolution (SR) algorithm where the hyperspectral image (HSI) is the only source of information. The main contribution of the proposed approach is to convert the ill-posed SR reconstruction (SRR) problem in the spectral domain to a quadratic optimization problem in the abundance map domain. In order to do so, Markov Random Field (MRF) based energy minimization approach is proposed and proved that the solution is quadratic. The proposed approach consists of five main steps. First, the number of endmembers in the scene is determined using virtual dimensionality. Second, the endmembers and their low resolution abundance maps are computed using simplex identification via the splitted augmented Lagrangian (SISAL) and fully constrained least squares (FCLS) algorithms. Third, high resolution (HR) abundance maps are obtained using our proposed maximum a posteriori (MAP) based energy function. This energy function is minimized subject to smoothness, unity and boundary constraints. Fourth, the HR abundance maps are further enhanced with texture preserving methods. Finally, HR HSI is reconstructed using the extracted endmembers and the enhanced abundance maps. The proposed method is tested on three real HSI datasets; namely the Cave, Harvard and Hyperspectral Remote Sensing Scenes (HRSS) and compared to state-of-the-art alternative methods using peak signal to noise ratio, structural similarity, spectral angle mapper and relative dimensionless global error in synthesis metrics. It is shown that the proposed method outperforms the state of the art methods in terms of quality while preserving the spectral consistency.
    Language English
    Publishing date 2018-03-09
    Publishing country United States
    Document type Journal Article
    ISSN 1941-0042
    ISSN (online) 1941-0042
    DOI 10.1109/TIP.2018.2814210
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Analysis of different urban spaces on thermal comfort in cold regions: a case from Erzurum

    Irmak, Mehmet Akif / Yilmaz, Sevgi / Mutlu, Emral / Yilmaz, Hasan

    Theoretical and applied climatology. 2020 Aug., v. 141, no. 3-4

    2020  

    Abstract: With the rapid rise in population density in urban areas, there has also been an increase in research on quality of life and the effects of green space on health and comfort in densely populated cities. A critical part of improving the quality of life in ...

    Abstract With the rapid rise in population density in urban areas, there has also been an increase in research on quality of life and the effects of green space on health and comfort in densely populated cities. A critical part of improving the quality of life in urban areas is the reduction of urban heat island effect, especially in hot climate cities, and the reduction of adverse effects of winter in cold climates. Urban planning and landscape design strategies can have a great impact on urban microclimates, thereby providing relief from the harsh effects of climate change. Studies reveal that the cultivation of wetlands and open green spaces can have a direct impact on microclimate and comfort in densely populated areas. Erzurum is under the cold stress of the decreasing temperature in winter and continues to experience extreme temperatures in summer. This study is focused on the effects of urban design and landscape architectural interventions in the city of Erzurum. For this purpose, meteorological stations were placed in intensive construction areas of the urban city center, in wetland areas, and in the forested area of Ata Botanical Park in the city center. Three stations, dense green areas (1), temporary wetlands (2), and urban city center areas (3), were selected as urban area use types. Meteorological data were collected during March–April when the wetlands were full due to heavier periods of rain, and during July–August, the hottest months in the city. Thermal comfort values have been analyzed for different areas using RayMan soft model. The average value of Physiologically Equivalent Temperature (PET) recorded in March–April was 3.5 °C in the city center, 2.8 °C in the dense green area, and − 0.3 °C around the temporary wetland area. In July and August, the average value of PET in the city center was 24.9 °C, 23.0 °C in dense green areas, and 21.2 °C around the wetland area. In cold cities, it was found that the water surfaces, which positively contribute to thermal comfort in summer, increased the cold stress in winter. It was determined that dense green areas function as balancing factors for thermal comfort of the city both for summer and winter seasons and they contributed positively in all conditions. As a result of this study, more accurate decisions can be made for future urban planning efforts by considering the effects of different environmental conditions on microclimates in the city, especially where this consideration can be applied to urban design and development, urban revitalization efforts, or when designing new settlements.
    Keywords climate change ; climatology ; cold ; cold stress ; forests ; green infrastructure ; heat island ; landscaping ; meteorological data ; microclimate ; models ; population density ; quality of life ; rain ; summer ; temperature ; wetlands ; winter
    Language English
    Dates of publication 2020-08
    Size p. 1593-1609.
    Publishing place Springer Vienna
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1463177-5
    ISSN 1434-4483 ; 0177-798X
    ISSN (online) 1434-4483
    ISSN 0177-798X
    DOI 10.1007/s00704-020-03289-y
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Plasmonic Titanium Nitride Nanohole Arrays for Refractometric Sensing.

    Günaydın, Beyza Nur / Gülmez, Mert / Torabfam, Milad / Pehlivan, Zeki Semih / Tütüncüoğlu, Atacan / Kayalan, Cemre Irmak / Saatçioğlu, Erhan / Bayazıt, Mustafa Kemal / Yüce, Meral / Kurt, Hasan

    ACS applied nano materials

    2023  Volume 6, Issue 22, Page(s) 20612–20622

    Abstract: Group IVB metal nitrides have attracted great interest as alternative plasmonic materials. Among them, titanium nitride (TiN) stands out due to the ease of deposition and relative abundance of Ti compared to those of Zr and Hf metals. Even though they do ...

    Abstract Group IVB metal nitrides have attracted great interest as alternative plasmonic materials. Among them, titanium nitride (TiN) stands out due to the ease of deposition and relative abundance of Ti compared to those of Zr and Hf metals. Even though they do not have Au or Ag-like plasmonic characteristics, they offer many advantages, from high mechanical stability to refractory behavior and complementary metal oxide semiconductor-compatible fabrication to tunable electrical/optical properties. In this study, we utilized reactive RF magnetron sputtering to deposit plasmonic TiN thin films. The flow rate and ratio of Ar/N
    Language English
    Publishing date 2023-11-14
    Publishing country United States
    Document type Journal Article
    ISSN 2574-0970
    ISSN (online) 2574-0970
    DOI 10.1021/acsanm.3c03050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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