Now showing 1 - 10 of 53
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    Q-FiberMapper-A framework for tractography and tractometry of clinical data
    (2022)
    Boshkovski, Tommy
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    Gallardo, Guillermo
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    Peria-Nogales, Oscar
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    Ramos, Marc
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    Smart city solution for early flood detection
    (IEEE, 2022-11-15)
    Stamenkova, Simona
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    Cavkovski, Pance
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    Risteska Stojkoska, Biljana
    Most of the world population is expected to live in urban areas in the future, therefore, there is an evident need for general smart city solutions, especially for big cities. The aim of this paper is: (i) to present an architecture for general smart city solution that collects different environmental parameters from different sites in a big city; (ii) to present implementation details of a separate module for flood detection that works on the top of the general solution; and (iii) to present a smart city application that monitors flood related parameters and informs residents if there is a flooded underpass, or increased water levels on a particular river or lake. The system collects environmental measurements using The Things Network, through LoRaWAN base stations.
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    Machine learning-supported MRI Radiomics to predict the volumetric response in meningiomas after Gamma Knife radiosurgery.
    (2022-01-02)
    Speckter, Herwin
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    Radulovic, Marko
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    Vranes, Velicko
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    Joaquin, Johanna
    Background: In previous studies, we analyzed the potential of both Diffusion Tensor Imaging and of Texture Analysis of Magnetic Resonance Imaging to predict the volumetric response of benign meningiomas to Gamma Knife radiosurgery (GKRS). In this study, we analyzed the value of meningioma morphology in the prediction of volumetric changes induced by GKRS. Methods: The retrospective prediction model of meningioma responsiveness to GKRS included T1- weighted, non-contrast enhanced MRI scans obtained from 93 patients before GKRS. Imaging data was processed and analyzed through the QMENTA cloud platform and meningioma morphology was quantified by calculation of 337 shape, first-order and second order radiomic features. This analysis was performed on original 3D unfiltered MR images and images modified by Laplacian of Gaussian (LoG), logarithm and exponential filters. Results: Sixty calculated features significantly correlated with the outcome defined as meningioma volume change per month. The predictive model was created based on all radiomic and twelve non-radiomic features using the LASSO regression machine learning method. Thereby, LoG-sigma-1-0-mm-3D_firstorder_InterquartileRange (coefficient weight = -9.916) and logarithm_ngtdm_ Busyness (coefficient = 0.002) were selected as the most predictively robust and non-redundant features. The radiomic score based on these two radiomic features produced an AUC = 0.81. Its values ranged between -2.89 and 2.48, whereby score values up to -1.31 defined a subgroup of 50 patients with consistent absence (0%) of tumor progression. Conclusions: This is the first report of a strong association between the MRI radiomic features and the volumetric meningioma response to radiosurgery. The clinical importance of the early and reliable prediction of meningioma responsiveness to GKRS is based on its potential to guide individualized treatment strategies.
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    A Survey of Graph Neural Network Architectures in Ligand Binding Affinity Prediction Models
    (IEEE, 2024-05-20)
    Fetaji, Fjolla
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    Ligand affinity prediction plays a pivotal role in drug discovery, influencing the efficiency and success of drug development processes. Traditional methods struggle in accurately capturing the complex interactions within molecular structures, prompting the exploration of advanced techniques such as Graph Neural Networks (GNNs). This paper provides an analysis of GNNs in the context of ligand affinity prediction, exploring their architecture, applications, and potential impact on revolutionizing drug discovery. Our findings suggest that GNNs can offer improvements over traditional computational methods, particularly in handling the dynamic and complex nature of molecular interactions. We highlight innovative GNN architectures that have shown notable success in predicting ligand binding affinities, such as heterogeneous graph representation and attention mechanisms. The implications of these advancements suggest a paradigm shift in drug discovery, where GNNs can lead to more accurate predictions and accelerate the identification of potential drug candidates. This study underscores the transformative potential of GNNs in enhancing predictive accuracy and efficiency in drug development.
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    O-076 Genomic and morphokinetic blueprint of mosaic embryos is evidence supporting their distinct clinical category
    (Oxford University Press, 2022-07-01)
    Madjunkov, M
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    Balakier, H
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    Abramov, R
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    Antes, R
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    Chen, S
    Study question Is there a correlation between blastocyst mosaicism, morphokinetic and morphologic characteristics and can it inform the clinical outcome of mosaic embryo transfers? Summary answer Mosaic (diploid/aneuploid) embryos have a distinct genetic, morphokinetic and morphologic signature that distinguishes them from euploid and abnormal embryos and supports their unique clinical identity. What is known already Advances in technologies for preimplantation aneuploidy testing (PGT-A) as the ultimate test for embryo selection has increased the resolution and sensitivity to detect intermediate chromosomal copy number as low as 20%. This has brought to light a biological phenomenon that has created clinical dilemma. Current recommendations support mosaic embryo transfer but with conflicting standpoints ranging from complete dismissal of mosaic embryos to arguing their existence. Time-lapse imaging technologies allow collection of morphokinetic data as a non-invasive assessment tool for embryo development. The aim of this study was to correlate genomic and morphokinetic data with clinical outcomes of mosaic embryos. Study design, size, duration This is a retrospective cohort study that took place in a single academic IVF centre, where we analysed the results from high resolution PGT-A, morphokinetic, morphologic and cell division features of 4113 embryos cultured in the time lapse imaging incubator (Embryoscope™) from 2016-2021. Associated patient data and transfer outcome of 770 euploid and 147 mosaic embryo transfers were analyzed. Participants/materials, setting, methods High resolution NGS PGT-A was performed using the Illumina platform and BluGnome and NxClinical for data analysis. Clinically relevant findings were aberrations >10Mb and mosaicism from 25%-75%. Time-lapse imaging was performed with an Embryoscope™. Comparison of clinical, morphological, morphokinetic characteristics of euploid, aneuploid, low-level mosaic (25%-<50% aneuploid cells in trophectoderm biopsy), and high-level mosaics (50% -75%) was done with R-statistical package, Mathlab and SSPS software were used, and p < 0.05 with CI 95% was considered significant. Main results and the role of chance Aneuploidy was detected in 26.2%, euploidy in 56.7% and diploid-aneuploid mosaicism in 17.1% of embryos included in this study. Compared with euploid embryos, mosaic embryos had significant delays in t2 (27.04±0.35vs.26.4±0.17 h-post-ICSI(hpi), p = 0.0029), which was not correlated with transfer outcome. Embryos with whole chromosome mosaicism (WCM) had longer t2 compared to those with segmental chromosome mosaicism (SCM) (27.29±0.59vs.26.4±0.3hpi,p=0.013). The time to first mitosis was also longer for mosaic vs. euploid embryos (4.57± 0.59vs.3.4±0.25hpi,p=0.000056) and for mosaic embryos with WCM vs SCM embryos (4.64± 0.9 vs 3.5 ±0.5hpi,p=0.04). Mosaic embryos had longer tB &tSB than euploid embryos (110.12±0.69vs.109.13hpi±0.4,p=0.01). Embryos with WCM had longer tB &tSB than those with SCM (111.07±1.09vs.108.7±0.8hpi,p=0.0006). Time to blast was longer for mosaic vs euploid embryos (13.69±0.52vs.12.7±0.4hpi,p=0.0035) and for mosaic WCM vs. SCM embryos (14.3±0.7vs.12.8±0.5hpi,p=0.00084). Both euploid and mosaic embryos that implanted had shorter time to tB&tSB than mosaic embryos that didn’t (p = 0.029; p = 0.007 and p = 0.002; p = 0.006 and p = 0.029 respectively); and mosaic embryos that implanted had shorter time to first mitosis than euploid embryos that didn’t (p = 0.00228). High level mosaic embryos had significantly more multinucleation at 2-cell stage (MN2) vs. euploid (p = 0.04,OD1.58-95%CI[1.01-2.45]),aneuploid (p = 0.02,OD1.7-95%CI[1.08-2.8]), as well as MN at 4-cell stage (euploid-p=0.0007,OD2.6-95CI1.4-4.7] and aneuploid-p=0.039,OD1.8-95CI1.02-3.4]). Limitations, reasons for caution Although this is the largest study to date that evaluated genomic, morphokinetic and outcome data of mosaic transfers, the numbers are still low to analyze the impact of specific chromosomal aberrations on morphokinetics and pregnancy outcome. The retrospective nature and cohort design limited the generalizability of our results. Wider implications of the findings Mosaic embryos have significant developmental potential and result in birth of healthy babies. Our study reveals the genomic interconnection of genomic and morphokinetic features of mosaic embryos and provides further evidence that mosaic embryos are a distinct category that requires specific clinical attention.
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    A Complete Air Pollution Monitoring and Prediction Framework
    (Institute of Electrical and Electronics Engineers (IEEE), 2023)
    Kalajdjieski, Jovan
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    Mirceva, Georgina
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    An Exploration of Autism Spectrum Disorder Classification from Structural and Functional MRI Images
    (Springer Nature Switzerland, 2022-09-29)
    Krajevski, Jovan
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    There are strong indications that structural and functional magnetic resonance imaging (MRI) may help identify biologically relevant phenotypes of neurodevelopmental disorders such as Autism spectrum disorder (ASD). Extracting patterns from MRI data is challenging due to the high dimensionality, limited cardinality and data heterogeneity. In this paper, we explore structural and resting state functional MRI (rs-fMRI) for ASD classification using available ABIDE II dataset, using several standard machine learning (ML) models and convolutional neural networks (CNNs). To overcome the high dimensionality problem, we propose a simple data transformation method based on histograms calculation for the standard ML models and a simple 3D-to-2D and 4D-to-3D data transformation method for the CNNs in ASD classification. Numerous research has been done for ASD classification using the online available ABIDE I dataset, and several with the ABIDE II dataset, the latter mostly working with single-site classification studies. Here, we take the whole ABIDE II dataset using all structural and functional raw data. Our results show that the proposed methods achive state-of-the art results of high 71.4% accuracy (functional) and 73.4% AUC (structural) compared to the best performing results in literature of 68% accuracy (functional) for ASD classification on all ABIDE dataset.
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    Is there an association between paternal age and aneuploidy? Evidence from young donor oocyte-derived embryos: a systematic review and individual patient data meta-analysis
    (Oxford University Press (OUP), 2021-05)
    Dviri, Michal
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    Madjunkova, Svetlana
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    Koziarz, Alex
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    Madjunkov, Mitko
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    Mashiach, Jordana
    Delayed parenthood, by both women and men, has become more common in developed countries. The adverse effect of advanced maternal age on embryo aneuploidy and reproductive outcomes is well known. However, whether there is an association between paternal age (PA) and embryonic chromosomal aberrations remains controversial. Oocyte donation (OD) is often utilized to minimize maternal age effects on oocyte and embryo aneuploidy, thus providing an optimal model to assess the effect of PA. Several studies have revealed a higher than expected rate of aneuploidy in embryos derived from young oocyte donors, which warrants examination as to whether this may be attributed to advanced PA (APA).
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    Check for updates Multiplex Collaboration Network of the Faculty of Computer Science and Engineering in Skopje
    (Springer Nature, 2024)
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    Multiplex collaboration networks facilitate intricate connections among individuals, enabling multidimensional collaborations across various domains and fostering synergistic knowledge exchange. This study focuses on the construction and basic analysis of a multiplex collaboration network among employees at the Faculty of Computer Science and Engineering (FCSE), Ss. Cyril and Methodius University in Skopje. The multiplex network is built with three layers based on: scientific collaborations resulting from joint project participations by FCSE employees, joint employees participations in the FCSE graduation thesis committees, and scientific FCSE employees collaborations defined by co-authorships in Google Scholar papers. The network's structure plays a vital role in determining the information accessibility and cooperative opportunities for individuals within FCSE institution. The aim here is to investigate the FCSE multiplex collaboration network's internal structure for discovering its latent knowledge and understand its implications. We perform identification of key individuals within the network, by computing various centrality and hubs detection network metrics. Additionally, we employ a community detection algorithm to reveal the underlying modular structure of the network. By comprehensively analyzing the acquired multiplex collaboration network model, we contribute to a better understanding of the collaboration patterns among FCSE employees. The findings can potentially inform decision-making processes and foster strategic planning aimed at enhancing collaboration and knowledge sharing within the institution.
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    Evaluation issues of different cryptography algorithms in wireless sensor networks
    (NATO-ARW, 2006-09-04)
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    Risteska Stojkoska, Biljana
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    Dimitrievski, Ace
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