@article{Bradshaw2022,

title = {Nuclear Medicine and Artificial Intelligence: Best Practices for Algorithm Development },

author = {Tyler J. Bradshaw and Ronald Boellaard and Joyita Dutta and Abhinav K. Jha and Paul Jacobs and Quanzheng Li and Chi Liu and Arkadiusz Sitek and Babak Saboury and Peter J.H. Scott and Piotr J. Slomka and John J. Sunderland and Richard L. Wahl and Fereshteh Yousefirizi and Sven Zuehlsdorff and Arman Rahmim and Ir\`{e}ne Buvat

},

url = {https://doi.org/10.2967/jnumed.121.262567},

doi = {https://doi.org/10.2967/jnumed.121.262567},

year  = {2022},

date = {2022-04-01},

journal = {Journal of Nuclear Medicine},

abstract = {The nuclear medicine field has seen a rapid expansion of academic and commercial interest in developing artificial intelligence (AI) algorithms. Users and developers can avoid some of the pitfalls of AI by recognizing and following best practices in AI algorithm development. In this article, recommendations on technical best practices for developing AI algorithms in nuclear medicine are provided, beginning with general recommendations and then continuing with descriptions of how one might practice these principles for specific topics within nuclear medicine. This report was produced by the AI Task Force of the Society of Nuclear Medicine and Molecular Imaging.



},

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tppubtype = {article}

}

@article{nokey,

title = {COVID-19 Drug Repurposing: a Network-based Framework for Exploring BioMedical Literature and Clinical Trials for Possible Treatments},

author = {Ahmed Abdeen Hamed and Tamer E. Fandy and Karolina L. Tkaczuk and Byung Suk Lee

},

url = {https://doi.org/10.3390/pharmaceutics14030567

},

doi = {https://doi.org/10.3390/pharmaceutics14030567},

year  = {2022},

date = {2022-03-04},

urldate = {2022-03-04},

journal = {Pharmaceutics },

abstract = {Background: With the Coronavirus becoming a new reality of our world, global efforts continue to seek answers to many questions regarding the spread, variants, vaccinations, and medications. Particularly, with the emergence of several strains (e.g., Delta, Omicron), vaccines will need further development to offer complete protection against the new variants. It is critical to identify antiviral treatments while the development of vaccines continues. In this regard, the repurposing of already FDA-approved drugs remains a major effort. In this paper, we investigate the hypothesis that a combination of FDA-approved drugs may be considered as a candidate for COVID-19 treatment if (1) there exists an evidence in the COVID-19 biomedical literature that suggests such a combination, and (2) there is match in the clinical trials space that validates this drug combination. Methods: We present a computational framework that is designed for detecting drug combinations, using the following components (a) a Text-mining module: to extract drug names from the abstract section of the biomedical publications and the intervention/treatment sections of clinical trial records. (b) a network model constructed from the drug names and their associations, (c) a clique similarity algorithm to identify candidate drug treatments. Result and Conclusions: Our framework has identified treatments in the form of two, three, or four drug combinations (e.g., hydroxychloroquine, doxycycline, and azithromycin). The identifications of the various treatment candidates provided sufficient evidence that supports the trustworthiness of our hypothesis. View Full-Text

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Justifying Short-Term Load Forecasts Obtained with the Use of Neural Models},

author = {Tadeusz A. Grzeszczyk and Michal K. Grzeszczyk 

},

url = {https://www.mdpi.com/1996-1073/15/5/1852/pdf},

doi = {https://doi.org/10.3390/en15051852},

year  = {2022},

date = {2022-03-02},

journal = {Energies 2022, 15(5), 1852;},

abstract = {There is a lot of research on the neural models used for short-term load forecasting (STLF), which is crucial for improving the sustainable operation of energy systems with increasing technical, economic, and environmental requirements. Neural networks are computationally powerful; however, the lack of clear, readable and trustworthy justification of STLF obtained using such models is a serious problem that needs to be tackled. The article proposes an approach based on the local interpretable model-agnostic explanations (LIME) method that supports reliable premises justifying and explaining the forecasts. The use of the proposed approach makes it possible to improve the reliability of heuristic and experimental neural modeling processes, the results of which are difficult to interpret. Explaining the forecasting may facilitate the justification of the selection and the improvement of neural models for STLF, while contributing to a better understanding of the obtained results and broadening the knowledge and experience supporting the enhancement of energy systems security based on reliable forecasts and simplifying dispatch decisions.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Deep learning fetal ultrasound video model match human observers in biometric measurements},

author = {Szymon P\lotka and Adam Klasa and Aneta Lisowska and Joanna Seliga-Siwecka and Micha\l Lipa and Tomasz Trzci\'{n}ski and Arkadiusz Sitek

},

url = {https://iopscience.iop.org/article/10.1088/1361-6560/ac4d85/pdf},

doi = {https://doi.org/10.1088/1361-6560/ac4d85 },

year  = {2022},

date = {2022-02-16},

urldate = {2022-02-16},

journal = {Physics in Medicine \& Biology},

abstract = {Objective. This work investigates the use of deep convolutional neural networks (CNN) to automatically perform measurements of fetal body parts, including head circumference, biparietal diameter, abdominal circumference and femur length, and to estimate gestational age and fetal weight using fetal ultrasound videos. Approach. We developed a novel multi-task CNN-based spatio-temporal fetal US feature extraction and standard plane detection algorithm (called FUVAI) and evaluated the method on 50 freehand fetal US video scans. We compared FUVAI fetal biometric measurements with measurements made by five experienced sonographers at two time points separated by at least two weeks. Intra- and inter-observer variabilities were estimated. Main results. We found that automated fetal biometric measurements obtained by FUVAI were comparable to the measurements performed by experienced sonographers The observed differences in measurement values were within the range of inter- and intra-observer variability. Moreover, analysis has shown that these differences were not statistically significant when comparing any individual medical expert to our model. Significance. We argue that FUVAI has the potential to assist sonographers who perform fetal biometric measurements in clinical settings by providing them with suggestions regarding the best measuring frames, along with automated measurements. Moreover, FUVAI is able perform these tasks in just a few seconds, which is a huge difference compared to the average of six minutes taken by sonographers. This is significant, given the shortage of medical experts capable of interpreting fetal ultrasound images in numerous countries.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Towards efficient GPGPU Cellular Automata model implementation using persistent active cells},

author = {Pawe\l Renc and Tomasz P\k{e}cak and Alessio De Rango and William Spataro and Giuseppe Mendicino and Jaros\law W\k{a}s

},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1877750321001964?via%3Dihub},

doi = {https://doi.org/10.1016/j.jocs.2021.101538},

year  = {2022},

date = {2022-01-10},

journal = {Journal of Computational Science},

abstract = {Natural complex phenomena simulation relies on the application of advanced numerical models. Nevertheless, due to their inherent temporal and spatial computational complexity, efficient parallel computing algorithms are required in order to speed up simulation execution times. In this paper, we apply the Nvidia CUDA architecture to the simulation of a groundwater hydrological model based on the Cellular Automata formalism. Different implementations, using different memory access patterns and optimizations, regarding the application of persistent active cells (i.e., once a cell is activated, it remains such throughout a simulation), are presented and evaluated. The obtained results have demonstrated the full suitability of the approach in speeding up simulation times, thus resulting in a valid support for complex system modeling.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Multi-institutional evaluation of a deep learning model for fully automated detection of aortic aneurysms in contrast and non-contrast CT},

author = {Xie Y and Graf B and Farzam P and Baker B and Lamoureux C and Sitek A

},

url = {https://spie.org/medical-imaging/presentation/Multi-institutional-evaluation-of-a-deep-learning-model-for-fully/12033-135},

year  = {2022},

date = {2022-01-01},

journal = {SPIE Medical Imaging},

abstract = {We developed and validated a research-only deep learning (DL) based automatic algorithm to detect thoracic and abdominal aortic aneurysms on contrast and non-contrast CT images and compared its performance with assessments obtained from retrospective radiology reports. The DL algorithm was developed using 556 CT scans. Manual annotations of aorta centerlines and cross-sectional aorta boundaries were created to train the algorithm. Aorta segmentation and aneurysm detection performances were evaluated on 2263 retrospective CT scans (154 thoracic and 176 abdominal aneurysms). Evaluation was performed by comparing the automatically detected aneurysm status to the aneurysm status reported in the radiology reports and the AUC was reported. In addition, a quantitative evaluation was performed to compare the automatically measured aortic diameters to manual diameters on a subset of 59 CT scans. Pearson correlation coefficient was used. For aneurysm detection, the AUC was 0.95 for thoracic aneurysm detection (95% confidence region [0.93, 0.97]) and 0.94 for abdominal aneurysm detection (95% confidence region [0.92, 0.96]). For aortic diameter measurement, the Pearson correlation coefficient was 0.973 (p<0.001).

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Improved myocardial blood flow estimation with residual activity correction and motion correction in 18 F-flurpiridaz PET myocardial perfusion imaging},

author = {Yuka Otaki and Serge D. Van Kriekinge and Chih-Chun Wei and Paul Kavanagh and Ananya Singh and Tejas Parekh and Marcelo Di Carli and Jamshid Maddahi and Arkadiusz Sitek and Christopher Buckley and Daniel S. Berman and Piotr J. Slomka

},

url = {https://doi.org/10.1007/s00259-021-05643-2 

},

doi = {https://doi.org/10.1007/s00259-021-05643-2 },

year  = {2021},

date = {2021-12-30},

journal = {European Journal of Nuclear Medicine and Molecular Imaging },

abstract = {We sought to evaluate the diagnostic performance for coronary artery disease (CAD) of myocardial blood flow (MBF) quantification with 18F-flurpiridaz PET using motion correction (MC) and residual activity correction (RAC).



In total, 231 patients undergoing same-day pharmacologic rest and stress 18F-flurpiridaz PET from Phase III Flurpiridaz trial (NCT01347710) were studied. Frame-by-frame MC was performed and RAC was accomplished by subtracting the rest residual counts from the dynamic stress polar maps. MBF and myocardial flow reserve (MFR) were derived with a two-compartment early kinetic model for the entire left ventricle (global), each coronary territory, and 17-segment. Global and minimal values of three territorial (minimal vessel) and segmental estimation (minimal segment) of stress MBF and MFR were evaluated in the prediction of CAD. MBF and MFR were evaluated with and without MC and RAC (1: no MC/no RAC, 2: no MC/RAC, 3: MC/RAC).



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins},

author = {Irena Roterman and Katarzyna Stapor and Krzysztof G\k{a}dek and Tomasz Guba\la and Piotr Nowakowski and Piotr Fabian and Leszek Konieczny

},

url = {https://www.mdpi.com/2077-0375/12/1/50/pdf},

doi = {https://doi.org/10.3390/membranes12010050},

year  = {2021},

date = {2021-12-30},

urldate = {2021-12-30},

journal = {Membrane Biological Function in Health and Disease},

abstract = {The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sousa2021,

title = {COVID-19 Symptoms App Analysis to Foresee Healthcare Impacts: Evidence from Northern Ireland},

author = {Jos\'{e} Sousa and Jo\~{a}oBarata and Hugo C van Woerdend and Frank Kee},

url = {https://doi.org/10.1016/j.asoc.2021.108324

},

doi = {https://doi.org/10.1016/j.asoc.2021.108324},

year  = {2021},

date = {2021-12-20},

journal = {Applied Soft Computing},

abstract = {Mobile health (mHealth) technologies, such as symptom tracking apps, are crucial for coping with the global pandemic crisis by providing near real-time, in situ information for the medical and governmental response. However, in such a dynamic and diverse environment, methods are still needed to support public health decision-making. This paper uses the lens of strong structuration theory to investigate networks of COVID-19 symptoms in the Belfast metropolitan area. A self-supervised machine learning method measuring information entropy was applied to the Northern Ireland COVIDCare app. The findings reveal: (1) relevant stratifications of disease symptoms, (2) particularities in health-wealth networks, and (3) the predictive potential of artificial intelligence to extract entangled knowledge from data in COVID-related apps. The proposed method proved to be effective for near real-time in-situ analysis of COVID-19 progression and to focus and complement public health decisions. Our contribution is relevant to an understanding of SARS-COV-2 symptom entanglements in localised environments. It can assist decision-makers in designing both reactive and proactive health measures that should be personalised to the heterogeneous needs of different populations. Moreover, near real-time assessment of pandemic symptoms using digital technologies will be critical to create early warning systems of emerging SARS-CoV-2 strains and predict the need for healthcare resources.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expression in Alzheimer's Disease},

author = {Samar S. M. Elsheikh and Emile R. Chimusa and Alzheimer's Disease Neuroimaging Initiative and Nicola J. Mulder and Alessandro Crimi

},

url = {https://www.frontiersin.org/articles/10.3389/fnhum.2021.761424/pdf},

doi = {https://doi.org/10.3389/fnhum.2021.761424},

year  = {2021},

date = {2021-12-17},

journal = {Front Hum Neurosci},

abstract = {Networks are present in many aspects of our lives, and networks in neuroscience have recently gained much attention leading to novel representations of brain connectivity. The integration of neuroimaging characteristics and genetics data allows a better understanding of the effects of the gene expression on brain structural and functional connections. The current work uses whole-brain tractography in a longitudinal setting, and by measuring the brain structural connectivity changes studies the neurodegeneration of Alzheimer's disease. This is accomplished by examining the effect of targeted genetic risk factors on the most common local and global brain connectivity measures. Furthermore, we examined the extent to which Clinical Dementia Rating relates to brain connections longitudinally, as well as to gene expression. For instance, here we show that the expression of PLAU gene increases the change over time in betweenness centrality related to the fusiform gyrus. We also show that the betweenness centrality metric impact dementia-related changes in distinct brain regions. Our findings provide insights into the complex longitudinal interplay between genetics and brain characteristics and highlight the role of Alzheimer's genetic risk factors in the estimation of regional brain connectivity alterations.



},

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pubstate = {published},

tppubtype = {article}

}