Article
Computer Science, Artificial Intelligence
Caglar Cakan, Nikola Jajcay, Klaus Obermayer
Summary: neurolib is a computational framework for whole-brain modeling written in Python, which can load structural and functional datasets, simulate and analyze whole-brain models, and optimize the models.
COGNITIVE COMPUTATION
(2023)
Review
Neurosciences
Guoshi Li, Pew-Thian Yap
Summary: Connectomics, as a newly emerging field, greatly advances our understanding of the wiring diagram and organizational features of the human brain. Generative modeling-based connectome analysis is crucial in deciphering the neural mechanisms of cognitive functions in health and dysfunction in diseases. The shift from descriptive connectome to mechanistic connectome opens up promising avenues for gaining mechanistic insights into the delicate operating principles of the human brain and their potential impairments in diseases.
FRONTIERS IN HUMAN NEUROSCIENCE
(2022)
Review
Engineering, Biomedical
Seokyoung Bang, Kyeong Seob Hwang, Sohyeon Jeong, Il-Joo Cho, Nakwon Choi, Jongbaeg Kim, Hong Nam Kim
Summary: The neural circuits of the central nervous system play crucial roles in various functions and dysfunctions are closely related to neurodegenerative diseases. In vitro human neural circuits provide a valuable alternative approach by allowing access to cellular compartments and real-time monitoring. These engineered neural circuit models recapitulate the characteristics of in vivo neural circuits, contributing to a better understanding of neural circuit physiology and potential applications in studying brain diseases.
ACTA BIOMATERIALIA
(2021)
Article
Materials Science, Multidisciplinary
Soheil Firooz, Stefan Kaessmair, Vasily Zaburdaev, Ali Javili, Paul Steinmann
Summary: Cellular aggregates play a significant role in the evolution of biological systems. This study proposes a non-linear continuum mechanics formulation and finite element simulation framework to model the physics of cellular aggregate formation, focusing on bacterial colony formation as an example. The study describes the aggregation process as an active phase separation phenomenon and investigates the influence of various parameters on the dynamics of cellular aggregate formation through numerical examples.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2022)
Article
Audiology & Speech-Language Pathology
Suyi Hu, Deborah A. Hall, Frederic Zubler, Raphael Sznitman, Lukas Anschuetz, Marco Caversaccio, Wilhelm Wimmer
Summary: This study developed a generative computational tinnitus perception model based on the Bayesian brain concept, successfully replicating behavioral responses during residual inhibition and simulating residual excitation and occurrence of tinnitus in non-tinnitus subjects after sensory deprivation. The model has the potential to quantitatively link experimental observations to theoretical hypotheses and support the search for neural signatures of tinnitus.
Article
Computer Science, Interdisciplinary Applications
Heber Fabbri, Marcelo Sanchez, Michael Maedo, Pedro Cleto, Osvaldo Manzoli
Summary: In this study, the fragmentation technique (MFT) is proposed to model evolving fractures in clays triggered by gas pressurization. The method is successfully verified against analytical solutions and applied to simulate gas breakthrough experiments in clays, showing a very satisfactory performance. This demonstrates the potential of the MFT to tackle multiphase flow problems in deformable porous media with evolving discontinuities.
COMPUTERS AND GEOTECHNICS
(2023)
Review
Engineering, Environmental
Jasir Jawad, Alaa H. Hawari, Syed Javaid Zaidi
Summary: Global population growth has resulted in freshwater scarcity, with artificial intelligence models emerging as popular tools for simulating and optimizing water treatment processes. Membrane processes and desalination techniques are being used to address household and industrial water demands.
CHEMICAL ENGINEERING JOURNAL
(2021)
Review
Cell Biology
Raj Bose, Soumyabrata Banerjee, Gary L. Dunbar
Summary: Brain organoids are important in vitro tools for modeling various aspects of brain development and disorders, providing insights into the molecular mechanisms involved in neurological diseases. Models derived from induced pluripotent stem cells (iPSCs), including 2D, 3D, and blood-brain barrier models, have advantages in disease modeling and can be used to develop vascularized and functional 3D models of brain processes. The applications of brain organoids for modeling major neurodegenerative diseases and neurodevelopmental disorders are also explored in this review.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Min Soo Kim, Da-Hyun Kim, Hyun Kyoung Kang, Myung Geun Kook, Soon Won Choi, Kyung-Sun Kang
Summary: Novel brain organoid model systems have been developed from adult dermal fibroblast-derived neural stem cells, exhibiting characteristics of the human cerebral cortex for studying neuronal proliferation and maturation. When subjected to hypoxic injury, reoxygenation restored neuronal cell proliferation but not maturation in these neural organoids, suggesting new opportunities for drug screening and personalized modeling of neurodegenerative diseases.
Article
Physics, Multidisciplinary
Prejaas Tewarie, Bastian Prasse, Jil Meier, Aine Byrne, Manlio De Domenico, Cornelis J. Stam, Matthew J. Brookes, Arjan Hillebrand, Andreas Daffertshofer, Stephen Coombes, Piet Van Mieghem
Summary: Recent studies suggest that treating neurophysiological networks separately for different frequency bands may be inadequate due to significant coupling between these bands. A multilayer network approach allows for analyzing frequency-specific networks in a unified framework, with interlayer connectivity playing a crucial role in network reconstruction.
NEW JOURNAL OF PHYSICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Chao Zhang, Lifeng Wang, Wenhua Ye, Junfeng Wu, Zhijun Shen, Igor Menshov
Summary: The article proposes a diffuse interface model for compressible multicomponent flows with mass, momentum, and energy transport phenomena. The model is reduced from a seven-equation model to a five-equation model by assuming different time scales for pressure and velocity relaxations. The proposed model maintains equilibrium near the diffused interface and shows good agreement with experimental results. The numerical methods used achieve second-order accuracy in space and time.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Guokai Zhang, Chenxi Huang, Jingwen Jiang, Weizhe Xu, Jianqing Chen, Xiaowen Xu
Summary: This paper proposes a brain magnetic resonance image denoising method based on multi-dilated blocks (MDB) to extract more contextual and attentive features, and improve the similarity between noisy and denoised images using a perceptual loss. Experimental results demonstrate that this method can predict higher resolution images compared to other methods.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Medicine, General & Internal
Kamireddy Rasool Reddy, Ravindra Dhuli
Summary: In recent years, there has been a substantial increase in brain tumor-related clinical cases, particularly in adults, due to environmental and genetic factors. Early diagnosis of brain tumors is crucial for treatment planning and improving patient condition. We developed an automated methodology for detecting and classifying brain tumors using magnetic resonance imaging (MRI).
Article
Radiology, Nuclear Medicine & Medical Imaging
Julia Kruger, Roland Opfer, Lothar Spies, Dennis Hedderich, Ralph Buchert
Summary: This study aimed to develop a deep convolutional neural network (CNN) for the detection of disease-specific brain atrophy without the need for a scanner-specific normal database. The CNN demonstrated similar performance to conventional methods and could potentially aid in the diagnosis of neurodegenerative diseases.
EUROPEAN RADIOLOGY
(2023)
Article
Neuroimaging
Guoshi Li, Yujie Liu, Yanting Zheng, Ye Wu, Danian Li, Xinyu Liang, Yaoping Chen, Ying Cui, Pew-Thian Yap, Shijun Qiu, Han Zhang, Dinggang Shen
Summary: This study demonstrates that major depressive disorder is primarily characterized by abnormal circuit interactions in the executive-limbic network rather than the default mode-salience network. Reduced frontoparietal effective connectivity in the former network potentially contributes to hypoactivity in the dorsolateral prefrontal cortex, while decreased intrinsic inhibition combined with increased excitation in the superior parietal cortex leads to amygdala hyperactivity. This activation imbalance in the PFC-amygdala circuit is prevalent in major depressive disorder.
NEUROIMAGE-CLINICAL
(2021)
Article
Engineering, Mechanical
Hatice Bulut, Meltem Golgeli, Fatihcan M. Atay
Summary: This paper examines the importance of personal caution during the COVID-19 pandemic, using a mathematical model to analyze the impact of personal caution on disease transmission, with a focus on Turkey and Italy as case studies.
NONLINEAR DYNAMICS
(2021)
Correction
Engineering, Mechanical
Hatice Bulut, Meltem Golgeli, Fatihcan M. Atay
NONLINEAR DYNAMICS
(2021)
Article
Instruments & Instrumentation
Thomas Froehlich, Johannes Sindram, Jens Haueisen, Alexander Hunold
Summary: The study proposes a calibrated setup to measure force-displacement curves for caps used in EEG and TES. Significant non-linearity and hysteresis effects were found in repeated measures of textile EEG-cap and TES-cap, indicating the importance of assessing cap fit for various head shapes and sizes.
TM-TECHNISCHES MESSEN
(2021)
Article
Multidisciplinary Sciences
Philipp Prinke, Jens Haueisen, Sascha Klee, Muhammad Qurhanul Rizqie, Eko Supriyanto, Karsten Koenig, Hans Georg Breunig, Lukasz Piatek
Summary: The proposed automatic segmentation algorithm effectively separates human skin cells components from tissue in fluorescence data, utilizing a multi-stage merging process and a cell model with novel features. This approach ensures high robustness in the segmentation process and accurately classifies cells based on depth-dependent data characteristics. The algorithm contributes to fully automated classification of human skin cells in multiphoton data and lays the foundation for non-invasive skin cancer detection.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Patrique Fiedler, Carlos Fonseca, Eko Supriyanto, Frank Zanow, Jens Haueisen
Summary: The new dry 256-channel HD-EEG electrode cap overcomes the principal limitations of HD-EEG in terms of preparation complexity, allowing rapid application by non-medically trained individuals, and enabling new use cases for HD-EEG. The dry electrodes make recording with state-of-the-art EEG amplifiers easier, while also demonstrating superior performance and wearing comfort.
HUMAN BRAIN MAPPING
(2022)
Article
Chemistry, Analytical
Claudia Lopes, Patrique Fiedler, Marco Sampaio Rodrigues, Joel Borges, Maurizio Bertollo, Eduardo Alves, Nuno Pessoa Barradas, Silvia Comani, Jens Haueisen, Filipe Vaz
Summary: In this study, a new type of nanostructured titanium-based thin film dry electrode for non-invasive monitoring of body surface biopotentials was proposed. Different Ti-Me metallic binary systems were prepared by magnetron sputtering, showing morphology dependent on chemical composition. In an in-vivo study on volunteers, Ti-Me dry electrodes demonstrated good reusability and reliability, with Ti-Au system performing excellently close to the Ag/AgCl reference electrodes.
Article
Chemistry, Analytical
Andreas Voss, Rico Schroeder, Steffen Schulz, Jens Haueisen, Stefanie Vogler, Paul Horn, Andreas Stallmach, Philipp Reuken
Summary: The purpose of this exploratory study was to determine whether liver dysfunction can be generally classified using a wearable electronic nose based on semiconductor metal oxide (MOx) gas sensors, and whether the extent of this dysfunction can be quantified. The study found that the wearable, non-invasive system could detect liver dysfunctions and accurately distinguish different degrees of cirrhosis patients and healthy controls.
Article
Engineering, Electrical & Electronic
Bojana Petkovic, Marek Ziolkowski, Hermann Kutschka, Hannes Toepfer, Jens Haueisen
Summary: This study numerically investigates a realistic two-layer magnetically shielded room using the finite element method and a measured B-H characteristic of Mumetal. It is found that extrapolating the magnetization curve linearly into the low magnetic field range yields no significant differences compared to using a constant permeability value. Furthermore, using a simple analytical method of images greatly reduces computation time and the difference in magnetic flux density calculation between this method and the finite element method is less than 1% at the center of the region of interest.
IEEE TRANSACTIONS ON MAGNETICS
(2022)
Article
Chemistry, Analytical
Chuen Rue Ng, Patrique Fiedler, Levin Kuhlmann, David Liley, Beatriz Vasconcelos, Carlos Fonseca, Gabriella Tamburro, Silvia Comani, Troby Ka-Yan Lui, Chun-Yu Tse, Indhika Fauzhan Warsito, Eko Supriyanto, Jens Haueisen
Summary: Dry electrodes for EEG have the potential for various applications and can provide reliable and reproducible results in different environments. Operator skill and experience are the main factors influencing channel reliability and signal quality.
Article
Engineering, Mechanical
Can Turkun, Meltem Golgeli, Fatihcan M. Atay
Summary: This study uses a SIR-type compartmental model to explain the seasonal exacerbations of bacterial meningitis, particularly in children outside the meningitis belt. The researchers introduce time-dependent transmission parameters to represent the outbreak of meningitis cases after the annual pilgrimage period or uncontrolled inflows of irregular immigrants. They present and analyze a mathematical model with time-dependent transmission, considering both periodic and non-periodic processes. The study demonstrates that the long-time average values of transmission functions can serve as a stability marker for equilibrium, and interprets the basic reproduction number in the case of time-dependent transmission functions. Numerical simulations are conducted to support and visually represent the theoretical findings.
NONLINEAR DYNAMICS
(2023)
Article
Chemistry, Analytical
Ricardo Spyrides Boabaid Pimentel Goncalves, Jens Haueisen
Summary: Three-dimensional scanning using rotation and immersion in a water-based fluid was developed as a low-cost alternative to traditional CT scanners. By utilizing a container filled with water and Xanthan gum, objects were submerged and scanned at various rotation angles. The results showed that this technique was feasible for producing reconstructed images of objects with irregular shapes or openings at a significantly lower cost.
Article
Engineering, Electrical & Electronic
Alexey Alexandrovich Korobkov, Marina Konstantinovna Diugurova, Jens Haueisen, Martin Haardt
Summary: This paper presents a novel robust to noise method called LineAr Regression of Global Eigenvalues (LaRGE) for model order estimation of noise-corrupted multi-dimensional low-rank data. The LaRGE method constructs global eigenvalues using the multi-linear singular values obtained from the HOSVD of the measurement tensor. Unlike the Modified Exponential Test (EFT), LaRGE does not require the calculation of the probability of false alarm and achieves significantly improved performance compared to popular state-of-the-art methods.
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2022)
Proceedings Paper
Automation & Control Systems
Dilan Ozturk, Hitay Ozbay, Fatihcan M. Atay
Summary: This paper investigates the robust stability of a gene regulatory network model with time delayed negative feedback. Through stability analysis and delay margin analysis, the impact of uncertainty on system stability is revealed, and a higher order extension model that can enhance system stability is proposed.
Article
Engineering, Biomedical
B. A. Sabel, A. Kresinsky, L. Cardenas-Morales, J. Haueisen, A. Hunold, M. Dannhauer, A. Antal
Summary: Phosphene threshold measurements were used as surrogate markers to investigate the relationship between phosphene thresholds evoked by transcranial alternating current stimulation (tACS) and current density estimates generated by head model-based computer simulations. Results showed that lower phosphene thresholds were associated with higher simulated current levels in unilateral montages of the model head, with the F7-F8 montage having the lowest phosphene threshold.
IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING
(2021)
Article
Computer Science, Information Systems
Yao Cheng, Michael Riesmeyer, Jens Haueisen, Martin Haardt
Summary: This article presents a new method for describing 200 Hz band activity using tensor decomposition, with experiments conducted on healthy volunteers. The novel multi-way component analysis approach can extract spectral features and separate signal components. Joint processing of EEG and MEG recordings has been shown to be qualitatively and quantitatively superior to separate processing.
