Hassan M Fathallah-Shaykh

Hassan M Fathallah-Shaykh
University of Alabama at Birmingham | UAB · Department of Neurology

M.D., Ph.D.

About

117
Publications
21,425
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2,477
Citations
Citations since 2016
31 Research Items
1749 Citations
20162017201820192020202120220100200300400500
20162017201820192020202120220100200300400500
20162017201820192020202120220100200300400500
20162017201820192020202120220100200300400500

Publications

Publications (117)
Preprint
Full-text available
Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors h...
Article
PURPOSE Multi-parametric MRI and artificial intelligence (AI) methods were previously used to predict peritumoral neoplastic cell infiltration and risk of future recurrence in glioblastoma, in single-institution studies. We hypothesize that important characteristics of peritumoral tissue heterogeneity captured, engineered/selected, and quantified b...
Article
PURPOSE Multi-parametric MRI based radiomic signatures have highlighted the promise of artificial intelligence (AI) in neuro-oncology. However, inter-institution heterogeneity hinders generalization to data from unseen clinical institutions. To this end, we formulated the ReSPOND (Radiomics Signatures for PrecisiON Diagnostics) consortium for gliob...
Preprint
Full-text available
Deep Learning (DL) holds great promise in reshaping the healthcare systems given its precision, efficiency, and objectivity. However, the brittleness of DL models to noisy and out-of-distribution inputs is ailing their deployment in the clinic. Most systems produce point estimates without further information about model uncertainty or confidence. T...
Preprint
Full-text available
Magnetic resonance imaging (MRI) is routinely used for brain tumor diagnosis, treatment planning, and post-treatment surveillance. Recently, various models based on deep neural networks have been proposed for the pixel-level segmentation of tumors in brain MRIs. However, the structural variations, spatial dissimilarities, and intensity inhomogeneit...
Article
Full-text available
Deep neural networks (DNNs) have surpassed human-level accuracy in various learning tasks. However, unlike humans who have a natural cognitive intuition for probabilities, DNNs cannot express their uncertainty in the output decisions. This limits the deployment of DNNs in mission-critical domains, such as warfighter decision-making or medical diagn...
Preprint
Full-text available
The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions (MICCAI) society. Since its inception, BraTS has been focusing on being a common benchmarking venue...
Preprint
Full-text available
This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often...
Chapter
Brain tumor segmentation refers to the process of pixel-level delineation of brain tumor structures in medical images, such as Magnetic Resonance Imaging (MRI). Brain tumor segmentation is required for radiotherapy treatment planning and can diagnosis through surveillance. Automatic segmentation of brain tumors is a challenging problem due to the c...
Article
No clear guidelines exist for the appropriate diagnostic workup of an intracranial mass suspected to be a metastasis from unknown primary origin. Dural metastasis from prostatic origin is very rare. Patients with a known history of metastatic prostate cancer who present with a newly discovered lesion on brain imaging require neurosurgical biopsy to...
Article
Full-text available
Magnetic resonance images of brain tumors are routinely used in neuro-oncology clinics for diagnosis, treatment planning, and post-treatment tumor surveillance. Currently, physicians spend considerable time manually delineating different structures of the brain. Spatial and structural variations, as well as intensity inhomogeneity across images, ma...
Article
Full-text available
Background Low-grade gliomas cause significant neurological morbidity by brain invasion. There is no universally accepted objective technique available for detection of enlargement of low-grade gliomas in the clinical setting; subjective evaluation by clinicians using visual comparison of longitudinal radiological studies is the gold standard. The...
Preprint
Full-text available
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions...
Article
Full-text available
Our research [Team Name: URAN] of 'Neuromorphic Neural Network for Multimodal Brain Tumor Segmentation and Survival analysis' demonstrates its performance on 'Overall Survival Prediction', without any prior training using multi-modal MRI Image segmentation by medical doctors (though provided by BraTS 2018 challenge data). Two segmentation categorie...
Article
Full-text available
Background Most existing algorithms for modeling and analyzing molecular networks assume a static or time-invariant network topology. Such view, however, does not render the temporal evolution of the underlying biological process as molecular networks are typically “re-wired” over time in response to cellular development and environmental changes....
Article
Tumor surveillance is a common practice in oncology; its goal is timely detection of cancer progression, which is typically diagnosed by Visual Comparison (VC) or bidirectional measurement of longitudinal radiological images. Low-grade gliomas (LGG) can cause significant neurological morbidity by progressive brain invasion over time. We analyzed th...
Preprint
Full-text available
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions...
Article
Full-text available
Tumor progression to higher grade is a fundamental property of cancer. The malignant advancement of the pathological features may either develop during the later stages of cancer growth (natural evolution) or it may necessitate new mutations or molecular events that alter the rates of growth, dispersion, or neovascularization (transformation). Here...
Article
Global asymptotic stability is of importance from a theoretical as well as an application point of view in several fields. We study a system of cubic polynomials that models biological networks. We classify the equilibria and show that the property that the interconnection matrix is Lyapunov diagonally stable is a key feature that determines conver...
Article
Full-text available
Glioblastoma (GBM) is a malignant brain tumor that continues to be associated with neurological morbidity and poor survival times. Brain invasion is a fundamental property of malignant glioma cells. The Go-or-Grow (GoG) phenotype proposes that cancer cell motility and proliferation are mutually exclusive. Here, we construct and apply a single gliom...
Article
We address the problem of fully automated region discovery and robust image segmentation by devising a new deformable model based on the level set method (LSM) and the probabilistic nonnegative matrix factorization (NMF). We describe the use of NMF to calculate the number of distinct regions in the image and to derive the local distribution of the...
Conference Paper
The 2016 BRATS includes imaging data on 191 patients diagnosed with low and high grade gliomas. We present a novel method for multimodal brain segmentation, which consists of (1) an automated, accurate and robust method for image segmentation, combined with (2) semi-automated and interactive multimodal labeling. The image segmentation applies Non-n...
Article
This Viewpoint provides examples of diseases to illustrate how the understanding of neurological disease has evolved from an elementary mendelian view.Technologic advances in genetic sequencing have revolutionized how physicians and scientists understand neurological disease, yet the full realized potential of these advances remains unclear. As our...
Article
Full-text available
Glioblastoma multiforme is a malignant brain tumor with poor prognosis and high morbidity due to its invasiveness. Hypoxia-driven motility and concentration-driven motility are two mechanisms of glioblastoma multiforme invasion in the brain. The use of anti-angiogenic drugs has uncovered new progression patterns of glioblastoma multiforme associate...
Article
Glioblastoma multiforme (GBM) causes significant neurological morbidity and short survival times. Brain invasion by GBM is associated with poor prognosis. Recent clinical trials of bevacizumab in newly-diagnosed GBM found no beneficial effects on overall survival times. We have reported a mathematical model of GBM growth and invasion, built at the...
Article
Melanoma is an aggressive cancer whose incidence continues to rise worldwide; furthermore, metastatic melanoma is associated with poor prognosis. Wnt signaling may lead to conflicting effects on the biology of melanoma as it may either decrease or increase the incidence of metastasis. Here, we show that Wnt5a enhances motility in 3/5 cell lines and...
Article
Full-text available
BACKGROUND: Tumor Treating Fields (TTFields) are low intensity, intermediate frequency alternating electric fields used to inhibit tumor cell division by impeding microtubular spindle formation during mitosis. Treatment is delivered by a portable medical device (Optune™) approved in the U.S. for adults with recurrent glioblastoma. Regulatory labell...
Article
This phase I study aimed to evaluate safety, maximum tolerated dose, pharmacokinetics, pharmacodynamics, and preliminary efficacy of voxtalisib (SAR245409, XL765), a pan-class I phosphoinositide 3-kinase (PI3K) and mammalian target of rapamycin (mTOR) inhibitor, in combination with temozolomide (TMZ), with or without radiation therapy (RT), in pati...
Chapter
The molecular networks of GBM include a large number of molecules and interactions, as well as multiple subnetworks and crosstalk. These large networks appear to have the ability to not only bypass therapeutic blockade, but to react to therapeutic modalities by activation of oncogenic subnetworks. We are not surprised that little progress has been...
Article
Full-text available
Bevacizumab is widely used for treatment of high-grade gliomas and other malignancies. Because bevacizumab has been shown to be associated with neurocognitive decline, this study is designed to investigate whether prolonged treatment with bevacizumab is also associated with brain atrophy. We identified 12 high-grade glioma patients who received bev...
Article
Full-text available
Glioblastoma multiforme (GBM) causes significant neurological morbidity and short survival times. Brain invasion by GBM is associated with poor prognosis. Recent clinical trials of bevacizumab in newly-diagnosed GBM found no beneficial effects on overall survival times; however, the baseline health-related quality of life and performance status wer...
Article
History A previously healthy 23-year-old white man presented to the emergency department of our hospital with a 2-month history of dysarthria, progressively worsening vertigo, and difficulty walking. A diagnosis of retinitis pigementosa was made in this patient's childhood. He did not have any history of congenital syphilis. He did not have a histo...
Article
Protein arginine methyltransferase 5 (PRMT5) catalyzes the formation of ω-NG,N′G-symmetric dimethylarginine residues on histones as well as other proteins. The modification play an important role in cell differentiation and tumor cell growth. However, the role of PRMT5 in human glioma cells has not been characterized. In this study, we assessed pro...
Article
The recent use of anti-angiogenesis (AA) drugs for the treatment of glioblastoma multiforme (GBM) has uncovered unusual tumor responses. Here, we derive a new mathematical model that takes into account the ability of proliferative cells to become invasive under hypoxic conditions; model simulations generate the multilayer structure of GBM, namely p...
Article
The objective of this study was to evaluate if peritumoral (PT) perfusion parameters obtained from dynamic susceptibility weighted contrast enhanced perfusion MRI can predict overall survival (OS) and progression free survival (PFS) in patients with newly diagnosed glioblastoma multiforme (GBM). Twenty-eight newly diagnosed GBM patients, who were t...
Article
Full-text available
Src family kinases (SFKs) are highly expressed and active in clinical glioblastoma multiforme (GBM) specimens. SFKs inhibitors have been demonstrated to inhibit prolifer-ation and migration of glioma cells. However, the role of SFKs in glioma stem cells (GSCs), which are important for treatment resistance and recurrence, has not been reported. Here...
Article
In Reply We appreciate the kind and thorough response of McNeil and colleagues to our queries on the Network for Excellence in Neuroscience Clinical Trials (NeuroNEXT).¹ We also thank them for their effort in putting together a framework that eases the immense burden of neurological disorders. Article Information Corresponding Author Hassan Fathal...
Article
Full-text available
Protein arginine methyltransferase 5 (PRMT5) catalyzes the formation of ω-NG,N'G-symmetric dimethylarginine residues on histones as well as other proteins. These modifications play an important role in cell differentiation and tumor cell growth. However, the role of PRMT5 in human glioma cells has not been characterized. In this study, we assessed...
Article
Proper orthogonal decomposition (POD) is frequently applied to estimate parameters of partial differential equations. This study examines the application of the POD method in estimating the parameters of an Ordinary Differential Equation (ODE) model of stable oscillating biological networks. The mathematical model used to simulate molecular interac...
Article
Full-text available
It is widely accepted that cellular requirements and environmental conditions dictate the architecture of genetic regulatory networks. Nonetheless, the status quo in regulatory network modeling and analysis assumes an invariant network topology over time. In this paper, we refocus on a dynamic perspective of genetic networks, one that can uncover s...
Article
Full-text available
Malignant gliomas remain associated with poor prognosis and high morbidity because of their ability to invade the brain; furthermore, human gliomas exhibit a phenotype of accelerated brain invasion in response to anti-angiogenic drugs. Here, we study 8 human glioblastoma cell lines; U251, U87, D54 and LN229 show accelerated motility in low ambient...
Article
The US National Institute of Neurological Disorders and Stroke (NINDS) recently launched the first trial that will take advantage of the Network for Excellence in Neuroscience Clinical Trials (NeuroNEXT).1- 3 Through this initiative, the National Institutes of Health and NINDS hope to accelerate the progress of biomarker validation studies and ther...
Article
Full-text available
Patients with primary glioblastoma multiforme (GBM) have one of the lowest overall survival rates among cancer patients, and reliable biomarkers are necessary to predict patient outcome. Cytochrome c oxidase (CcO) promotes the switch from glycolytic to OXPHOS metabolism, and increased CcO activity in tumors has been associated with tumor progressio...
Chapter
The cell maintains its function via an elaborate network of interconnecting positive and negative feedback loops of genes, RNAs, and proteins that send different signals to a large number of pathways and molecules. These structures are referred to as genetic regulatory networks, and their dynamics are used to understand the mechanisms and character...
Article
Genetic regulatory networks undergo rewiring over time in response to cellular developments and environmental stimuli. The main challenge in estimating time-varying genetic interactions is the limited number of observations at each time point; thus making the problem unidentifiable. We formulate the recovery of temporally-rewiring genetic networks...
Article
Full-text available
In this paper, we address the problem of inferring sparse biomolecular networks from a limited number of noisy measurements. We model the gene expression dynamics using a system of ordinary differential equations corrupted by additive white noise. We derive the gene interactions that maximize the likelihood function while constraining the network t...
Article
Full-text available
Primary angiosarcoma of the brain is extremely rare; only 15 cases have been reported in adults over the last 25 years. We describe two cases of primary angiosarcoma of the brain that are well characterized by imaging, histopathology, and immunohistochemistry. Case 1: our first patient was a 35-year-old woman who developed exophthalmos. Subtotal re...
Conference Paper
Full-text available
We cast the problem of reverse-engineering the connectivity matrix of genetic regulatory networks from a limited number of measurements as a regularized multivariate regression problem. The regularization term incorporates the prior knowledge of sparsity of genetic regulatory networks. Moreover, the genetic profiles within a measurement are assumed...
Article
Fractal geometry can adequately represent many complex and irregular objects in nature. The fractal dimension is typically computed by the box-counting procedure. Here I compute the box-counting and the Kaplan-Yorke dimensions of the 14-dimensional models of the Drosophila circadian clock. Clockwork Orange (CWO) is transcriptional repressor of dire...