37 results on '"Prakash KN"'
Search Results
2. An end-end deep learning framework for lesion segmentation on multi-contrast MR images—an exploratory study in a rat model of traumatic brain injury
- Author
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Bhanu Prakash KN, Arvind CS, Abdalla Mohammed, Krishna Kanth Chitta, Xuan Vinh To, Hussein Srour, and Fatima Nasrallah
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Biomedical Engineering ,Computer Science Applications - Published
- 2023
3. Multimodal assessments of Zika virus immune pathophysiological responses in marmosets
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Lum, Fok-Moon, Zhang, Wei, Lim, Kheng-Choon, Malleret, Benoit, Teo, Teck-Hui, Koh, Jun-Jia, Lee, Kuan J., Chua, Tze-Kwang, Kam, Yiu-Wing, Yee, Wearn-Xin, Huen, Isaac, Tan, Jeslin J. L., Amrun, Siti Naqiah, Prakash KN, Bhanu, Cozzone, Patrick J., Renia, Laurent, Lee, Philip T. H., and Ng, Lisa F. P.
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- 2018
- Full Text
- View/download PDF
4. CAFT: a deep learning-based comprehensive abdominal fat analysis tool for large cohort studies
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Prakash Kn Bhanu, Cher Heng Tan, Wen Xiang Chen, Ling Yun Yeow, Wee Shiong Lim, and Channarayapatna Srinivas Arvind
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medicine.medical_specialty ,Abdominal Fat ,Subcutaneous Fat ,Biophysics ,Adipose tissue ,Type 2 diabetes ,Intra-Abdominal Fat ,Cohort Studies ,Deep Learning ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Sarcopenic obesity ,Segmentation ,Obesity ,Aged ,Ground truth ,Radiological and Ultrasound Technology ,business.industry ,Deep learning ,Reproducibility of Results ,Middle Aged ,medicine.disease ,Magnetic Resonance Imaging ,Diabetes Mellitus, Type 2 ,Female ,Radiology ,Artificial intelligence ,Metabolic syndrome ,business - Abstract
There is increasing appreciation of the association of obesity beyond co-morbidities, such as cancers, Type 2 diabetes, hypertension, and stroke to also impact upon the muscle to give rise to sarcopenic obesity. Phenotypic knowledge of obesity is crucial for profiling and management of obesity, as different fat—subcutaneous adipose tissue depots (SAT) and visceral adipose tissue depots (VAT) have various degrees of influence on metabolic syndrome and morbidities. Manual segmentation is time consuming and laborious. Study focuses on the development of a deep learning-based, complete data processing pipeline for MRI-based fat analysis, for large cohort studies which include (1) data augmentation and preprocessing (2) model zoo (3) visualization dashboard, and (4) correction tool, for automated quantification of fat compartments SAT and VAT. Our sample comprised 190 healthy community-dwelling older adults from the Geri-LABS study with mean age of 67.85 ± 7.90 years, BMI 23.75 ± 3.65 kg/m2, 132 (69.5%) female, and mainly Chinese ethnicity. 3D-modified Dixon T1-weighted gradient-echo MR images were acquired. Residual global aggregation-based 3D U-Net (RGA-U-Net) and standard 3D U-Net were trained to segment SAT, VAT, superficial and deep subcutaneous adipose tissue depots (SSAT and DSAT). Manual segmentation from 26 subjects was used as ground truth during training. Data augmentations, random bias, noise and ghosting were carried out to increase the number of training datasets to 130. Segmentation accuracy was evaluated using Dice and Hausdorff metrics. The accuracy of segmentation was SSAT:0.92, DSAT:0.88 and VAT:0.9. Average Hausdorff distance was less than 5 mm. Automated segmentation significantly correlated R2 > 0.99 (p
- Published
- 2021
5. Narciclasine attenuates diet-induced obesity by promoting oxidative metabolism in skeletal muscle.
- Author
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Sofi G Julien, Sun-Yee Kim, Reinhard Brunmeir, Joanna R Sinnakannu, Xiaojia Ge, Hongyu Li, Wei Ma, Jadegoud Yaligar, Bhanu Prakash Kn, Sendhil S Velan, Pia V Röder, Qiongyi Zhang, Choon Kiat Sim, Jingyi Wu, Marta Garcia-Miralles, Mahmoud A Pouladi, Wei Xie, Craig McFarlane, Weiping Han, and Feng Xu
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Obesity develops when caloric intake exceeds metabolic needs. Promoting energy expenditure represents an attractive approach in the prevention of this fast-spreading epidemic. Here, we report a novel pharmacological strategy in which a natural compound, narciclasine (ncls), attenuates diet-induced obesity (DIO) in mice by promoting energy expenditure. Moreover, ncls promotes fat clearance from peripheral metabolic tissues, improves blood metabolic parameters in DIO mice, and protects these mice from the loss of voluntary physical activity. Further investigation suggested that ncls achieves these beneficial effects by promoting a shift from glycolytic to oxidative muscle fibers in the DIO mice thereby enhancing mitochondrial respiration and fatty acid oxidation (FAO) in the skeletal muscle. Moreover, ncls strongly activates AMPK signaling specifically in the skeletal muscle. The beneficial effects of ncls treatment in fat clearance and AMPK activation were faithfully reproduced in vitro in cultured murine and human primary myotubes. Mechanistically, ncls increases cellular cAMP concentration and ADP/ATP ratio, which further lead to the activation of AMPK signaling. Blocking AMPK signaling through a specific inhibitor significantly reduces FAO in myotubes. Finally, ncls also enhances mitochondrial membrane potential and reduces the formation of reactive oxygen species in cultured myotubes.
- Published
- 2017
- Full Text
- View/download PDF
6. CT-based morphologic and radiomics features for the classification of MYCN gene amplification status in pediatric neuroblastoma
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Eelin Tan, Khurshid Merchant, Bhanu Prakash KN, Arvind CS, Joseph J. Zhao, Seyed Ehsan Saffari, Poh Hwa Tan, and Phua Hwee Tang
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N-Myc Proto-Oncogene Protein ,Neuroblastoma ,Pediatrics, Perinatology and Child Health ,Gene Amplification ,Humans ,Neurology (clinical) ,General Medicine ,Child ,Tomography, X-Ray Computed ,Retrospective Studies - Abstract
MYCN onco-gene amplification in neuroblastoma confers patients to the high-risk disease category for which prognosis is poor and more aggressive multimodal treatment is indicated. This retrospective study leverages machine learning techniques to develop a computed tomography (CT)-based model incorporating semantic and non-semantic features for non-invasive prediction of MYCN amplification status in pediatric neuroblastoma.From 2009 to 2020, 54 pediatric patients treated for neuroblastoma at a specialized children's hospital with pre-treatment contrast-enhanced CT and MYCN status were identified (training cohort, n = 44; testing cohort, n = 10). Six morphologic features and 107 quantitative gray-level texture radiomics features extracted from manually drawn volume-of-interest were analyzed. Following feature selection and class balancing, the final predictive model was developed with eXtreme Gradient Boosting (XGBoost) algorithm. Accumulated local effects (ALE) plots were used to explore main effects of the predictive features. Tumor texture maps were also generated for visualization of radiomics features.One morphologic and 2 radiomics features were selected for model building. The XGBoost model from the training cohort yielded an area under the receiver operating characteristics curve (AUC-ROC) of 0.930 (95% CI, 0.85-1.00), optimized F1-score of 0.878, and Matthews correlation coefficient (MCC) of 0.773. Evaluation on the testing cohort returned AUC-ROC of 0.880 (95% CI, 0.64-1.00), optimized F1-score of 0.933, and MCC of 0.764. ALE plots and texture maps showed higher "GreyLevelNonUniformity" values, lower "Strength" values, and higher number of image-defined risk factors contribute to higher predicted probability of MYCN amplification.The machine learning model reliably classified MYCN amplification in pediatric neuroblastoma and shows potential as a surrogate imaging biomarker.
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- 2022
7. CAFT: a deep learning-based comprehensive abdominal fat analysis tool for large cohort studies
- Author
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Bhanu, Prakash KN, primary, Arvind, Channarayapatna Srinivas, additional, Yeow, Ling Yun, additional, Chen, Wen Xiang, additional, Lim, Wee Shiong, additional, and Tan, Cher Heng, additional
- Published
- 2021
- Full Text
- View/download PDF
8. Quantification of abdominal fat depots in rats and mice during obesity and weight loss interventions.
- Author
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Bhanu Prakash Kn, Venkatesh Gopalan, Swee Shean Lee, and S Sendhil Velan
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Medicine ,Science - Abstract
BACKGROUND & AIMS:Obesity is a leading healthcare issue contributing to metabolic diseases. There is a great interest in non-invasive approaches for quantitating abdominal fat in obese animals and humans. In this work, we propose an automated method to distinguish and quantify subcutaneous and visceral adipose tissues (SAT and VAT) in rodents during obesity and weight loss interventions. We have also investigated the influence of different magnetic resonance sequences and sources of variability in quantification of fat depots. MATERIALS AND METHODS:High-fat diet fed rodents were utilized for investigating the changes during obesity, exercise, and calorie restriction interventions (N = 7/cohort). Imaging was performed on a 7T Bruker ClinScan scanner using fast spin echo (FSE) and Dixon imaging methods to estimate the fat depots. Finally, we quantified the SAT and VAT volumes between the L1-L5 lumbar vertebrae using the proposed automatic hybrid geodesic region-based curve evolution algorithm. RESULTS:Significant changes in SAT and VAT volumes (p
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- 2014
- Full Text
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9. Multimodal assessments of Zika virus immune pathophysiological responses in marmosets
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Philip Lee, Patrick Cozzone, Bhanu Prakash Kn, Jeslin J. L. Tan, Teck-Hui Teo, Wei Zhang, Isaac Huen, Tze-Kwang Chua, Laurent Rénia, Jun-Jia Koh, Yiu-Wing Kam, Fok-Moon Lum, Benoit Malleret, Siti Naqiah Amrun, Kuan J. Lee, Kheng-Choon Lim, Lisa F. P. Ng, and Wearn-Xin Yee
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0301 basic medicine ,lcsh:Medicine ,CD8-Positive T-Lymphocytes ,Biology ,Antibodies, Viral ,Article ,Epitope ,Cell Line ,Zika virus ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Immunity ,biology.animal ,Animals ,Humans ,030212 general & internal medicine ,lcsh:Science ,B-Lymphocytes ,Multidisciplinary ,Zika Virus Infection ,lcsh:R ,Marmoset ,Callithrix ,Zika Virus ,biology.organism_classification ,Antibodies, Neutralizing ,Killer Cells, Natural ,HEK293 Cells ,030104 developmental biology ,Immunology ,biology.protein ,RNA, Viral ,lcsh:Q ,Antibody ,CD8 - Abstract
Animal models that recapitulate the human pathophysiology have been developed as useful research tools. Although laboratory mice are widely used, they are phylogenetically “distant” to humans. New world monkeys, such as the common marmoset (Callithrix jacchus) have steadily gained prominence. In this report, marmosets are explored as an alternate in vivo model to investigate infection and immunity of Zika virus (ZIKV). Multimodal platforms, including ultrasound and magnetic resonance imaging (MRI), flow cytometry, and multiplex microbead immunoassays were established to comprehensively decipher immune responses and pathophysiological outcomes. While ZIKV-infected marmosets had detectable ZIKV RNA load in various body fluids, animals did not develop any observable lesions in their testes and brains as shown by ultrasound and MRI. Immune-phenotyping detected differences in the numbers of B cells, CD8+ T cells and HLADR+ NK cells during the first two weeks of infection. Neutralizing ZIKV-specific antibodies were elicited to high levels and targeted epitopes in the E protein. This study presents a one-stop-shop platform to study infection and pathophysiology in marmosets. While marmoset-specific research tools are being refined, the research values of these animals present them as a good model for immune-based therapies.
- Published
- 2018
10. Identification, Segmentation, and Image Property Study of Acute Infarcts in Diffusion-Weighted Images by Using a Probabilistic Neural Network and Adaptive Gaussian Mixture Model
- Author
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Bhanu Prakash, KN, Gupta, Varsha, Bilello, Michel, Beauchamp, Norman J., and Nowinski, Wieslaw L.
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- 2006
- Full Text
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11. Rodent Abdominal Adipose Tissue Imaging by MR
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Bhanu Prakash, Kn, Jadegoud, Yaligar, Sanjay K, Verma, Venkatesh, Gopalan, and S, Sendhil Velan
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Mice ,Abdominal Fat ,Image Processing, Computer-Assisted ,Animals ,Body Fat Distribution ,Intra-Abdominal Fat ,Magnetic Resonance Imaging ,Rats - Abstract
Rodents including rats and mice are important models to study obesity, diabetes, and metabolic syndrome in a preclinical setting. Translational and longitudinal imaging of these rodents permit investigation of metabolic diseases and identification of imaging biomarkers suitable for clinical translation. Here we describe the imaging protocols for achieving quantitative abdominal imaging in small animals followed by segmentation and quantification of fat volumes.
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- 2018
12. Rodent Abdominal Adipose Tissue Imaging by MR
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S. Sendhil Velan, Jadegoud Yaligar, Sanjay Kumar Verma, Venkatesh Gopalan, and Bhanu Prakash Kn
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Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,Rodent ,biology ,business.industry ,Adipose tissue ,Magnetic resonance imaging ,Longitudinal imaging ,medicine.disease ,Subcutaneous fat ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,Diabetes mellitus ,biology.animal ,medicine ,Abdomen ,Metabolic syndrome ,business ,030217 neurology & neurosurgery - Abstract
Rodents including rats and mice are important models to study obesity, diabetes, and metabolic syndrome in a preclinical setting. Translational and longitudinal imaging of these rodents permit investigation of metabolic diseases and identification of imaging biomarkers suitable for clinical translation. Here we describe the imaging protocols for achieving quantitative abdominal imaging in small animals followed by segmentation and quantification of fat volumes.
- Published
- 2018
13. Multi-echo susceptibility-weighted imaging and histology of open-field blast-induced traumatic brain injury in a rat model
- Author
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Mui Hong Tan, S. Sendhil Velan, Yong Chiat Wong, Jia Lu, Kian Chye Ng, Sankar Seramani, Bhanu Prakash Kn, Enci Mary Kan, Eng-Ang Ling, and Sanjay Kumar Verma
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Pathology ,medicine.medical_specialty ,business.industry ,Traumatic brain injury ,Ischemia ,Poison control ,medicine.disease ,Blast injury ,medicine.anatomical_structure ,Cerebral blood flow ,Cerebral cortex ,Susceptibility weighted imaging ,medicine ,Molecular Medicine ,Radiology, Nuclear Medicine and imaging ,business ,Spectroscopy ,Oxygen saturation (medicine) - Abstract
Blast-induced traumatic brain injury is on the rise, predominantly as a result of the use of improvised explosive devices, resulting in undesirable neuropsychological dysfunctions, as demonstrated in both animals and humans. This study investigated the effect of open-field blast injury on the rat brain using multi-echo, susceptibility-weighted imaging (SWI). Multi-echo SWI provided phase maps with better signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), making it a sensitive technique for brain injury. Male Sprague-Dawley rats were subjected to a survivable blast of 180 kPa. The visibility of blood vessels of varying sizes improved with multi-echo SWI. Reduced signal intensity from major vessels post-blast indicates increased deoxyhaemoglobin. Relative cerebral blood flow was computed from filtered phase SWI images using inferred changes in oxygen saturation from major blood vessels. Cerebral blood flow decreased significantly at day 3 and day 5 post-blast compared with that pre-blast. This was substantiated by the upregulation of β-amyloid precursor protein (β-APP), a marker of ischaemia, in the neuronal perikaya of the cerebral cortex, as observed by immunofluorescence, and in the cortical tissue by western blot analysis. Our findings indicate the presence of brain ischaemia in post-blast acute phase of injury with possible recovery subsequently. Our results from cerebrovascular imaging, histology and staining provide an insight into the ischaemic state of the brain post-blast and may be useful for prognosis and outcome.
- Published
- 2015
14. Fat Storage-inducing Transmembrane Protein 2 Is Required for Normal Fat Storage in Adipose Tissue
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Long N. Nguyen, Bhanu Prakash Kn, Wang Cheng, Vera J. Goh, Ji-Hyun Kim, David L. Silver, Bryan C. Tan, S. Sendhil Velan, Jolene S.Y. Tan, Jadegoud Yaligar, Hongyan Wang, and Diego A Miranda
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endocrine system ,medicine.medical_specialty ,FGF21 ,Adipose tissue macrophages ,Adipose tissue ,White adipose tissue ,Biology ,Biochemistry ,Mice ,chemistry.chemical_compound ,Lipid droplet ,Internal medicine ,Adipocyte ,Brown adipose tissue ,Adipocytes ,medicine ,Animals ,Molecular Biology ,Triglycerides ,Mice, Knockout ,Triglyceride ,technology, industry, and agriculture ,Membrane Proteins ,Cell Biology ,Lipids ,eye diseases ,humanities ,body regions ,medicine.anatomical_structure ,Endocrinology ,Adipose Tissue ,chemistry - Abstract
Triglycerides within the cytosol of cells are stored in a phylogenetically conserved organelle called the lipid droplet (LD). LDs can be formed at the endoplasmic reticulum, but mechanisms that regulate the formation of LDs are incompletely understood. Adipose tissue has a high capacity to form lipid droplets and store triglycerides. Fat storage-inducing transmembrane protein 2 (FITM2/FIT2) is highly expressed in adipocytes, and data indicate that FIT2 has an important role in the formation of LDs in cells, but whether FIT2 has a physiological role in triglyceride storage in adipose tissue remains unproven. Here we show that adipose-specific deficiency of FIT2 (AF2KO) in mice results in progressive lipodystrophy of white adipose depots and metabolic dysfunction. In contrast, interscapular brown adipose tissue of AF2KO mice accumulated few but large LDs without changes in cellular triglyceride levels. High fat feeding of AF2KO mice or AF2KO mice on the genetically obese ob/ob background accelerated the onset of lipodystrophy. At the cellular level, primary adipocyte precursors of white and brown adipose tissue differentiated in vitro produced fewer but larger LDs without changes in total cellular triglyceride or triglyceride biosynthesis. These data support the conclusion that FIT2 plays an essential, physiological role in fat storage in vivo.
- Published
- 2014
15. Narciclasine attenuates diet-induced obesity by promoting oxidative metabolism in skeletal muscle
- Author
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Jadegoud Yaligar, Marta Garcia-Miralles, Joanna R. Sinnakannu, Pia V. Röder, Jingyi Wu, Weiping Han, Bhanu Prakash Kn, Mahmoud A. Pouladi, Hongyu Li, Wei Ma, Reinhard Brunmeir, Craig McFarlane, Wei Xie, Sofi G. Julien, Qiongyi Zhang, S. Sendhil Velan, Xiaojia Ge, Choon Kiat Sim, Feng Xu, and Sun Yee Kim
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Male ,0301 basic medicine ,Muscle Fibers, Skeletal ,AMP-Activated Protein Kinases ,Mitochondrion ,Biochemistry ,Fats ,Mice ,Adenosine Triphosphate ,Drug Metabolism ,Animal Cells ,Cyclic AMP ,Medicine and Health Sciences ,Glycolysis ,Biology (General) ,Musculoskeletal System ,Beta oxidation ,Cells, Cultured ,Energy-Producing Organelles ,Statistical Data ,Membrane Potential, Mitochondrial ,Myogenesis ,Muscles ,General Neuroscience ,Fatty Acids ,Lipids ,Mitochondria ,Phenanthridines ,Adenosine Diphosphate ,Slow-Twitch Muscle Fiber ,Muscle Fibers, Slow-Twitch ,medicine.anatomical_structure ,Physical Sciences ,Anatomy ,Cellular Structures and Organelles ,Cellular Types ,General Agricultural and Biological Sciences ,Oxidation-Reduction ,Statistics (Mathematics) ,Signal Transduction ,Research Article ,medicine.medical_specialty ,QH301-705.5 ,Cell Respiration ,Slow-Twitch Muscle Fibers ,Oxidative phosphorylation ,Bioenergetics ,Biology ,Diet, High-Fat ,Protective Agents ,Muscle Fibers ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Physical Conditioning, Animal ,Internal medicine ,medicine ,Animals ,Humans ,Pharmacokinetics ,Obesity ,Muscle, Skeletal ,Pharmacology ,General Immunology and Microbiology ,Biology and Life Sciences ,Skeletal muscle ,AMPK ,Cell Biology ,Skeletal Muscle Fibers ,Diet ,Enzyme Activation ,Mice, Inbred C57BL ,030104 developmental biology ,Endocrinology ,Skeletal Muscles ,Amaryllidaceae Alkaloids ,Reactive Oxygen Species ,Energy Metabolism ,Biomarkers ,Mathematics - Abstract
Obesity develops when caloric intake exceeds metabolic needs. Promoting energy expenditure represents an attractive approach in the prevention of this fast-spreading epidemic. Here, we report a novel pharmacological strategy in which a natural compound, narciclasine (ncls), attenuates diet-induced obesity (DIO) in mice by promoting energy expenditure. Moreover, ncls promotes fat clearance from peripheral metabolic tissues, improves blood metabolic parameters in DIO mice, and protects these mice from the loss of voluntary physical activity. Further investigation suggested that ncls achieves these beneficial effects by promoting a shift from glycolytic to oxidative muscle fibers in the DIO mice thereby enhancing mitochondrial respiration and fatty acid oxidation (FAO) in the skeletal muscle. Moreover, ncls strongly activates AMPK signaling specifically in the skeletal muscle. The beneficial effects of ncls treatment in fat clearance and AMPK activation were faithfully reproduced in vitro in cultured murine and human primary myotubes. Mechanistically, ncls increases cellular cAMP concentration and ADP/ATP ratio, which further lead to the activation of AMPK signaling. Blocking AMPK signaling through a specific inhibitor significantly reduces FAO in myotubes. Finally, ncls also enhances mitochondrial membrane potential and reduces the formation of reactive oxygen species in cultured myotubes., Narciclasine is a natural compound that attenuates diet-induced obesity in mice by promoting energy expenditure; it also induces a number of beneficial metabolic effects and activates AMPK signaling in skeletal muscle., Author summary Obesity results from the imbalance of food intake and energy expenditure. Since the restriction of food intake is difficult and inefficient in maintaining long-term weight loss, enhancing energy expenditure is now an attractive approach in combating obesity. Here, we analysed the role in this process of a natural compound called narciclasine. We showed that narciclasine treatment reduces excess fat accumulation in peripheral metabolic tissues, improves blood metabolic parameters and insulin sensitivity in obese mice, and protects these mice from the loss of voluntary physical activity. Further investigation suggested that narciclasine enhances mitochondrial respiration and fatty acid consumption in the skeletal muscle. In addition, narciclasine strongly activates the AMP-activated protein kinase (AMPK) signaling, which is a central sensor of the cellular energy status and a key player in maintaining energy homeostasis, specifically in the skeletal muscle. Mechanistically, we found that narciclasine increases cAMP concentration and ADP/ATP ratio in muscle cells, which further lead to AMPK activation. Finally, we observed that narciclasine increases mitochondrial membrane potential and reduces the production of reactive oxygen species in muscle cells. Our findings suggest that narciclasine is a natural compound that attenuates diet-induced obesity in mice by promoting energy expenditure.
- Published
- 2017
16. Multi-echo susceptibility-weighted imaging and histology of open-field blast-induced traumatic brain injury in a rat model
- Author
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Sanjay Kumar, Verma, Enci Mary, Kan, Jia, Lu, Kian Chye, Ng, Eng Ang, Ling, Sankar, Seramani, Bhanu Prakash, Kn, Yong Chiat, Wong, Mui Hong, Tan, and S Sendhil, Velan
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Male ,Rats, Sprague-Dawley ,Amyloid beta-Protein Precursor ,Disease Models, Animal ,Blast Injuries ,Brain Injuries ,Cerebrovascular Circulation ,Animals ,Signal-To-Noise Ratio ,Magnetic Resonance Imaging ,Rats - Abstract
Blast-induced traumatic brain injury is on the rise, predominantly as a result of the use of improvised explosive devices, resulting in undesirable neuropsychological dysfunctions, as demonstrated in both animals and humans. This study investigated the effect of open-field blast injury on the rat brain using multi-echo, susceptibility-weighted imaging (SWI). Multi-echo SWI provided phase maps with better signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), making it a sensitive technique for brain injury. Male Sprague-Dawley rats were subjected to a survivable blast of 180 kPa. The visibility of blood vessels of varying sizes improved with multi-echo SWI. Reduced signal intensity from major vessels post-blast indicates increased deoxyhaemoglobin. Relative cerebral blood flow was computed from filtered phase SWI images using inferred changes in oxygen saturation from major blood vessels. Cerebral blood flow decreased significantly at day 3 and day 5 post-blast compared with that pre-blast. This was substantiated by the upregulation of β-amyloid precursor protein (β-APP), a marker of ischaemia, in the neuronal perikaya of the cerebral cortex, as observed by immunofluorescence, and in the cortical tissue by western blot analysis. Our findings indicate the presence of brain ischaemia in post-blast acute phase of injury with possible recovery subsequently. Our results from cerebrovascular imaging, histology and staining provide an insight into the ischaemic state of the brain post-blast and may be useful for prognosis and outcome.
- Published
- 2014
17. Comparison of 3-segmentation techniques for intraventricular and intracerebral hemorrhages in unenhanced computed tomography scans
- Author
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Timothy C. Morgan, Wieslaw L. Nowinski, Daniel F. Hanley, Jianbo Hu, and Bhanu Prakash Kn
- Subjects
Normalization (statistics) ,Male ,Pathology ,medicine.medical_specialty ,Sensitivity and Specificity ,Cerebral Ventricles ,Hounsfield scale ,Medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Segmentation ,Longitudinal Studies ,Cerebral Hemorrhage ,Intracerebral hemorrhage ,Artifact (error) ,business.industry ,medicine.disease ,Thresholding ,Intraventricular hemorrhage ,Radiographic Image Interpretation, Computer-Assisted ,Female ,Tomography ,business ,Nuclear medicine ,Artifacts ,Tomography, X-Ray Computed ,Algorithms - Abstract
Objectives The Clot Lysis Evaluating Accelerated Resolution of Intraventricular Hemorrhage Trial phase III is a multicenter, randomized clinical trial in the management and treatment of subjects with small intracerebral hemorrhage and large intraventricular hemorrhage. Accurate localization, segmentation, and quantification of hemorrhage are necessary for decision making and treatment. Our studies are aimed at developing algorithms for accurate and automatic hemorrhage segmentation for this trial. Methods Two hundred one computed tomography scans of 41 patients with 2.5- to 10-mm slice thickness from 10 hospitals were used. Techniques based on thresholding, clustering, and graph theory modified using textural energy-based normalization were used along with preprocessing (filtering, skull stripping) and postprocessing (artifact removal). The segmented results of each method are compared with the ground truths. Results The median sensitivity, specificity, and dice statistical index (DSI) are 86.19%, 99.94%, and 0.8655 for modified thresholding; 83.23%, 99.93%, and 0.8410 for modified fuzzy C-means; and 87.28%, 99.81%, and 0.7917 for modified normalized cut method, respectively. The preprocessing and postprocessing enhanced the DSI by 10% and 3%, respectively. Usage of textural energy along with the Hounsfield value in the modified methods increased the DSI by about 8% to 10%. The methods reduced the time needed for processing from 20 to 30 minutes to 2 to 3 minutes per case. Conclusions The modified thresholding provided the highest accuracy, least computation time, and implementation complexity compared with other 2 methods. The method reduces the time to localize and segment the hemorrhagic regions and also provides quantitative information that is critical to precise therapeutic decision making.
- Published
- 2012
18. An investigation into the feasibility of fetal lung maturity prediction using statistical textural features
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T.W.P. Chow, Prakash Kn, A. G. Ramakrishnan, and S. Suresh
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Pathology ,medicine.medical_specialty ,01 natural sciences ,Ultrasonography, Prenatal ,03 medical and health sciences ,0302 clinical medicine ,Fetal Organ Maturity ,Region of interest ,Pregnancy ,0103 physical sciences ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Lung region ,010301 acoustics ,Lung ,030219 obstetrics & reproductive medicine ,Radiological and Ultrasound Technology ,business.industry ,Ultrasound ,Gestational age ,medicine.anatomical_structure ,Fetal lung maturity ,Ultrasound imaging ,Feasibility Studies ,Fetal lung ,Female ,business - Abstract
Fetal lung and liver tissues were examined by ultrasound in 240 subjects during 24 to 38 weeks of gestational age in order to investigate the feasibility of predicting the maturity of the lung from the textural features of sonograms. A region of interest of 64 × 64 pixels is used for extracting textural features. Since the histological properties of the liver are claimed to remain constant with respect to gestational age, features obtained from the lung region are compared with those from liver. Though the mean values of some of the features show a specific trend with respect to gestation age, the variance is too high to guarantee definite prediction of the gestational age. Thus, we restricted our purview to an investigation into the feasibility of fetal lung maturity prediction using statistical textural features. Out of 64 features extracted, those features that are correlated with gestation age and less computationally intensive are selected. The results of our study show that the sonographic features hold some promise in determining whether the fetal lung is mature or immature.
- Published
- 2001
19. Harnessing artificial intelligence in radiology to augment population health.
- Author
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Sim JZT, Bhanu Prakash KN, Huang WM, and Tan CH
- Abstract
This review article serves to highlight radiological services as a major cost driver for the healthcare sector, and the potential improvements in productivity and cost savings that can be generated by incorporating artificial intelligence (AI) into the radiology workflow, referencing Singapore healthcare as an example. More specifically, we will discuss the opportunities for AI in lowering healthcare costs and supporting transformational shifts in our care model in the following domains: predictive analytics for optimising throughput and appropriate referrals, computer vision for image enhancement (to increase scanner efficiency and decrease radiation exposure) and pattern recognition (to aid human interpretation and worklist prioritisation), natural language processing and large language models for optimising reports and text data-mining. In the context of preventive health, we will discuss how AI can support population level screening for major disease burdens through opportunistic screening and democratise expertise to increase access to radiological services in primary and community care., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (© 2023 Sim, Bhanu Prakash, Huang and Tan.)
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- 2023
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20. Correction to: CAFT: a deep learning-based comprehensive abdominal fat analysis tool for large cohort studies.
- Author
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Bhanu Prakash KN, Arvind CS, Yeow LY, Chen WX, Lim WS, and Tan CH
- Published
- 2022
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21. Early postnatal irradiation-induced age-dependent changes in adult mouse brain: MRI based characterization.
- Author
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Ren BX, Huen I, Wu ZJ, Wang H, Duan MY, Guenther I, Bhanu Prakash KN, and Tang FR
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- Animals, Animals, Newborn, Brain growth & development, Female, Male, Mice, Mice, Inbred BALB C, Brain radiation effects, Cranial Irradiation adverse effects, Neurogenesis radiation effects
- Abstract
Background: Brain radiation exposure, in particular, radiotherapy, can induce cognitive impairment in patients, with significant effects persisting for the rest of their life. However, the main mechanisms leading to this adverse event remain largely unknown. A study of radiation-induced injury to multiple brain regions, focused on the hippocampus, may shed light on neuroanatomic bases of neurocognitive impairments in patients. Hence, we irradiated BALB/c mice (male and female) at postnatal day 3 (P3), day 10 (P10), and day 21 (P21) and investigated the long-term radiation effect on brain MRI changes and hippocampal neurogenesis., Results: We found characteristic brain volume reductions in the hippocampus, olfactory bulbs, the cerebellar hemisphere, cerebellar white matter (WM) and cerebellar vermis WM, cingulate, occipital and frontal cortices, cerebellar flocculonodular WM, parietal region, endopiriform claustrum, and entorhinal cortex after irradiation with 5 Gy at P3. Irradiation at P10 induced significant volume reduction in the cerebellum, parietal region, cingulate region, and olfactory bulbs, whereas the reduction of the volume in the entorhinal, parietal, insular, and frontal cortices was demonstrated after irradiation at P21. Immunohistochemical study with cell division marker Ki67 and immature marker doublecortin (DCX) indicated the reduced cell division and genesis of new neurons in the subgranular zone of the dentate gyrus in the hippocampus after irradiation at all three postnatal days, but the reduction of total granule cells in the stratum granulosun was found after irradiation at P3 and P10., Conclusions: The early life radiation exposure during different developmental stages induces varied brain pathophysiological changes which may be related to the development of neurological and neuropsychological disorders later in life.
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- 2021
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22. CD10 marks non-canonical PPARγ-independent adipocyte maturation and browning potential of adipose-derived stem cells.
- Author
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Chakraborty S, Ong WK, Yau WWY, Zhou Z, Bhanu Prakash KN, Toh SA, Han W, Yen PM, and Sugii S
- Subjects
- Adipogenesis, Cell Differentiation, Cells, Cultured, Humans, Neprilysin, Prospective Studies, Stem Cells, Adipocytes, PPAR gamma genetics
- Abstract
Background: Effective stem cell therapy is dependent on the stem cell quality that is determined by their differentiation potential, impairment of which leads to poor engraftment and survival into the target cells. However, limitations in our understanding and the lack of reliable markers that can predict their maturation efficacies have hindered the development of stem cells as an effective therapeutic strategy. Our previous study identified CD10, a pro-adipogenic, depot-specific prospective cell surface marker of human adipose-derived stem cells (ASCs). Here, we aim to determine if CD10 can be used as a prospective marker to predict mature adipocyte quality and play a direct role in adipocyte maturation., Methods: We first generated 14 primary human subject-derived ASCs and stable immortalized CD10 knockdown and overexpression lines for 4 subjects by the lentiviral transduction system. To evaluate the role of CD10 in adipogenesis, the adipogenic potential of the human subject samples were scored against their respective CD10 transcript levels. Assessment of UCP1 expression levels was performed to correlate CD10 levels to the browning potential of mature ASCs. Quantitative polymerase chain reaction (qPCR) and Western blot analysis were performed to determine CD10-dependent regulation of various targets. Seahorse analysis of oxidative metabolism and lipolysis assay were studied. Lastly, as a proof-of-concept study, we used CD10 as a prospective marker for screening nuclear receptor ligands library., Results: We identified intrinsic CD10 levels as a positive determinant of adipocyte maturation as well as browning potential of ASCs. Interestingly, CD10 regulates ASC's adipogenic maturation non-canonically by modulating endogenous lipolysis without affecting the classical peroxisome proliferator-activated receptor gamma (PPARγ)-dependent adipogenic pathways. Furthermore, our CD10-mediated screening analysis identified dexamethasone and retinoic acid as stimulator and inhibitor of adipogenesis, respectively, indicating CD10 as a useful biomarker for pro-adipogenic drug screening., Conclusion: Overall, we establish CD10 as a functionally relevant ASC biomarker, which may be a prerequisite to identify high-quality cell populations for improving metabolic diseases.
- Published
- 2021
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23. Fast Adipogenesis Tracking System (FATS)-a robust, high-throughput, automation-ready adipogenesis quantification technique.
- Author
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Yuan C, Chakraborty S, Chitta KK, Subramanian S, Lim TE, Han W, Bhanu Prakash KN, and Sugii S
- Subjects
- Adipogenesis, Animals, Humans, Mice, Adipocytes metabolism, High-Throughput Screening Assays methods
- Abstract
Adipogenesis is essential in in vitro experimentation to assess differentiation capability of stem cells, and therefore, its accurate measurement is important. Quantitative analysis of adipogenic levels, however, is challenging and often susceptible to errors due to non-specific reading or manual estimation by observers. To this end, we developed a novel adipocyte quantification algorithm, named Fast Adipogenesis Tracking System (FATS), based on computer vision libraries. The FATS algorithm is versatile and capable of accurately detecting and quantifying percentage of cells undergoing adipogenic and browning differentiation even under difficult conditions such as the presence of large cell clumps or high cell densities. The algorithm was tested on various cell lines including 3T3-L1 cells, adipose-derived mesenchymal stem cells (ASCs), and induced pluripotent stem cell (iPSC)-derived cells. The FATS algorithm is particularly useful for adipogenic measurement of embryoid bodies derived from pluripotent stem cells and was capable of accurately distinguishing adipogenic cells from false-positive stains. We then demonstrate the effectiveness of the FATS algorithm for screening of nuclear receptor ligands that affect adipogenesis in the high-throughput manner. Together, the FATS offer a universal and automated image-based method to quantify adipocyte differentiation of different cell lines in both standard and high-throughput workflows.
- Published
- 2019
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24. Adipocyte Ceramides Regulate Subcutaneous Adipose Browning, Inflammation, and Metabolism.
- Author
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Chaurasia B, Kaddai VA, Lancaster GI, Henstridge DC, Sriram S, Galam DL, Gopalan V, Prakash KN, Velan SS, Bulchand S, Tsong TJ, Wang M, Siddique MM, Yuguang G, Sigmundsson K, Mellet NA, Weir JM, Meikle PJ, Bin M Yassin MS, Shabbir A, Shayman JA, Hirabayashi Y, Shiow ST, Sugii S, and Summers SA
- Subjects
- Adipocytes drug effects, Adipose Tissue, Brown drug effects, Adrenergic beta-Agonists pharmacology, Adult, Aged, Animals, Body Mass Index, Cell Differentiation drug effects, Cell Differentiation genetics, Cold Temperature, Diabetes Mellitus metabolism, Dioxoles pharmacology, Energy Metabolism drug effects, Fatty Liver metabolism, Fatty Liver pathology, Gene Deletion, Gene Expression Regulation drug effects, Glucose metabolism, Humans, Inflammation genetics, Mice, Middle Aged, Obesity metabolism, Obesity pathology, Organ Specificity drug effects, Serine C-Palmitoyltransferase metabolism, Sphingolipids biosynthesis, Sphingolipids metabolism, Subcutaneous Fat drug effects, Subcutaneous Fat metabolism, Thermogenesis drug effects, Thermogenesis genetics, Young Adult, Adipocytes metabolism, Adipose Tissue, Brown metabolism, Adipose Tissue, Brown pathology, Ceramides pharmacology, Inflammation pathology, Subcutaneous Fat pathology
- Abstract
Adipocytes package incoming fatty acids into triglycerides and other glycerolipids, with only a fraction spilling into a parallel biosynthetic pathway that produces sphingolipids. Herein, we demonstrate that subcutaneous adipose tissue of type 2 diabetics contains considerably more sphingolipids than non-diabetic, BMI-matched counterparts. Whole-body and adipose tissue-specific inhibition/deletion of serine palmitoyltransferase (Sptlc), the first enzyme in the sphingolipid biosynthesis cascade, in mice markedly altered adipose morphology and metabolism, particularly in subcutaneous adipose tissue. The reduction in adipose sphingolipids increased brown and beige/brite adipocyte numbers, mitochondrial activity, and insulin sensitivity. The manipulation also increased numbers of anti-inflammatory M2 macrophages in the adipose bed and induced secretion of insulin-sensitizing adipokines. By comparison, deletion of serine palmitoyltransferase from macrophages had no discernible effects on metabolic homeostasis or adipose function. These data indicate that newly synthesized adipocyte sphingolipids are nutrient signals that drive changes in the adipose phenotype to influence whole-body energy expenditure and nutrient metabolism., (Copyright © 2016 Elsevier Inc. All rights reserved.)
- Published
- 2016
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25. Effect of Exercise and Calorie Restriction on Tissue Acylcarnitines, Tissue Desaturase Indices, and Fat Accumulation in Diet-Induced Obese Rats.
- Author
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Gopalan V, Michael N, Ishino S, Lee SS, Yang AY, Bhanu Prakash KN, Yaligar J, Sadananthan SA, Kaneko M, Zhou Z, Satomi Y, Hirayama M, Kamiguchi H, Zhu B, Horiguchi T, Nishimoto T, and Velan SS
- Subjects
- Animals, Carnitine metabolism, Disease Models, Animal, Humans, Insulin Resistance, Liver metabolism, Male, Muscle, Skeletal metabolism, Obesity chemically induced, Rats, Rats, Inbred F344, Treatment Outcome, Caloric Restriction methods, Carnitine analogs & derivatives, Diet, High-Fat adverse effects, Fatty Acid Desaturases metabolism, Obesity therapy, Physical Conditioning, Animal methods
- Abstract
Both exercise and calorie restriction interventions have been recommended for inducing weight-loss in obese states. However, there is conflicting evidence on their relative benefits for metabolic health and insulin sensitivity. This study seeks to evaluate the differential effects of the two interventions on fat mobilization, fat metabolism, and insulin sensitivity in diet-induced obese animal models. After 4 months of ad libitum high fat diet feeding, 35 male Fischer F344 rats were grouped (n = 7 per cohort) into sedentary control (CON), exercise once a day (EX1), exercise twice a day (EX2), 15% calorie restriction (CR1) and 30% calorie restriction (CR2) cohorts. Interventions were carried out over a 4-week period. We found elevated hepatic and muscle long chain acylcarnitines with both exercise and calorie restriction, and a positive association between hepatic long chain acylcarnitines and insulin sensitivity in the pooled cohort. Our result suggests that long chain acylcarnitines may not indicate incomplete fat oxidation in weight loss interventions. Calorie restriction was found to be more effective than exercise in reducing body weight. Exercise, on the other hand, was more effective in reducing adipose depots and muscle triglycerides, favorably altering muscle/liver desaturase activity and improving insulin sensitivity.
- Published
- 2016
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- View/download PDF
26. A method for the automatic segmentation of brown adipose tissue.
- Author
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Bhanu Prakash KN, Srour H, Velan SS, and Chuang KH
- Subjects
- Adipose Tissue, Brown anatomy & histology, Adipose Tissue, White anatomy & histology, Algorithms, Animals, Female, Image Enhancement methods, Machine Learning, Mice, Mice, Inbred C57BL, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Adipose Tissue, Brown diagnostic imaging, Adipose Tissue, White diagnostic imaging, Image Interpretation, Computer-Assisted methods, Magnetic Resonance Imaging methods, Pattern Recognition, Automated methods
- Abstract
Objective: Brown adipose tissue (BAT) plays a key role for thermogenesis in mammals and infants. Recent confirmation of BAT presence in adult humans has aroused great interest for its potential to initiate weight-loss and normalize metabolic disorders in diabetes and obesity. Reliable detection and differentiation of BAT from the surrounding white adipose tissue (WAT) and muscle is critical for assessment/quantification of BAT volume. This study evaluates magnetic resonance (MR) acquisition for BAT and the efficacy of different automated methods for MR features-based BAT segmentation to identify the best suitable method., Materials and Methods: Multi-point Dixon and multi-echo T2 spin-echo images were acquired from 12 mice using an Agilent 9.4T scanner. Four segmentation methods: multidimensional thresholding (MTh); region-growing (RG); fuzzy c-means (FCM) and neural-network (NNet) were evaluated for the interscapular region and validated against manually defined BAT, WAT and muscle., Results: Statistical analysis of BAT segmentation yielded a median Dice-Statistical-Index, and sensitivity of 89.92% for NNet, 82.86% for FCM, 72.74% for RG, and 72.70%, for MTh, respectively., Conclusion: This study demonstrates that NNet improves the specificity to BAT from surrounding tissue based on 3-point Dixon and T2 MRI. This method facilitates quantification and longitudinal measurement of BAT in preclinical-models and human subjects.
- Published
- 2016
- Full Text
- View/download PDF
27. Segmentation and characterization of interscapular brown adipose tissue in rats by multi-parametric magnetic resonance imaging.
- Author
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Bhanu Prakash KN, Verma SK, Yaligar J, Goggi J, Gopalan V, Lee SS, Tian X, Sugii S, Leow MK, Bhakoo K, and Velan SS
- Subjects
- Adipose Tissue, Brown anatomy & histology, Animals, Male, Rats, Rats, Wistar, Reproducibility of Results, Scapula anatomy & histology, Sensitivity and Specificity, Shoulder Joint anatomy & histology, Adipose Tissue, Brown diagnostic imaging, Cold Temperature, Image Interpretation, Computer-Assisted methods, Multimodal Imaging methods, Scapula diagnostic imaging, Shoulder Joint diagnostic imaging
- Abstract
Objective: The aim was to auto-segment and characterize brown adipose, white adipose and muscle tissues in rats by multi-parametric magnetic resonance imaging with validation by histology and UCP1., Materials and Methods: Male Wistar rats were randomized into two groups for thermoneutral (n = 8) and cold exposure (n = 8) interventions, and quantitative MRI was performed longitudinally at 7 and 11 weeks. Prior to imaging, rats were maintained at either thermoneutral body temperature (36 ± 0.5 °C), or short term cold exposure (26 ± 0.5 °C). Neural network based automatic segmentation was performed on multi-parametric images including fat fraction, T2 and T2* maps. Isolated tissues were subjected to histology and UCP1 analysis., Results: Multi-parametric approach showed precise delineation of the interscapular brown adipose tissue (iBAT), white adipose tissue (WAT) and muscle regions. Neural network based segmentation results were compared with manually drawn regions of interest, and showed 96.6 and 97.1% accuracy for WAT and BAT respectively. Longitudinal assessment of the iBAT volumes showed a reduction at 11 weeks of age compared to 7 weeks. The cold exposed group showed increased iBAT volume compared to thermoneutral group at both 7 and 11 weeks. Histology and UCP1 expression analysis supported our imaging results., Conclusion: Multi-parametric MR based neural network auto-segmentation provides accurate separation of BAT, WAT and muscle tissues in the interscapular region. The cold exposure improves the classification and quantification of heterogeneous BAT.
- Published
- 2016
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- View/download PDF
28. Segmentation and quantification of intra-ventricular/cerebral hemorrhage in CT scans by modified distance regularized level set evolution technique.
- Author
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Prakash KN, Zhou S, Morgan TC, Hanley DF, and Nowinski WL
- Subjects
- Algorithms, Humans, Randomized Controlled Trials as Topic, Cerebral Hemorrhage diagnostic imaging, Cerebral Ventriculography, Image Enhancement methods, Tomography, X-Ray Computed
- Abstract
Purpose: An automatic, accurate and fast segmentation of hemorrhage in brain Computed Tomography (CT) images is necessary for quantification and treatment planning when assessing a large number of data sets. Though manual segmentation is accurate, it is time consuming and tedious. Semi-automatic methods need user interactions and might introduce variability in results. Our study proposes a modified distance regularized level set evolution (MDRLSE) algorithm for hemorrhage segmentation., Methods: Study data set (from the ongoing CLEAR-IVH phase III clinical trial) is comprised of 200 sequential CT scans of 40 patients collected at 10 different hospitals using different machines/vendors. Data set contained both constant and variable slice thickness scans. Our study included pre-processing (filtering and skull removal), segmentation (MDRLSE which is a two-stage method with shrinking and expansion) with modified parameters for faster convergence and higher accuracy and post-processing (reduction in false positives and false negatives)., Results: Results are validated against the gold standard marked manually by a trained CT reader and neurologist. Data sets are grouped as small, medium and large based on the volume of blood. Statistical analysis is performed for both training and test data sets in each group. The median Dice statistical indices (DSI) for the 3 groups are 0.8971, 0.8580 and 0.9173 respectively. Pre- and post-processing enhanced the DSI by 8 and 4% respectively., Conclusions: The MDRLSE improved the accuracy and speed for segmentation and calculation of the hemorrhage volume compared to the original DRLSE method. The method generates quantitative information, which is useful for specific decision making and reduces the time needed for the clinicians to localize and segment the hemorrhagic regions.
- Published
- 2012
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29. A Brain Parenchyma Model-Based Segmentation of Intraventricular and Intracerebral Haemorrhage in CT Scans.
- Author
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Bhanu Prakash KN, Morgan TC, Hanley DM, and Nowinski WL
- Abstract
Accurate quantification of haemorrhage volume in a computed tomography (CT) scan is critical in the management and treatment planning of intraventricular (IVH) and intracerebral haemorrhage (ICH). Manual and semi-automatic methods are laborious and time-consuming limiting their applicability to small data sets. In clinical trials measurements are done at different locations and on a large number of data; an accurate, consistent and automatic method is preferred. A fast and efficient method based on texture energy for identification and segmentation of hemorrhagic regions in the CT scans is proposed. The data set for the study was obtained from CLEAR-IVH clinical trial phase III (41 patients' 201 sequential CT scans from ten different hospitals, slice thickness 2.5-10 mm and from different scanners). The DICOM data were windowed, skull stripped, convolved with textural energy masks and segmented using a hybrid method (a combination of thresholding and fuzzy c-means). Artifacts were removed by statistical analysis and morphological processing. Segmentation results were compared with the ground truth. Descriptive statistics, Dice statistical index (DSI), Bland-Altman and mean difference analysis were carried out. The median sensitivity, specificity and DSI for slice identification and haemorrhage segmentation were 86.25%, 100%, 0.9254 and 84.90%, 99.94%, 0.8710, respectively. The algorithm takes about one minute to process a scan in MATLAB(®). A hybrid method-based volumetry of haemorrhage in CT is reliable, observer independent, efficient, reduces the time and labour. It also generates quantitative data that is important for precise therapeutic decision-making.
- Published
- 2012
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- View/download PDF
30. A Simple and Fast Method of 3D Registration and Statistical Landmark Localization for Sparse Multi-Modal/Time-Series Neuroimages Based on Cortex Ellipse Fitting.
- Author
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Volkau I, Puspitasari F, Ng TT, Bhanu Prakash KN, Gupta V, and Nowinski WL
- Abstract
Existing methods of neuroimage registration typically require high quality scans and are time-consuming. We propose a simple and fast method which allows intra-patient multi-modal and time-series neuroimage registration as well as landmark identification (including commissures and superior/inferior brain landmarks) for sparse data. The method is based on elliptical approximation of the brain cortical surface in the vicinity of the midsagittal plane (MSP). Scan registration is performed by a 3D affine transformation based on parameters of the cortex elliptical fit and by aligning the MSPs. The landmarks are computed using a statistical localization method based on analysis of 53 structural scans without detectable pathology. The method is illustrated for multi-modal registration, analysis of hemorrhagic stroke time series, and ischemic stroke follow ups, as well as for localization of hardly visible or not discernible landmarks in sparse neuroimages. The method also enables a statistical localization of landmarks in sparse morphological/non-morphological images, where landmark points may be invisible.
- Published
- 2012
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31. Extraction of the midsagittal plane from morphological neuroimages using the Kullback-Leibler's measure.
- Author
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Volkau I, Bhanu Prakash KN, Ananthasubramaniam A, Aziz A, and Nowinski WL
- Subjects
- Arachnoid Cysts pathology, Brain diagnostic imaging, Brain pathology, Brain Neoplasms pathology, Ependymoma pathology, Humans, Magnetic Resonance Imaging, Meningioma pathology, Phantoms, Imaging, Tomography, X-Ray Computed, Brain anatomy & histology, Image Interpretation, Computer-Assisted
- Abstract
A theoretically simple and computationally efficient method to extract the midsagittal plane (MSP) from volumetric neuroimages is presented. The method works in two stages (coarse and fine) and is based on calculation of the Kullback and Leibler's (KL) measure, which characterizes the difference between two distributions. Slices along the sagittal direction are analyzed with respect to a reference slice to determine the coarse MSP. To calculate the final MSP, a local search algorithm is applied. The proposed method does not need any preprocessing, like reformatting, skull stripping, etc. The algorithm was validated quantitatively on 75 MRI datasets of different pulse sequences (T1WI, T2WI, FLAIR and SPGR) and MRA. The angular and distance errors between the calculated MSP and the ground truth lines marked by the expert were calculated. The average distance and angular deviation were 1.25 pixels and 0.63 degrees , respectively. In addition, the algorithm was tested qualitatively on PD, FLAIR, MRA, and CT datasets. To analyze the robustness of the method against rotation, inhomogeneity and noise, the phantom data were used.
- Published
- 2006
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- View/download PDF
32. Fast Talairach Transformation for magnetic resonance neuroimages.
- Author
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Nowinski WL, Qian G, Bhanu Prakash KN, Hu Q, and Aziz A
- Subjects
- Algorithms, Humans, Phantoms, Imaging, Software, Brain anatomy & histology, Brain Mapping methods, Image Interpretation, Computer-Assisted methods, Image Processing, Computer-Assisted methods, Magnetic Resonance Imaging
- Abstract
We introduce and validate the Fast Talairach Transformation (FTT). FTT is a rapid version of the Talairach transformation (TT) with the modified Talairach landmarks. Landmark identification is fully automatic and done in 3 steps: calculation of midsagittal plane, computing of anterior commissure (AC) and posterior commissure (PC) landmarks, and calculation of cortical landmarks. To perform these steps, we use fast and anatomy-based algorithms employing simple operations. FTT was validated for 215 diversified T1-weighted and spoiled gradient recalled (SPGR) MRI data sets. It calculates the landmarks and warps the Talairach-Tournoux atlas fully automatically in about 5 sec on a standard computer. The average distance errors in landmark localization are (in mm): 1.16 (AC), 1.49 (PC), 0.08 (left), 0.13 (right), 0.48 (anterior), 0.16 (posterior), 0.35 (superior), and 0.52 (inferior). Extensions to FTT by introducing additional landmarks and applying nonlinear warping against the ventricular system are addressed. Application of FTT to other brain atlases of anatomy, function, tracts, cerebrovasculature, and blood supply territories is discussed. FTT may be useful in a clinical setting and research environment: (1) when the TT is used traditionally, (2) when a global brain structure positioning with quick searching and labeling is required, (3) in urgent cases for quick image interpretation (eg, acute stroke), (4) when the difference between nonlinear and piecewise linear warping is negligible, (5) when automatic processing of a large number of cases is required, (6) as an initial atlas-scan alignment before performing nonlinear warping, and (7) as an initial atlas-guided segmentation of brain structures before further local processing.
- Published
- 2006
- Full Text
- View/download PDF
33. Morphologic relationship among the corpus callosum, fornix, anterior commissure, and posterior commissure MRI-based variability study.
- Author
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Prakash KN and Nowinski WL
- Subjects
- Humans, Image Processing, Computer-Assisted, Reference Values, Brain Mapping methods, Cerebral Cortex anatomy & histology, Corpus Callosum anatomy & histology, Fornix, Brain anatomy & histology, Magnetic Resonance Imaging methods
- Abstract
Rationale and Objectives: This study explores morphological relationships and structural variability of the corpus callosum (CC), fornix (Fo), anterior (AC), and posterior commissures (PC)., Materials and Methods: These structures are extracted automatically on the midsagittal plane. The CC and Fo are modeled using best-fit ellipses. The parameters characterizing these structures and relationships among them are points, distances, angles, and eccentricities. The minimum, maximum and mean values, standard deviations, and coefficients of variation for all parameters are calculated for 62 diversified MRI datasets. Subsequently, the regression analysis and parameter distribution study are performed., Results: The parameters have at least 10% variations. The major axis of CC and eccentricities of CC and Fo vary much less than the other parameters The major axis of CC is approximately parallel to the AC-PC line. The mean eccentricity of each of CC and Fo is greater than 0.95. The most significant correlation (P < .05) is observed between various angles and the angle between the major axes of CC and Fo. The correlation is also significant between other angles and distances. The Weibull distribution characterizes the major axis of CC, and distance between the AC and the most superior point of CC. Distribution of angle between the major axes of CC and Fo is log (logistic), and normal for the AC-PC distance., Conclusions: The AC-PC distance, used prevalently for brain normalization, is not correlated with any parameters except with the distance between the AC and the most superior point on the body of the CC with P < .05.
- Published
- 2006
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- View/download PDF
34. Rapid and automatic localization of the anterior and posterior commissure point landmarks in MR volumetric neuroimages.
- Author
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Bhanu Prakash KN, Hu Q, Aziz A, and Nowinski WL
- Subjects
- Algorithms, Brain Stem anatomy & histology, Corpus Callosum anatomy & histology, Fornix, Brain anatomy & histology, Humans, Image Processing, Computer-Assisted, Reference Values, Brain Mapping methods, Cerebral Cortex anatomy & histology, Magnetic Resonance Imaging methods
- Abstract
Rationale and Objective: Accurate identification of the anterior commissure (AC) and posterior commissure (PC) is critical in neuroradiology, functional neurosurgery, human brain mapping, and neuroscience research. Moreover, major stereotactic brain atlases are based on the AC and PC. Our goal is to provide an algorithm for a rapid, robust, accurate and automatic identification of AC and PC., Materials and Method: The method exploits anatomical and radiological properties of AC, PC and surrounding structures, including morphological variability. The localization is done in two stages: coarse and fine. The coarse stage locates the AC and PC on the midsagittal plane by analyzing their relationships with the corpus callosum, fornix, and brainstem. The fine stage refines the AC and PC in a well-defined volume of interest, analyzing locations of lateral and third ventricles, interhemispheric fissure, and massa intermedia., Results: The algorithm was developed using simple operations, like histogramming, thresholding, region growing, 1D projections. It was tested on 94 diversified T1W and SPGR datasets. After the fine stage, 71 (76%) volumes had an error between 0-1 mm for the AC and 55 (59%) for the PC. The mean errors were 1.0 mm (AC) and 1.0 mm (PC). The accuracy has improved twice due to fine stage processing. The algorithm took about 1 second for coarse and 4 seconds for fine processing on P4, 2.5 GHz., Conclusion: The use of anatomical and radiological knowledge including variability in algorithm formulation aids in localization of structures more accurately and robustly. This fully automatic algorithm is potentially useful in clinical setting and for research.
- Published
- 2006
- Full Text
- View/download PDF
35. Dorsoventral extension of the talairach transformation and its automatic calculation for magnetic resonance neuroimages.
- Author
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Nowinski WL and Prakash KN
- Subjects
- Algorithms, Corpus Callosum pathology, Electronic Data Processing methods, Humans, Image Interpretation, Computer-Assisted methods, Image Processing, Computer-Assisted methods, Magnetic Resonance Imaging standards, Magnetic Resonance Imaging statistics & numerical data, Models, Theoretical, Phantoms, Imaging, Reproducibility of Results, Brain anatomy & histology, Brain Mapping methods, Magnetic Resonance Imaging methods
- Abstract
The Talairach transformation (TT), the most prevalent method for brain normalization and atlas-to-data warping, is conceptually simple, fast and can be automated. Two problems with the TT in the clinical setting that are addressed in this article are reduced accuracy at the orbitofrontal cortex and upper corpus callosum (CC) and unsuitability for functional neurosurgery because of incomplete scanning. To increase dorsoventral accuracy, we introduce 2 additional landmarks: the top of the CC (SM) and the most ventral point of the orbitofrontal cortex on the midsagittal slab (IM). A method for their automatic calculation is proposed and validated against 55 diversified magnetic resonance (MR) imaging cases. The SM and IM landmarks are identified accurately and robustly in an automatic way. The average error of SM localization is 0.69 mm, and 91% of all cases have an error not greater than 1 mm. The average error of IM localization is 0.98 mm, approximately three quarters of cases have an error not greater than 1 mm, and 95% of all cases have an error not larger than 2 mm. The SM is correlated (R(2) = 0.72) with the most superior cortical landmark, whereas the IM is only loosely correlated (R(2) = 0.22) with the most inferior cortical landmark. On average, the original TT overlays the atlas axial plate at -24 on the orbitofrontal cortex as opposed to the correct plate at -28. Therefore, 1-dimensional ventral scaling in the original TT is insufficient to cope with variability in the orbitofrontal cortex. The key advantages of our approach are the preserved conceptual simplicity of the TT, fully automatic identification of the new landmarks, improved accuracy of the atlas-to-data match without compromising performance, and enabled TT use in functional neurosurgery when a dorsal part of the brain is not available in the scan.
- Published
- 2005
- Full Text
- View/download PDF
36. Fetal lung maturity analysis using ultrasound image features.
- Author
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Prakash KN, Ramakrishnan AG, Suresh S, and Chow TW
- Subjects
- Female, Humans, Lung diagnostic imaging, Pilot Projects, Pregnancy, Pregnancy Trimester, Second, Pregnancy Trimester, Third, Ultrasonography, Lung embryology
- Abstract
This pilot study was carried out to find the feasibility of analyzing the maturity of the fetal lung using ultrasound images. Data were collected from normal pregnant women at intervals of two weeks from the gestation age of 24 to 38 weeks. Images were acquired at two centers located at different geographical locations. The total data acquired consisted of 750 images of immature and 250 images of mature class. A region of interest of 64 x 64 pixels was used for extracting the features. Various textural features were computed from the fetal lung and liver images. The ratios of fetal lung to liver feature values were investigated as possible indexes for classifying the images into those from mature (reduced pulmonary risk) and immature (possible pulmonary risk) lung. The features used are fractal dimension, lacunarity, and features derived from the histogram of the images. The following classifiers were used to classify the fetal lung images as belonging to mature or immature lung: nearest neighbor, k-nearest neighbor, modified k-nearest neighbor, multilayer perceptron, radial basis function network, and support vector machines. The classification accuracy obtained for the testing set ranges from 73% to 96%.
- Published
- 2002
- Full Text
- View/download PDF
37. An investigation into the feasibility of fetal lung maturity prediction using statistical textural features.
- Author
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Prakash KN, Ramakrishnan AG, Suresh S, and Chow TW
- Subjects
- Feasibility Studies, Female, Fetal Organ Maturity, Humans, Pregnancy, Lung embryology, Ultrasonography, Prenatal statistics & numerical data
- Abstract
Fetal lung and liver tissues were examined by ultrasound in 240 subjects during 24 to 38 weeks of gestational age in order to investigate the feasibility of predicting the maturity of the lung from the textural features of sonograms. A region of interest of 64 x 64 pixels is used for extracting textural features. Since the histological properties of the liver are claimed to remain constant with respect to gestational age, features obtained from the lung region are compared with those from liver. Though the mean values of some of the features show a specific trend with respect to gestation age, the variance is too high to guarantee definite prediction of the gestational age. Thus, we restricted our purview to an investigation into the feasibility of fetal lung maturity prediction using statistical textural features. Out of 64 features extracted, those features that are correlated with gestation age and less computationally intensive are selected. The results of our study show that the sonographic features hold some promise in determining whether the fetal lung is mature or immature.
- Published
- 2001
- Full Text
- View/download PDF
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