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Promises and pitfalls of Topological Data Analysis for brain connectivity analysis [article]

Luigi Caputi, Anna Pidnebesna, Jaroslav Hlinka
2021 bioRxiv   pre-print
Therefore, we assess the potential of persistent homology to directed brain network analysis by testing its discriminatory power in two enigmatic examples of disease-related brain connectivity alterations  ...  We conjecture its prominent tool of persistent homology may benefit from going beyond analysing structural and functional connectivity to effective connectivity graphs capturing the direct causal interactions  ...  Acknowledgment The authors thank Jakub Kopal for sharing the preprocessed fMRI time series and Barbora Bučková for sharing scripts for classification pipeline.  ... 
doi:10.1101/2021.02.10.430469 fatcat:axyfsv3c4vhvflvdgusep6wcpe

Promises and pitfalls of Topological Data Analysis for brain connectivity analysis

Luigi Caputi, Anna Pidnebesna, Jaroslav Hlinka
2021 NeuroImage  
In the easier task of seizure discrimination from scalp electroencephalography data, classification based on persistent homology features generally reached comparable performance to using raw connectivity  ...  Therefore, we assess the potential of persistent homology to directed brain network analysis by testing its discriminatory power in two distinctive examples of disease-related brain connectivity alterations  ...  Acknowledgment The authors thank Jakub Kopal for sharing the preprocessed fMRI time series and Barbora Bučková for sharing scripts for classification pipeline.  ... 
doi:10.1016/j.neuroimage.2021.118245 pmid:34111515 fatcat:ubawhvm5fzf5hndgamc5rpiccu

Fast and Accurate Tumor Segmentation of Histology Images using Persistent Homology and Deep Convolutional Features [article]

Talha Qaiser, Yee-Wah Tsang, Daiki Taniyama, Naoya Sakamoto, Kazuaki Nakane, David Epstein, Nasir Rajpoot
2018 arXiv   pre-print
Overall the proposed framework highlights the utility of persistent homology for histopathology image analysis.  ...  For a given image patch, the homology profiles are derived by efficient computation of persistent homology, which is an algebraic tool from homology theory.  ...  Here we characterize these phenomena with the help of persistent homology for tumor regions in CRC histology images.  ... 
arXiv:1805.03699v1 fatcat:5mo75v2oxbfo3oat2577hlgpmm

Small bowel adenocarcinoma in Lynch syndrome: A case report

Ke-Kang Sun, Gang Liu, Xiaojun Shen, Xiaoyang Wu
2016 Oncology Letters  
This case highlights the importance of considering the possibility of small bowel adenocarcinoma in patients with upper bowel obstruction, particularly for patients with Lynch syndrome.  ...  The laparotomy revealed a completely obstructing mass. Intraoperative frozen section showed a small bowel adenocarcinoma. Subsequent genetic testing confirmed the germline mutation of mutL homolog 1.  ...  In view of the improved accessibility of the small bowel with the introduction of capsule endoscopy and double balloon enteroscopy, the question of whether patients should be screened for small bowel neoplasia  ... 
doi:10.3892/ol.2016.4753 pmid:27446478 pmcid:PMC4950888 fatcat:moqvlo6uqndxlpb6xsmghmxlxq

Topological Information Retrieval with Dilation-Invariant Bottleneck Comparative Measures [article]

Athanasios Vlontzos, Yueqi Cao, Luca Schmidtke, Bernhard Kainz, Anthea Monod
2021 arXiv   pre-print
Computing persistent homology on a variety of embedded datasets reveals that some commonly used embeddings fail to preserve the connectivity.  ...  We use these measures to perform the first instance of topology-based information retrieval and demonstrate its increased performance over the standard bottleneck distance for persistent homology.  ...  A.M. wishes to acknowledge start-up funding from the Department of Mathematics at Imperial College London. L.S.'  ... 
arXiv:2104.01672v2 fatcat:65o4z7o4yrgnbjrchierrpkhlm

Endoscopic and histologic characteristics of serrated lesions

Driffa Moussata
2015 World Journal of Gastroenterology  
In recent years, a second pathway for colonic carcinogenesis, distinct from the adenomatous pathway, has been explored. This is referred to as MINIREVIEWS Submit a Manuscript  ...  Chromo-endoscopy: The crypt opening is star-shaped, corresponding to type Ⅱ in the Kudo classification [23] .  ...  Narrow-band imaging: According to narrow-band imaging (NBI) International Colorectal Endoscopic classification system (NICE), SSA present a mixed spectrum of features between HP and adenomas [24] and  ... 
doi:10.3748/wjg.v21.i10.2896 pmid:25780286 pmcid:PMC4356908 fatcat:by33x5wznjctnodhh5mwbrk3oy

(Quasi)Periodicity Quantification in Video Data, Using Topology

Christopher J. Tralie, Jose A. Perea
2018 SIAM Journal of Imaging Sciences  
The approach combines ideas from nonlinear time series analysis (delay embeddings) and computational topology (persistent homology), by translating the problem of finding recurrent dynamics in video data  ...  , into the problem of determining the circularity or toroidality of an associated geometric space.  ...  ACKNOWLEDGMENTS The authors would like to thank Juergen Neubauer, Dimitar Deliyski, Robert Hillman, Alessandro de Alarcon, Dariush Mehta, and Stephanie Zacharias for providing videos of vocal folds.  ... 
doi:10.1137/17m1150736 fatcat:iil55fgmqbgtnj4fgi3pokmrhm

British Society of Gastroenterology guidelines on the diagnosis and management of patients at risk of gastric adenocarcinoma

Matthew Banks, David Graham, Marnix Jansen, Takuji Gotoda, Sergio Coda, Massimiliano di Pietro, Noriya Uedo, Pradeep Bhandari, D Mark Pritchard, Ernst J Kuipers, Manuel Rodriguez-Justo, Marco R Novelli (+3 others)
2019 Gut  
Image-enhanced endoscopy combined with biopsy sampling for histopathology is the best approach to detect and accurately risk-stratify GA and GIM.  ...  High-quality endoscopy with full mucosal visualisation is an important part of improving early detection.  ...  In the absence of evidence, we would suggest 3-yearly endoscopy with high-definition endoscopy and image enhancement as a possible protocol.  ... 
doi:10.1136/gutjnl-2018-318126 pmid:31278206 pmcid:PMC6709778 fatcat:yopalcw7z5fmbnzhylqzsnelhq

(Quasi)Periodicity Quantification in Video Data, Using Topology [article]

Christopher J. Tralie, Jose A. Perea
2018 arXiv   pre-print
The approach combines ideas from nonlinear time series analysis (delay embeddings) and computational topology (persistent homology), by translating the problem of finding recurrent dynamics in video data  ...  , into the problem of determining the circularity or toroidality of an associated geometric space.  ...  Acknowledgments The authors would like to thank Juergen Neubauer, Dimitar Deliyski, Robert Hillman, Alessandro de Alarcon, Dariush Mehta, and Stephanie Zacharias for providing videos of vocal folds.  ... 
arXiv:1704.08382v2 fatcat:2zw6mylrbjablcfzt7gd7grjzu

Close and regular surveillance is key to prevent severe complications for Peutz-Jeghers syndrome patients without gastrointestinal polyps: case report of a novel STK11 mutation (c.471_472delCT) in a Chinese girl

Zi-Ye Zhao, Yu-Liang Jiang, Bai-Rong Li, Jing Li, Xiao-Wei Jin, En-Da Yu, Shou-Bin Ning
2018 BMC Surgery  
We speculate close and regular endoscopy especially enteroscopy is necessary for complication prevention when the former endoscopy discovers no polyps temporarily in a child of suspect PJS.  ...  Endoscopy revealed no obvious polyps in the stomach or the colon until 10 years old, when she received enteroscopy.  ...  Acknowledgements We thank the subjects for their participation. We appreciate very much for Dr. Wen-Sheng LIN's kindly help with the pathologic pictures of the polyps. We also appreciate Dr.  ... 
doi:10.1186/s12893-018-0357-8 pmid:29685139 pmcid:PMC5914036 fatcat:32qj2ls2enf6dkt2j7dcp3cizm

Deep Learning Based Earlier Detection of Esophageal Cancer Using Improved Empirical Wavelet Transform From Endoscopic Image

Yuan Xue, Na Li, Xiaojie Wei, Ren'an Wan, Chunyan Wang
2020 IEEE Access  
Such results suggest that a new identification technique of early esophageal cancer may be established using the characteristics obtained from the homology persistent and the frequency components.  ...  The formula of the method of counting is the following: (1) Binary image with a '0s and' 1's 'dynamical threshold approach to achieve an optimized image.  ... 
doi:10.1109/access.2020.3006106 fatcat:ablzhsmwmvgl5nglltjj3x76gi

Diagnosis and therapy of neuroendocrine neoplasms of the gastrointestinal tract

Andrzej Deptała, Aleksandra Izabela Czerw
2016 Family Medicine & Primary Care Review  
In the diagnosing nens, imaging methods based on morphology (such as UsG, eUs, CT, MrI, and endoscopy) and functional techniques (like somatostatin receptor scintigraphy and gallium isotope PeT-CT) are  ...  GeP nens are relatively rare neoplasms (around 2% of the overall number of neoplasms of the digestive system) with an incidence of around 6 cases per 100,000 per year.  ...  ) in respect of survival. trasound, computed tomography, magnetic resonance imaging, endoscopy, capsule endoscopy, double-balloon enteroscopy, the choice depending on the location of the GeP nen.  ... 
doi:10.5114/fmpcr/64146 fatcat:y7bhprc2s5be5juozyoqg77m6m

Therapeutic strategies in eosinophilic esophagitis: Induction, maintenance and refractory disease

Jamie Sodikoff, Ikuo Hirano
2015 Baillière's Best Practice & Research : Clinical Gastroenterology  
Little is known about the natural history of EoE, however, raising controversy regarding the necessity of maintenance and therapy in asymptomatic or treatment-refractory patients.  ...  Eosinophilic esophagitis (EoE) is a chronic, immune-mediated disease that is increasingly recognized as one of the most common causes of dysphagia and foregut symptoms in adults and children.  ...  Clinical Research Network, an initiative of the Office of Rare Disease Research and is funded through a collaboration between NIAID, NIDDK and NCATS) and an American Society of Gastrointestinal Endoscopy  ... 
doi:10.1016/j.bpg.2015.09.002 pmid:26552781 pmcid:PMC4946566 fatcat:uzb2s4awsbdfnh2ze6zwi5kg5e

Consensus on the Prevention, Screening, Early Diagnosis and Treatment of Colorectal Tumors in China: Chinese Society of Gastroenterology, October 14-15, 2011, Shanghai, China

Jing-Yuan Fang, Shu Zheng, Bo Jiang, Mao-De Lai, Dian-Chun Fang, Ying Han, Qian-Jiu Sheng, Jing-Nan Li, Ying-Xuan Chen, Qin-Yan Gao
2014 Gastrointestinal Tumors  
Furthermore, because of high risk of recurrence after removal of adenomas under endoscopy, factors contributing to recurrence, the follow-up mode and the interval established, and the feasibility of application  ...  The follow-up interval after the removal or surgery of colorectal tumors should be different with lesions.  ...  A screening cycle of 3 years is recommended for persistent interventions.  ... 
doi:10.1159/000362585 pmid:26672726 pmcid:PMC4645581 fatcat:tsds2idndrfxdnxskaugntcdse

Enhanced tumor response to radiotherapy after PD-1 blockade in metastatic gastric cancer

Akinori Sasaki, Yoshiaki Nakamura, Yosuke Togashi, Hirofumi Kuno, Hidehiro Hojo, Shunichiro Kageyama, Naoki Nakamura, Kenji Takashima, Tomohiro Kadota, Yusuke Yoda, Saori Mishima, Kentaro Sawada (+12 others)
2020 Gastric Cancer  
Five out of eight patients in the anti-PD-1-exposed group, who underwent endoscopy after RT showed partial response, but none in the anti-PD-1-naïve patients showed response (P = 0.026).  ...  Immune profiling suggests that anti-PD-1 therapy may enhance the efficacy of RT by immunoactivation in the TME.  ...  Anti-mutL homolog 1 MSH2 Anti-mutS homolog 2 PMS2 Anti-postmeiotic segregation increased 2 Introduction Systemic chemotherapy is the standard treatment option for patients with metastatic gastric cancer  ... 
doi:10.1007/s10120-020-01058-4 pmid:32180056 fatcat:67scuz6zxffhdcjzgil2jlrthq
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