Review of ependymomas: assessment of consensus in pathological diagnosis and correlations with genetic profiles and outcome

2019 ◽  
Vol 36 (2) ◽  
pp. 92-101 ◽  
Author(s):  
Atsushi Sasaki ◽  
Junko Hirato ◽  
Takanori Hirose ◽  
Kohei Fukuoka ◽  
Yonehiro Kanemura ◽  
...  
Keyword(s):  
Pathological Diagnosis ◽  
Genetic Profiles

Acinar Dysplasia, Clinical and Pathological Diagnosis Dilemma in Term Infants

2006 ◽  
Vol 210 (S 5) ◽  
Author(s):  
A Adnan Amin ◽  
A Halabi ◽  
T Melaiki
Keyword(s):  
Pathological Diagnosis ◽  
Term Infants

The Power of Matrix Factorization: Methods for Deconvoluting Genetic Heterogeneous Data at Expression Level

2021 ◽  
Vol 15 (8) ◽  
pp. 841-853
Author(s):  
Yuan Liu ◽  
Zhining Wen ◽  
Menglong Li
Keyword(s):  
Artificial Intelligence ◽  
Matrix Factorization ◽  
In Silico ◽  
Genetic Data ◽  
Heterogeneous Data ◽  
Expression Level ◽  
Mathematical Methods ◽  
Challenges And Opportunities ◽  
Factorization Methods ◽  
Genetic Profiles

Background:: The utilization of genetic data to investigate biological problems has recently become a vital approach. However, it is undeniable that the heterogeneity of original samples at the biological level is usually ignored when utilizing genetic data. Different cell-constitutions of a sample could differentiate the expression profile, and set considerable biases for downstream research. Matrix factorization (MF) which originated as a set of mathematical methods, has contributed massively to deconvoluting genetic profiles in silico, especially at the expression level. Objective: With the development of artificial intelligence algorithms and machine learning, the number of computational methods for solving heterogeneous problems is also rapidly abundant. However, a structural view from the angle of using MF to deconvolute genetic data is quite limited. This study was conducted to review the usages of MF methods on heterogeneous problems of genetic data on expression level. Methods: MF methods involved in deconvolution were reviewed according to their individual strengths. The demonstration is presented separately into three sections: application scenarios, method categories and summarization for tools. Specifically, application scenarios defined deconvoluting problem with applying scenarios. Method categories summarized MF algorithms contributed to different scenarios. Summarization for tools listed functions and developed web-servers over the latest decade. Additionally, challenges and opportunities of relative fields are discussed. Results and Conclusion: Based on the investigation, this study aims to present a relatively global picture to assist researchers to achieve a quicker access of deconvoluting genetic data in silico, further to help researchers in selecting suitable MF methods based on the different scenarios.

Molecular basis of adaptive evolution of sperm motility involved in in vivo fertilization of terrestrial animals

Impact ◽  
2020 ◽  
Vol 2020 (6) ◽  
pp. 73-75
Author(s):  
Akihiko Watanabe
Keyword(s):  
Sexual Reproduction ◽  
Sperm Motility ◽  
Asexual Reproduction ◽  
Acrosome Reaction ◽  
Sperm Morphology ◽  
Adaptive Potential ◽  
Selective Pressures ◽  
The Face ◽  
Genetic Profiles

One of the unifying traits of life on this planet is reproduction, or life's ability to make copies of itself. The mode of reproduction has evolved over time, having almost certainly begun with simple asexual reproduction when the ancestral single celled organism divided into two. Since these beginnings' life has tried out numerous strategies, and perhaps one of the most important and successful has been sexual reproduction. This form of reproduction relies on the union of gametes, otherwise known as sperm and egg. Evolutionarily, sexual reproduction allows for greater adaptive potential because the genes of two unique individuals have a chance to recombine and mix in order to produce a new individual. Unlike asexual reproduction which produces genetically-identical clones of the parent individual, sex produces offspring with novel genes and combinations of genes. Therefore, in the face of new selective pressures there is a higher chance that one of these novel genetic profiles will produce an adaptation that is advantageous in the new circumstances. Dr Akihiko Watanabe is a reproductive biologist based in the Department of Biology, Faculty of Science Yamagata University in Japan, he is currently working on three research projects; a comparative study on the signalling pathways for inducing sperm motility and acrosome reaction in amphibians, the mechanism behind the adaptive modification of sperm morphology and motility, and the origin of sperm motility initiating substance (SMIS).

scholarly journals Diverse Genetic Landscape of Suspected Retinitis Pigmentosa in a Large Korean Cohort

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 675
Author(s):  
Yoon-Jeon Kim ◽  
You-Na Kim ◽  
Young-Hee Yoon ◽  
Eul-Ju Seo ◽  
Go-Hun Seo ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Detection Rate ◽  
Mutation Detection ◽  
Retinal Disease ◽  
Mutation Detection Rate ◽  
Targeted Next Generation Sequencing ◽  
Initial Symptoms ◽  
Genetic Landscape ◽  
History Of ◽  
Genetic Profiles

We conducted targeted next-generation sequencing (TGS) and/or whole exome sequencing (WES) to assess the genetic profiles of clinically suspected retinitis pigmentosa (RP) in the Korean population. A cohort of 279 unrelated Korean patients with clinically diagnosed RP and available family members underwent molecular analyses using TGS consisting of 88 RP-causing genes and/or WES with clinical variant interpretation. The combined genetic tests (TGS and/or WES) found a mutation in the 44 RP-causing genes and seven inherited retinal disease (IRD)-causing genes, and the total mutation detection rate was 57%. The mutation detection rate was higher in patients who experienced visual deterioration at a younger age (75.4%, age of symptom onset under 10 years) and who had a family history of RP (70.7%). The most common causative genes were EYS (8.2%), USH2A (6.8%), and PDE6B (4.7%), but mutations were dispersed among the 51 RP/IRD genes generally. Meanwhile, the PDE6B mutation was the most common in patients experiencing initial symptoms in their first decade, EYS in their second to third decades, and USH2A in their fifth decades and older. Of note, WES revealed some unexpected genotypes: ABCC6, CHM, CYP4V2, RS1, TGFBI, VPS13B, and WDR19, which were verified by ophthalmological re-phenotyping.

scholarly journals “Masato de Yuca” and “Chicha de Siete Semillas” Two Traditional Vegetable Fermented Beverages from Peru as Source for the Isolation of Potential Probiotic Bacteria

2021 ◽  
Author(s):  
Teresa D. Rebaza-Cardenas ◽  
Kenneth Silva-Cajaleón ◽  
Carlos Sabater ◽  
Susana Delgado ◽  
Nilda D. Montes-Villanueva ◽  
...  
Keyword(s):  
Gastrointestinal Transit ◽  
Probiotic Strain ◽  
In Vitro Digestion ◽  
Intestinal Cell ◽  
Adhesion Ability ◽  
Intestinal Cell Line ◽  
Carbohydrate Fermentation ◽  
Traditional Vegetable ◽  
Genetic Profiles

AbstractIn this work, two Peruvian beverages “Masato de Yuca,” typical of the Amazonian communities made from cassava (Manihot esculenta), and “Chicha de Siete Semillas,” made from different cereal, pseudo-cereal, and legume flours, were explored for the isolation of lactic acid bacteria after obtaining the permission of local authorities following Nagoya protocol. From an initial number of 33 isolates, 16 strains with different RAPD- and REP-PCR genetic profiles were obtained. In Chicha, all strains were Lactiplantibacillus plantarum (formerly Lactobacillus plantarum), whereas in Masato, in addition to this species, Limosilactobacillus fermentum (formerly Lactobacillus fermentum), Pediococcus acidilactici, and Weissella confusa were also identified. Correlation analysis carried out with their carbohydrate fermentation patterns and enzymatic profiles allowed a clustering of the lactobacilli separated from the other genera. Finally, the 16 strains were submitted to a static in vitro digestion (INFOGEST model) that simulated the gastrointestinal transit. Besides, their ability to adhere to the human epithelial intestinal cell line HT29 was also determined. Following both procedures, the best probiotic candidate was Lac. plantarum Ch13, a robust strain able to better face the challenging conditions of the gastrointestinal tract and showing higher adhesion ability to the intestinal epithelium in comparison with the commercial probiotic strain 299v. In order to characterize its benefit for human health, this Ch13 strain will be deeply studied in further works.

scholarly journals Is There Pathological Uniformity between the Periphery and Center of a Gastrointestinal Stromal Tumor?

2021 ◽  
Vol 10 (4) ◽  
pp. 687
Author(s):  
Seong Ji Choi ◽  
Kwan Hong Lee ◽  
Chan Kyoo Yoo ◽  
Jai Hoon Yoon ◽  
Ki Seok Jang ◽  
...  
Keyword(s):  
Risk Stratification ◽  
Mitotic Index ◽  
High Power ◽  
Malignant Potential ◽  
Mitotic Count ◽  
Pathological Diagnosis ◽  
High Power Field ◽  
Gastric Gists ◽  
Significant Difference ◽  
The Mean

Background: Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors and have some malignant potential. Mitotic count is important for predicting the malignant potential of GISTs. Proper treatment of GISTs requires accurate pathological diagnosis. In general, endoscopic ultrasound-guided fine-needle aspiration and deep biopsy are used for pathological diagnosis of GIST before making decisions about surgery. This study sought to evaluate the pathological uniformity of gastric GISTs for mitotic index of the center and periphery of the GIST. Methods: We retrospectively reviewed the data of 37 gastric GIST patients who underwent wedge resection at Hanyang University Hospital. We used Armed Forces Institute of Pathology criteria to classify gastric GISTs. To determine the pathological uniformity of gastric GISTs, we compared GIST risk stratification between the center and periphery of GISTs. Results: The mean size of GISTs was 3.56 ± 2.10 cm. Three lesions were located in the antrum, 11 in the fundus, 9 in the cardia, and 14 in the body. The mean age of patients was 58.65 ± 9.44 years; 18 patients were male and 19 were female. Thirty-five patients (94.6%) showed the same level of risk stratification between the center and periphery of gastric GISTs, while two patients (5.4%) presented different levels of risk between the two sites. No significant difference in mitotic count was observed between the two sites (kappa value = 0.863; p = 0.001). Conclusions: Mitotic index category (either more than five mitoses per high-power field or five or fewer mitoses per high-power field) of GISTs showed good concurrence between the center and periphery.

scholarly journals Real-time intraoperative glioma diagnosis using fluorescence imaging and deep convolutional neural networks

2021 ◽  
Author(s):  
Biluo Shen ◽  
Zhe Zhang ◽  
Xiaojing Shi ◽  
Caiguang Cao ◽  
Zeyu Zhang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Real Time ◽  
Fluorescence Imaging ◽  
Convolutional Neural Networks ◽  
Frozen Section ◽  
Fluorescent Imaging ◽  
Pathological Diagnosis ◽  
Pathological Examination ◽  
Deep Convolutional Neural Networks ◽  
Fluorescence Images

Abstract Purpose Surgery is the predominant treatment modality of human glioma but suffers difficulty on clearly identifying tumor boundaries in clinic. Conventional practice involves neurosurgeon’s visual evaluation and intraoperative histological examination of dissected tissues using frozen section, which is time-consuming and complex. The aim of this study was to develop fluorescent imaging coupled with artificial intelligence technique to quickly and accurately determine glioma in real-time during surgery. Methods Glioma patients (N = 23) were enrolled and injected with indocyanine green for fluorescence image–guided surgery. Tissue samples (N = 1874) were harvested from surgery of these patients, and the second near-infrared window (NIR-II, 1000–1700 nm) fluorescence images were obtained. Deep convolutional neural networks (CNNs) combined with NIR-II fluorescence imaging (named as FL-CNN) were explored to automatically provide pathological diagnosis of glioma in situ in real-time during patient surgery. The pathological examination results were used as the gold standard. Results The developed FL-CNN achieved the area under the curve (AUC) of 0.945. Comparing to neurosurgeons’ judgment, with the same level of specificity >80%, FL-CNN achieved a much higher sensitivity (93.8% versus 82.0%, P < 0.001) with zero time overhead. Further experiments demonstrated that FL-CNN corrected >70% of the errors made by neurosurgeons. FL-CNN was also able to rapidly predict grade and Ki-67 level (AUC 0.810 and 0.625) of tumor specimens intraoperatively. Conclusion Our study demonstrates that deep CNNs are better at capturing important information from fluorescence images than surgeons’ evaluation during patient surgery. FL-CNN is highly promising to provide pathological diagnosis intraoperatively and assist neurosurgeons to obtain maximum resection safely. Trial registration ChiCTR ChiCTR2000029402. Registered 29 January 2020, retrospectively registered

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