Ensembling Descendant Term Classifiers to Improve Gene - Abnormal Phenotype Predictions

2019 ◽  
pp. 70-80
Author(s):  
Marco Notaro ◽  
Max Schubach ◽  
Marco Frasca ◽  
Marco Mesiti ◽  
Peter N. Robinson ◽  
...  
Keyword(s):  
Abnormal Phenotype

scholarly journals Combining WV-2 images and tree physiological factors to detect damage stages of Populus gansuensis by Asian longhorned beetle (Anoplophora glabripennis) at the tree level

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Quan Zhou ◽  
Xudong Zhang ◽  
Linfeng Yu ◽  
Lili Ren ◽  
Youqing Luo
Keyword(s):  
Remote Sensing ◽  
Gansu Province ◽  
Tree Level ◽  
Anoplophora Glabripennis ◽  
Longhorned Beetle ◽  
Asian Longhorned Beetle ◽  
Remote Sensing Images ◽  
Physiological Factors ◽  
Abnormal Phenotype ◽  
Damage Degree

Abstract Background Anoplophora glabripennis (Motschulsky), commonly known as Asian longhorned beetle (ALB), is a wood-boring insect that can cause lethal infestation to multiple borer leaf trees. In Gansu Province, northwest China, ALB has caused a large number of deaths of a local tree species Populus gansuensis. The damaged area belongs to Gobi desert where every single tree is artificially planted and is extremely difficult to cultivate. Therefore, the monitoring of the ALB infestation at the individual tree level in the landscape is necessary. Moreover, the determination of an abnormal phenotype that can be obtained directly from remote-sensing images to predict the damage degree can greatly reduce the cost of field investigation and management. Methods Multispectral WorldView-2 (WV-2) images and 5 tree physiological factors were collected as experimental materials. One-way ANOVA of the tree’s physiological factors helped in determining the phenotype to predict damage degrees. The original bands of WV-2 and derived vegetation indices were used as reference data to construct the dataset of a prediction model. Variance inflation factor and stepwise regression analyses were used to eliminate collinearity and redundancy. Finally, three machine learning algorithms, i.e., Random Forest (RF), Support Vector Machine (SVM), Classification And Regression Tree (CART), were applied and compared to find the best classifier for predicting the damage stage of individual P. gansuensis. Results The confusion matrix of RF achieved the highest overall classification accuracy (86.2%) and the highest Kappa index value (0.804), indicating the potential of using WV-2 imaging to accurately detect damage stages of individual trees. In addition, the canopy color was found to be positively correlated with P. gansuensis’ damage stages. Conclusions A novel method was developed by combining WV-2 and tree physiological index for semi-automatic classification of three damage stages of P. gansuensis infested with ALB. The canopy color was determined as an abnormal phenotype that could be directly assessed using remote-sensing images at the tree level to predict the damage degree. These tools are highly applicable for driving quick and effective measures to reduce damage to pure poplar forests in Gansu Province, China.

A case of deletion 8q22.2q22.3 in a child with de novo balanced translocation t(1;6)

2021 ◽  
pp. 49-56
Author(s):  
М.Е. Миньженкова ◽  
Ж.Г. Маркова ◽  
И.В. Анисимова ◽  
И.В. Канивец ◽  
Н.В. Шилова
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Current Trend ◽  
Chromosomal Microarray ◽  
Congenital Defects ◽  
Chromosomal Microarray Analysis ◽  
Balanced Translocation ◽  
Genomic Imbalance ◽  
Abnormal Phenotype ◽  
Balanced Translocations

Выяснение этиопатогенеза аномального фенотипа у пациентов со сбалансированными транслокациями является актуальным аспектом в современной клинической цитогенетике. Формирование аномалий развития может быть ассоциировано с наличием скрытого геномного дисбаланса как в точках разрывов, так и на хромосомах, не задействованных в перестройке. Целью данного исследования явилась этиологическая диагностика геномного дисбаланса у пациента со сбалансированной транслокацией и аномалиями развития. Для детекции геномного дисбаланса у пациента со сбалансированной транслокацией использовали хромосомный микроматричный анализ (ХМА) и FISH-исследование. У пациента со сбалансированной транслокацией при ХМА была выявлена делеция на хромосоме 8, не задействованной в транслокации. Таким образом, в статье представлен новый случай делеции 8q22.2q22.3 у пациента со сбалансированной транслокацией t(1;6) и аномалиями развития вследствие делеции. Identification of the etiopathogenesis of the abnormal phenotype in patients with balanced translocations is current trend in cytogenetic laboratories. The formation of developmental anomalies can be associated with the presence of a cryptic genomic imbalance both at breakpoints and on chromosomes not involved in rearrangements.The aim of this study is diagnostics of genomic imbalance in a patient with balanced translocation and abnormal phenotype. The case was characterized by GTG-banding, chromosomal microarray analysis and FISH diagnosis. We present a new case of deletion 8q22.2-q22.3 in child with balanced translocation t(1;6) and developmental delay/congenital defects due to deletion.

Gastric smooth muscle cells manifest an abnormal phenotype in Parkinson’s disease rats with gastric dysmotility

2020 ◽  
Vol 381 (2) ◽  
pp. 217-227 ◽  
Author(s):  
Xiao-Lin Xiu ◽  
Li-Fei Zheng ◽  
Xiao-Yu Liu ◽  
Yan-Yan Fan ◽  
Jin-Xia Zhu
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Muscle Cells ◽  
Abnormal Phenotype ◽  
Gastric Smooth Muscle

scholarly journals Overexpressing TPTE2 (TPIP), a homolog of the human tumor suppressor gene PTEN, rescues the abnormal phenotype of the PTEN−/− mutant

Oncotarget ◽  
2018 ◽  
Vol 9 (30) ◽  
pp. 21100-21121 ◽  
Author(s):  
Daniel F. Lusche ◽  
Emma C. Buchele ◽  
Kanoe B. Russell ◽  
Benjamin A. Soll ◽  
Michele I. Vitolo ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Tumor Suppressor Gene ◽  
Human Tumor ◽  
Suppressor Gene ◽  
Abnormal Phenotype

Prenatal detection of mosaic isochromosome 20q: a fourth report with abnormal phenotype

2005 ◽  
Vol 25 (8) ◽  
pp. 653-655 ◽  
Author(s):  
C. Goumy ◽  
A. M. Beaufrère ◽  
C. Francannet ◽  
A. Tchirkov ◽  
H. Laurichesse Delmas ◽  
...  
Keyword(s):  
Abnormal Phenotype ◽  
Prenatal Detection ◽  
Fourth Report

De novo dup(X)(q22.1q25) in a girl with an abnormal phenotype

1999 ◽  
Vol 87 (4) ◽  
pp. 302-305 ◽  
Author(s):  
Fr�d�rique Tihy ◽  
Emmanuelle Lemyre ◽  
Nicole Lemieux ◽  
Louis Dallaire
Keyword(s):  
De Novo ◽  
Abnormal Phenotype

scholarly journals Abnormal phenotype of in vitro dermal fibroblasts from patients with pseudoxanthoma elasticum (PXE)

2000 ◽  
Vol 1501 (1) ◽  
pp. 51-62 ◽  
Author(s):  
D Quaglino ◽  
F Boraldi ◽  
D Barbieri ◽  
A Croce ◽  
R Tiozzo ◽  
...  
Keyword(s):  
Pseudoxanthoma Elasticum ◽  
Dermal Fibroblasts ◽  
Abnormal Phenotype

Mosaic trisomy of a small r(1) with an abnormal phenotype

2002 ◽  
Vol 110 (4) ◽  
pp. 413-413
Author(s):  
Alan L. Shanske ◽  
Robert W. Marion
Keyword(s):  
Abnormal Phenotype ◽  
Mosaic Trisomy

De novo and complex imbalanced chromosomal rearrangements revealed by array CGH in a patient with an abnormal phenotype and apparently “balanced” paracentric inversion of 14(q21q23)

2008 ◽  
Vol 146A (15) ◽  
pp. 1986-1993 ◽  
Author(s):  
Yong-Hui Jiang ◽  
Jose E. Martinez ◽  
Zhishuo Ou ◽  
M. Lance Cooper ◽  
Sung-Hae L. Kang ◽  
...  
Keyword(s):  
Array Cgh ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Paracentric Inversion ◽  
Abnormal Phenotype
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