-
Using Evolutionary Trees for the Colorectal Cancer Prognosis Prediction
Hung-Yu Yan,
Dun-Wei Cheng,
Peng-Chan Lin,
Hsin-Hung Chou,
Meng-Ru Shen,
Sun-Yuan Hsieh
Issue:
Volume 9, Issue 1, June 2021
Pages:
1-14
Received:
2 January 2021
Accepted:
29 January 2021
Published:
10 February 2021
Abstract: The measurement of tree similarity based on structure comparison has been long used in diverse fields. We applied the evolutionary tree method to study the cancer genome. Cancer evolutionary trees, representing cancer diversity, provide information on the clonal evolution and the clinical outcome of cancer patients. This study considered 107 colorectal cancer (CRC) patients who received deep targeted sequencing of cancer tissues. The evolutionary trees of individual cancer patients were reconstructed from genome sequencing data based on variant allele frequencies (VAFs) of point mutations and small insertions or deletions (indels). The main purpose of this study was to predict cancer recurrence. We mapped the structure of a cancer evolutionary tree to a rooted tree and developed a canonical-form transformation for solving tree isomorphism to ensure that each patient has a unique tree structure. We proposed an algorithm for comparing tree similarity in terms of cost calculation between evolutionary structure trees. The cost was calculated using the node position, tree size (or number of nodes), tree height, node depth, number of descendants of the node (the size of the subtree with the node as a root), and relationship of the node with other nodes. After tree similarity comparison, the cancer patients were clustered into two groups through k-means clustering. The clustering information indicated that the evolutionary structure trees were associated with gender and tumor invasion stage. Several machine-learning strategies including random forest, support vector machine (SVM), bagging, and boosting were used to predict cancer recurrence in these patients. Our results revealed that combining the clustering information of evolutionary structure trees increased the prediction performance compared with using clinical information alone, and tree similarity comparison can help in the prognostic analysis of cancer patients.
Abstract: The measurement of tree similarity based on structure comparison has been long used in diverse fields. We applied the evolutionary tree method to study the cancer genome. Cancer evolutionary trees, representing cancer diversity, provide information on the clonal evolution and the clinical outcome of cancer patients. This study considered 107 colore...
Show More
-
A Comprehensive Review of Predicting Method of RNA Tertiary Structure
Yurong Yang,
Zhendong Liu
Issue:
Volume 9, Issue 1, June 2021
Pages:
15-20
Received:
6 February 2021
Accepted:
1 March 2021
Published:
10 March 2021
Abstract: In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and RNA tertiary interaction, so the RNA tertiary structure prediction has also attracted extensive attention. There are many RNA tertiary structure prediction algorithms. According to the traditional classification methods, the existing RNA tertiary structure prediction algorithms can be divided into two categories: the RNA tertiary structure prediction algorithm based on knowledge mining and the RNA tertiary structure prediction algorithm based on physics. On this basis, this paper further refines the RNA tertiary structure prediction algorithm based on physics in traditional classification, and proposes a new refinement classification method based on conformational sampling method, namely RNA tertiary structure prediction algorithm based on physical fragment assembly conformational sampling method and RNA tertiary structure prediction algorithm based on Stepwise ansatz conformational sampling method. We make a comparative analysis of RNA tertiary structure prediction algorithms, and put forward some suggestions for improving the energy function in the next step, in order to find an RNA tertiary structure prediction algorithm that can achieve atomic accuracy.
Abstract: In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and RNA tertiary interaction, so the RNA tertiary structure prediction has also attracted extensive...
Show More
-
Prey Fragmentation and Transport in Six Tropical Arboreal Ant Species
Tadu Zephirin,
Messop-Youbi Edith Blandine,
Fomekong Lontchi Judicael,
Alene Desiree Chantal,
Djieto-Lordon Champlain
Issue:
Volume 9, Issue 1, June 2021
Pages:
21-30
Received:
17 May 2021
Accepted:
3 June 2021
Published:
25 June 2021
Abstract: Prey fragmentation and transport modalities were studied in Myrmicaria opaciventris, Platythyrea conradti, Cremtogaster sp., Crematogaster clariventris, Tetramorium aculeatum and Oecophylla longinoda, six tropical ant species with varying levels of adaptation to foraging in the tree canopy. Termites and grasshoppers of different sizes were used as prey and deposited on a hunting arena. After prey capture, we investigated the strategy adopted by each ant species to fragment and transport their prey. The data were analyzed with classification tree, using Chi-squared Automatic Interaction Detection method to find the variation in prey fragmentation strategies and transportation modalities between arboreal ant species in relation with prey type and prey size. The results showed that prey fragmentation did not occur systematically after capture and varied between ant species with prey type and prey size. Studied ant species cut their prey either completely into tiny pieces or partially into two or three large pieces before cutting them totally into tiny pieces or not at all. Fragmentation strategy, induced variation in transport modalities including (a) transport of large pieces, each by a single worker; (b) transport of large pieces, each, by a group of workers; (c) transport of tiny pieces after total cutting, and (c) transport of entire prey in the nest without fragmentation. Prey fragmentation and transport modalities varied between ant species in relation with their level of adaptation to arboreal area.
Abstract: Prey fragmentation and transport modalities were studied in Myrmicaria opaciventris, Platythyrea conradti, Cremtogaster sp., Crematogaster clariventris, Tetramorium aculeatum and Oecophylla longinoda, six tropical ant species with varying levels of adaptation to foraging in the tree canopy. Termites and grasshoppers of different sizes were used as ...
Show More
