Hasil untuk "q-bio.SC"

Dong Young Chung, Pietro P. Lopes, Pedro Farinazzo Bergamo Dias Martins et al.

F. H. Jackson

Huiqi Li, Rui Zeng, Zixiao Shi et al.

Denitsa R. Baykusheva, Deven Carmichael, Clara S. Weber et al.

V. M. Semenov, T. N. Lebedeva, D. A. Sokolov et al.

Cecile M. Cres, Andrew Tritt, Kristofer E. Bouchard et al.

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

N. A. Aziz, A. A. Latiff, M. Q. Lokman et al.

G. Kersh

M. Chaichian, P. Kulish

Ross J. Anderson, S. Vaudenay

K. Chandran, D. Aggarwal, R. Migrino et al.

Doxorubicin (DOX) is used for treating various cancers. Its clinical use is, however, limited by its dose-limiting cardiomyopathy. The exact mechanism of DOX-induced cardiomyopathy still remains unknown. The goals were to investigate the molecular mechanism of DOX-induced cardiomyopathy and cardioprotection by mitoquinone (Mito-Q), a triphenylphosphonium-conjugated analog of coenzyme Q, using a rat model. Rats were treated with DOX, Mito-Q, and DOX plus Mito-Q for 12 weeks. The left ventricular function as measured by two-dimensional echocardiography decreased in DOX-treated rats but was preserved during Mito-Q plus DOX treatment. Using low-temperature ex vivo electron paramagnetic resonance (EPR), a time-dependent decrease in heme signal was detected in heart tissues isolated from rats administered with a cumulative dose of DOX. DOX attenuated the EPR signals characteristic of the exchange interaction between cytochrome c oxidase (CcO)-Fe(III) heme a3 and CuB. DOX and Mito-Q together restored these EPR signals and the CcO activity in heart tissues. DOX strongly downregulated the stable expression of the CcO subunits II and Va and had a slight inhibitory effect on CcO subunit I gene expression. Mito-Q restored CcO subunit II and Va expressions in DOX-treated rats. These results suggest a novel cardioprotection mechanism by Mito-Q during DOX-induced cardiomyopathy involving CcO.

Himanshu Joshi, H. Sigmarsson, Sungwook Moon et al.

I. T. Ellingsen, I. Størksen, P. Stephens

C. Quesenberry

B. Gayral, J. Gerard, A. Lemaître et al.

Dachun Yang, Wen Yuan

A. Armani, K. Vahala

G. Tesauro

Arild Palmström, E. Broch

S. Best