Tianren Jiang

This study addresses doctrinal inconsistencies arising from inconsistent statements within Yogācāra literature regarding the cessation or non-cessation of _ālayavijñāna_ upon achieving _nirvāṇa_. In _Yogācārabhūmi_, _ālayavijñāna_ is defined as a type of consciousness that supports and conceals itself within the practitioner’s body, serving as a foundational consciousness for the continuity of life during _nirodhasamāpatti_. As the doctrine evolves, _ālayavijñāna_ is understood as inherently polluted, and it is proposed that arhatship, signifying the eradication of all defilements, leads to its cessation. However, two key doctrinal inconsistencies arise: the first concerns how an arhat, whose _ālayavijñāna_ has ceased, can still possess a living body during _nirodhasamāpatti_ in _nirvāṇa_ with remainder (_sopadhiśeṣanirvāṇa_); the second pertains to how _jñeyāvaraṇa_ (the hindrance regarding what is to be known) —which renders the _nirvāṇa_ of arhats and pratyekabuddhas inferior to Buddhahood—can persist while they no longer possess either bodies nor minds in _nirvāṇa_ without remainder (_nirupadhiśeṣanirvāṇa_)_._ This study examines these doctrinal challenges by analyzing various Yogācāra texts, including the _Yogācārabhūmi_, _Mahāyānasaṃgraha_, _Triṃśikāvijñaptikārikā_, as well as the commentaries of the latter two, and _Laṅkāvatārasūtra_, offering a comparative analysis of how these texts attempt to resolve the tensions surrounding _nirvāṇa_ and the ontological implications of the cessation of _ālayavijñāna_.

This study addresses doctrinal inconsistencies arising from inconsistent statements within Yogācāra literature regarding the cessation or non-cessation of ālayavijñāna upon achieving nirvāṇa. In Yogācārabhūmi, ālayavijñāna is defined as a type of consciousness that supports and conceals itself within the practitioner’s body, serving as a foundational consciousness for the continuity of life during nirodhasamāpatti. As the doctrine evolves, ālayavijñāna is understood as inherently polluted, and it is proposed that arhatship, signifying the eradication of all defilements, leads to its cessation. However, two key doctrinal inconsistencies arise: the first concerns how an arhat, whose ālayavijñāna has ceased, can still possess a living body during nirodhasamāpatti in nirvāṇa with remainder (sopadhiśeṣanirvāṇa); the second pertains to how jñeyāvaraṇa (the hindrance regarding what is to be known) —which renders the nirvāṇa of arhats and pratyekabuddhas inferior to Buddhahood—can persist while they no longer possess either bodies nor minds in nirvāṇa without remainder (nirupadhiśeṣanirvāṇa). This study examines these doctrinal challenges by analyzing various Yogācāra texts, including the Yogācārabhūmi, Mahāyānasaṃgraha, Triṃśikāvijñaptikārikā, as well as the commentaries of the latter two, and Laṅkāvatārasūtra, offering a comparative analysis of how these texts attempt to resolve the tensions surrounding nirvāṇa and the ontological implications of the cessation of ālayavijñāna.

© 2015 Macmillan Publishers Limited All rights reserved. Genome-wide gene expression measurements have enabled comprehensive studies that integrate the changes of gene expression and phenotypic information to uncover their novel associations. Here we reported the association analysis between psychophysical phenotypes and genome-wide gene expression changes in human adaptation to one of the most extreme climates on Earth, the Antarctic Dome Argus. Dome A is the highest ice feature in Antarctica, and may be the coldest, driest and windiest location on earth. It is considered unapproachable due to its hostile environment. In 2007, a Chinese team of 17 male explorers made the expedition to Dome A for scientific investigation. Overall, 133 psychophysical phenotypes were recorded, and genome-wide gene expression profiles from the blood samples of the explorers were measured before their departure and upon their arrival at Dome A. We found that mood disturbances, including tension, depression, anger and fatigue, had a strong, positive, linear relationship with the level of a male sex hormone, testosterone, using the Pearson correlation coefficient analysis. We also demonstrated that significantly lowest-level Gene Ontology groups in changes of gene expression in blood cells with erythrocyte removal were consistent with the adaptation of the psychophysical characteristics. Interestingly, we discovered a list of genes that were strongly related to significant phenotypes using phenotype and gene expression PCC analysis. Importantly, among the 70 genes that were identified, most were significantly related to mood disturbances, where 42 genes have been reported in the literature mining, suggesting that the other 28 genes were likely novel genes involved in the mood disturbance mechanism. Taken together, our association analysis provides a reliable method to uncover novel genes and mechanisms related to phenotypes, although further studies are needed.

© 2014 The Author. Motivation: Although many gene set analysis methods have been proposed to explore associations between a phenotype and a group of genes sharing common biological functions or involved in the same biological process, the underlying biological mechanisms of identified gene sets are typically unexplained. Results: We propose a method called Differential Regulation-based enrichment Analysis for GENe sets to identify gene sets in which a significant proportion of genes have their transcriptional regulatory patterns changed in a perturbed phenotype. We conduct comprehensive simulation studies to demonstrate the capability of our method in identifying differentially regulated gene sets. We further apply our method to three human microarray expression datasets, two with hormone treated and control samples and one concerning different cell cycle phases. Results indicate that the capability of DRAGEN in identifying phenotype-associated gene sets is significantly superior to those of four existing methods for analyzing differentially expressed gene sets.We conclude that the proposed differential regulation enrichment analysis method, though exploratory in nature, complements the existing gene set analysis methods and provides a promising new direction for the interpretation of gene expression data.

Motivation: De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species. Results: Here we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows us to extend the initial assemblies, while avoiding incorrect extensions and early terminations. In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7-62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9-94.5% and 80.3-165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph's efficiency in improving genome assemblies by taking advantage of closely related references. © 2014 The Author. Published by Oxford University Press. All rights reserved.