SHEsis PCA: A GPU-Based Software to Correct for Population Stratification that Efficiently Accelerates the Process for Handling Genome-Wide Datasets

Population stratification is a problem in genetic association studies because it is likely to highlight loci that underlie the population structure rather than disease-related loci. At present, principal component analysis （PCA） has been proven to be an effective way to correct for population stratification. However, the conventional PCA algorithm is time-consuming when dealing with large datasets. We developed a Graphic processing unit （GPU）-based PCA software named SHEsisPCA （http：//analysis.bio-x.cn/SHEsisMain.htm） that is highly parallel with a highest speedup greater than 100 compared with its CPU version. A cluster algorithm based on X-means was also implemented as a way to detect population subgroups and to obtain matched cases and controls in order to reduce the genomic inflation and increase the power. A study of both simulated and real datasets showed that SHEsisPCA ran at an extremely high speed while the accuracy was hardly reduced. Therefore, SHEsisPCA can help correct for population stratification much more efficiently than the conventional CPU-based algorithms.

Inhalation of Roman chamomile essential oil attenuates depressive-like behaviors in Wistar Kyoto rats

The idea of aromatherapy, using essential oils, has been considered as an alternative antidepressant treatment. In the present study, we investigated the effect of Roman chamomile essential oil inhalation for two weeks on depressive-like behaviors in Wistar-Kyoto(WKY) rats. We found that inhalation of either Roman chamomile or one of its main components α-pinene,attenuated depressive-like behavior in WKY rats in the forced swim test. Using isobaric tags for relative and absolute quantitation analysis(iTRAQ), we found that inhalation of α-pinene increased expression of proteins that are involved in oxidative phosphorylation, such as cytochrome c oxidase subunit 6C-2, cytochrome c oxidase subunit 7A2, ATPase inhibitor in the hippocampus, and cytochrome c oxidase subunit 6C-2, ATP synthase subunit e, Acyl carrier protein, and Cytochrome b-c1 complex subunit 6 in the PFC(prefrontal cortex). In addition, using the quantitative real-time polymerase chain reaction technique, we confirmed an increase of parvalbumin mRNA expression in the hippocampus, which was shown to be upregulated by 2.8-fold in iTRAQ analysis, in α-pinene treated WKY rats. These findings collectively suggest the involvement of mitochondrial functions and parvalbumin-related signaling in the antidepressant effect of α-pinene inhalation.

Electroencephalogram Features of Anxiety Relieving During Music Listening

With the fast-accelerating pace of life,most of the population is troubled by anxious feelings,or they even developed anxiety disorders,which affect their life qualities viciously.The current treatment is not without drawbacks,such as exhibiting slow or acute effects only.Music therapy has shown promising outcomes in significantly reducing tension and anxiety in many studies.To explore the underlying mechanism,we recruited 12 undergraduate student volunteers from Shanghai Jiao Tong University with habits of music listening.We explored the changes in the electroencephalogram(EEG)power spectrum both during and after listening to self-select favorite music,and the relation between EEG signals and anxiety-relieving during music listening.The results showed that the power of the band in the right parietal area was significantly higher in those who were self-report able to relax during music listening compared with those who could not get relaxed.We observed power increased in the right parietal area of self-reports,not able to relax while music playing.Also,a significant difference inband power in the left frontal area and band in the right frontal area before and after music listening was observed between high anxiety group and low anxiety group.These results imply that band activity in the left frontal area is associated with the anxiety-relieving capability of anxiety,which provides evidence for further elucidating the mechanism underlying anxiety-relieving during music listening.