Sequence dependence of cross-hybridization on short oligo microarrays

One of the critical problems in the short oligo microarray technology is how to deal with cross-hybridization that produces spurious data. Little is known about the details of cross-hybridization effect at molecular level. Here, we report a free energy analysis of cross-hybridization on short oligo microarrays using data from a spike-in study. Our analysis revealed that cross-hybridization on the arrays is mostly caused by oligo fragments with a run of 10–16 nt complementary to the probes. Mismatches were estimated to be energetically much more costly in cross-hybridization than that in gene-specific hybridization, implying that the sources of cross-hybridization must be very different between a PM–MM probe pair. Consequently, it is unreliable to use MM probe signal to track cross-hybridizing signal on a corresponding PM probe. Our results also showed that the oligo fragments tend to bind to the 5′ ends of the probes, and are rarely seen at the 3′ ends. These results are useful for microarray design and data analysis

The Cure: Making a game of gene selection for breast cancer survival prediction

Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biological interpretability. Methods that take advantage of structured prior knowledge (e.g. protein interaction networks) show promise in helping to define better signatures but most knowledge remains unstructured. Crowdsourcing via scientific discovery games is an emerging methodology that has the potential to tap into human intelligence at scales and in modes previously unheard of. Here, we developed and evaluated a game called The Cure on the task of gene selection for breast cancer survival prediction. Our central hypothesis was that knowledge linking expression patterns of specific genes to breast cancer outcomes could be captured from game players. We envisioned capturing knowledge both from the players prior experience and from their ability to interpret text related to candidate genes presented to them in the context of the game. Results: Between its launch in Sept. 2012 and Sept. 2013, The Cure attracted more than 1,000 registered players who collectively played nearly 10,000 games. Gene sets assembled through aggregation of the collected data clearly demonstrated the accumulation of relevant expert knowledge. In terms of predictive accuracy, these gene sets provided comparable performance to gene sets generated using other methods including those used in commercial tests. The Cure is available at http://genegames.org/cure

Bivariate functions with low cc-differential uniformity

Starting with the multiplication of elements in $\mathbb{F}_{q}^2$ which is consistent with that over $\mathbb{F}_{q^2}$, where $q$ is a prime power, via some identification of the two environments, we investigate the $c$-differential uniformity for bivariate functions $F(x,y)=(G(x,y),H(x,y))$. By carefully choosing the functions $G(x,y)$ and $H(x,y)$, we present several constructions of bivariate functions with low $c$-differential uniformity. Many P$c$N and AP$c$N functions can be produced from our constructions.Comment: Low $c$-differential uniformity, perfect and almost perfect $c$-nonlinearity, the bivariate functio

Imaging the Centromedian Thalamic Nucleus Using Quantitative Susceptibility Mapping.

The centromedian (CM) nucleus is an intralaminar thalamic nucleus that is considered as a potentially effective target of deep brain stimulation (DBS) and ablative surgeries for the treatment of multiple neurological and psychiatric disorders. However, the structure of CM is invisible on the standard T1- and T2-weighted (T1w and T2w) magnetic resonance images, which hamper it as a direct DBS target for clinical applications. The purpose of the current study is to demonstrate the use of quantitative susceptibility mapping (QSM) technique to image the CM within the thalamic region. Twelve patients with Parkinson's disease, dystonia, or schizophrenia were included in this study. A 3D multi-echo gradient recalled echo (GRE) sequence was acquired together with T1w and T2w images on a 3-T MR scanner. The QSM image was reconstructed from the GRE phase data. Direct visual inspection of the CM was made on T1w, T2w, and QSM images. Furthermore, the contrast-to-noise ratios (CNRs) of the CM to the adjacent posterior part of thalamus on T1w, T2w, and QSM images were compared using the one-way analysis of variance (ANOVA) test. QSM dramatically improved the visualization of the CM nucleus. Clear delineation of CM compared to the surroundings was observed on QSM but not on T1w and T2w images. Statistical analysis showed that the CNR on QSM was significantly higher than those on T1w and T2w images. Taken together, our results indicate that QSM is a promising technique for improving the visualization of CM as a direct targeting for DBS surgery

The influence of challenge research stressors on research creativity among Chinese doctoral students: a mediated moderation model

The research creativity of doctoral students is not solely fueled by their intrinsic motivation, but also thrives in an environment that offers challenging research opportunities, substantial support, and feedback from significant others. Based on the job demands-resources model, this study aims to explore the impact of challenge research stressors on the research creativity of Chinese doctoral students. A mediated moderation model was constructed to examine the mediating effect of achievement motivation and the moderating effect of supervisor developmental feedback on the relationship between challenge research stressors and research creativity. A total of 538 valid questionnaires were collected from doctoral students using convenience sampling and snowball sampling. The questionnaires included the Challenge Research Stressors Scale, the Research Creativity Scale, the Achievement Motivation Scale, and the Supervisor Developmental Feedback Scale. Regression analyses, bootstrap testing, and simple slope analyses were used to estimate the various relationships. The findings indicated that challenge research stressors had a positive effect on doctoral students’ research creativity. Supervisor developmental feedback positively moderated the impact of challenge research stressors on the achievement motivation and research creativity of doctoral students. Achievement motivation partially mediated the influence of challenge research stressors on doctoral students’ research creativity, and further fully mediated the interaction effect of challenge research stressors and supervisor developmental feedback on doctoral students’ research creativity. These findings contribute not only to our understanding of the mechanisms and boundary conditions through which challenge research stressors impact the research creativity of doctoral students, but also provide valuable insights into how to stimulate and maintain their research creativity