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Search: authors:"Shuai Li"

11 papers found.
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Predicting interval and screen-detected breast cancers from mammographic density defined by different brightness thresholds

Case–control studies show that mammographic density is a better risk factor when defined at higher than conventional pixel-brightness thresholds. We asked if this applied to interval and/or screen-detected cancers. We conducted a nested case–control study within the prospective Melbourne Collaborative Cohort Study including 168 women with interval and 422 with screen-detected...

Reconstructing directed gene regulatory network by only gene expression data

Background Accurately identifying gene regulatory network is an important task in understanding in vivo biological activities. The inference of such networks is often accomplished through the use of gene expression data. Many methods have been developed to evaluate gene expression dependencies between transcription factor and its target genes, and some methods also eliminate...

Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study

BackgroundSmoking has been reported to be associated with peripheral blood DNA methylation, but the causal aspects of the association have rarely been investigated. We aimed to investigate the association and underlying causation between smoking and blood methylation.MethodsThe methylation profile of DNA from the peripheral blood, collected as dried blood spots stored on Guthrie...

IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination

Background Information in the brain is often segregated into spatially organized layers that reflect the function of the embedded circuits. This is perhaps best exemplified in the layering, or lamination, of the retinal inner plexiform layer (IPL). The neurites of the retinal ganglion, amacrine and bipolar cell subtypes that form synapses in the IPL are precisely organized in...

Structural neighboring property for identifying protein-protein binding sites

Background The protein-protein interaction plays a key role in the control of many biological functions, such as drug design and functional analysis. Determination of binding sites is widely applied in molecular biology research. Therefore, many efficient methods have been developed for identifying binding sites. In this paper, we calculate structural neighboring property through...

Limb remote ischemic postconditioning protects cerebral ischemia from injury associated with expression of HIF-1α in rats

Background Limb remote ischemic postconditioning (LRIP) can ameliorate cerebral ischemia–reperfusion injury (IRI), while the underlying mechanism remains elusive. Hypoxia-inducible factor 1α (HIF-1α) is an important transcription factor during cerebral ischemia damage. However, whether the neuroprotective effect of LRIP could be associated with HIF-1α is somewhat unclear. Here we...

Limb remote ischemic postconditioning protects cerebral ischemia from injury associated with expression of HIF-1α in rats

Limb remote ischemic postconditioning (LRIP) can ameliorate cerebral ischemia–reperfusion injury (IRI), while the underlying mechanism remains elusive. Hypoxia-inducible factor 1α (HIF-1α) is an important transcription factor during cerebral ischemia damage. However, whether the neuroprotective effect of LRIP could be associated with HIF-1α is somewhat unclear. Here we tested the...

Protein-protein binding site identification by enumerating the configurations

Background The ability to predict protein-protein binding sites has a wide range of applications, including signal transduction studies, de novo drug design, structure identification and comparison of functional sites. The interface in a complex involves two structurally matched protein subunits, and the binding sites can be predicted by identifying structural matches at protein...

Calibur: a tool for clustering large numbers of protein decoys

Background Ab initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. The decoy with the most number of neighbors of up to a threshold distance is typically identified as the most representative decoy. However, the clustering of decoys needed for this criterion involves computations with runtimes that are at best...

Incorporating Ab Initio energy into threading approaches for protein structure prediction

Background Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how...

SEL1L deficiency impairs growth and differentiation of pancreatic epithelial cells

Background The vertebrate pancreas contains islet, acinar and ductal cells. These cells derive from a transient pool of multipotent pancreatic progenitors during embryonic development. Insight into the genetic determinants regulating pancreatic organogenesis will help the development of cell-based therapies for the treatment of diabetes mellitus. Suppressor enhancer lin12/Notch 1...