Automatic Bayesian single molecule identification for localization microscopy

Single molecule localization microscopy (SMLM) is on its way to become a mainstream imaging technique in the life sciences. However, analysis of SMLM data is biased by user provided subjective parameters required by the analysis software. To remove this human bias we introduce here the Auto-Bayes method that executes the analysis of SMLM data automatically. We demonstrate the success of the method using the photoelectron count of an emitter as selection characteristic. Moreover, the principle can be used for any characteristic that is bimodally distributed with respect to false and true emitters. The method also allows generation of an emitter reliability map for estimating quality of SMLM-based structures. The potential of the Auto-Bayes method is shown by the fact that our first basic implementation was able to outperform all software packages that were compared in the ISBI online challenge in 2015, with respect to molecule detection (Jaccard index)

Application of new probabilistic graphical models in the genetic regulatory networks studies

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

Quantum confined peptide assemblies with tunable visible to near-infrared spectral range

Quantum confined materials have been extensively studied for photoluminescent applications. Due to intrinsic limitations of low biocompatibility and challenging modulation, the utilization of conventional inorganic quantum confined photoluminescent materials in bio-imaging and bio-machine interface faces critical restrictions. Here, we present aromatic cyclo-dipeptides that dimerize into quantum dots, which serve as building blocks to further self-assemble into quantum confined supramolecular structures with diverse morphologies and photoluminescence properties. Especially, the emission can be tuned from the visible region to the near-infrared region (420 nm to 820 nm) by modulating the self-assembly process. Moreover, no obvious cytotoxic effect is observed for these nanostructures, and their utilization for in vivo imaging and as phosphors for light-emitting diodes is demonstrated. The data reveal that the morphologies and optical properties of the aromatic cyclo-dipeptide self-assemblies can be tuned, making them potential candidates for supramolecular quantum confined materials providing biocompatible alternatives for broad biomedical and opto-electric applications

Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information

<p>Abstract</p> <p>Background</p> <p>In parallel with the quick development of high-throughput technologies, <it>in vivo (vitro) </it>experiments for genome-wide identification of protein-DNA interactions have been developed. Nevertheless, a few questions remain in the field, such as how to distinguish true protein-DNA binding (functional binding) from non-specific protein-DNA binding (non-functional binding). Previous researches tackled the problem by integrated analysis of multiple available sources. However, few systematic studies have been carried out to examine the possible relationships between histone modification and protein-DNA binding. Here this issue was investigated by using publicly available histone modification data in yeast.</p> <p>Results</p> <p>Two separate histone modification datasets were studied, at both the open reading frame (ORF) and the promoter region of binding targets for 37 yeast transcription factors. Both results revealed a distinct histone modification pattern between the functional protein-DNA binding sites and non-functional ones for almost half of all TFs tested. Such difference is much stronger at the ORF than at the promoter region. In addition, a protein-histone modification interaction pathway can only be inferred from the functional protein binding targets.</p> <p>Conclusions</p> <p>Overall, the results suggest that histone modification information can be used to distinguish the functional protein-DNA binding from the non-functional, and that the regulation of various proteins is controlled by the modification of different histone lysines such as the protein-specific histone modification levels.</p

Schiff Base Mediated Dipeptide Assembly toward Nanoarchitectonics

Dynamic covalent chemistry (DCC) is fascinating because of its dual nature. It perfectly combines the reversible nature of noncovalent bonds with the robustness of covalent bonds, effectively enhancing the stability of assemblies and meanwhile giving rise to unprecedented properties. Therefore, integration of DCC with supramolecular chemistry has emerged as a versatile and an extraordinarily useful approach in directing peptide assembly. This Minireview focuses on a recent strategy, which exploits dynamic Schiff base chemistry in combination with supramolecular chemistry, to mediate dipeptide assembly toward nanoarchitectonics. Diversified structures, new emergent properties, and their related applications are highlighted. Lastly, the opportunities and prospects in this exciting field are also introduced

Schiff Base Mediated Dipeptide Assembly toward Nanoarchitectonics

Dynamic covalent chemistry (DCC) is fascinating because of its dual nature. It perfectly combines the reversible nature of noncovalent bonds with the robustness of covalent bonds, effectively enhancing the stability of assemblies and meanwhile giving rise to unprecedented properties. Therefore, integration of DCC with supramolecular chemistry has emerged as a versatile and an extraordinarily useful approach in directing peptide assembly. This Minireview focuses on a recent strategy, which exploits dynamic Schiff base chemistry in combination with supramolecular chemistry, to mediate dipeptide assembly toward nanoarchitectonics. Diversified structures, new emergent properties, and their related applications are highlighted. Lastly, the opportunities and prospects in this exciting field are also introduced

An efficient methodology of simultaneous three-phase withstand voltage and sensitive partial discharge testing of medium voltage power cables

Withstand voltage tests and partial discharge (PD) measurement are widely accepted as indispensable techniques for assessing the insulation condition of power equipment. To reduce testing time, a favorable tool that can perform insulation tests simultaneously for three-core medium voltage (MV) power cables is urgently needed. This study aims to develop a high-efficiency solution for this purpose. The proposed methodology’s topology and operation principle are presented and illustrated, which can be used to conduct three-phase withstand voltage tests and sensitive PD measurement of MV cables simultaneously under different excitation voltages. Circuit analysis and parameter optimization are carried out to adapt the system to the application. Thus, the proposed methodology is implemented, and a prototype is built. A new method for achieving high sensitivity in screening PD pulses is proposed, and some experimental tests on a three-core MV power cable with artificial defects are performed to validate the effectiveness and practicality of the proposed methodology