scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization.

MOTIVATION: Single cell RNA-seq data offers us new resource and resolution to study cell type identity and its conversion. However, data analyses are challenging in dealing with noise, sparsity and poor annotation at single cell resolution. Detecting cell-type-indicative markers is promising to help denoising, clustering and cell type annotation. RESULTS: We developed a new method, scTIM, to reveal cell-type-indicative markers. scTIM is based on a multi-objective optimization framework to simultaneously maximize gene specificity by considering gene-cell relationship, maximize gene's ability to reconstruct cell-cell relationship and minimize gene redundancy by considering gene-gene relationship. Furthermore, consensus optimization is introduced for robust solution. Experimental results on three diverse single cell RNA-seq datasets show scTIM's advantages in identifying cell types (clustering), annotating cell types and reconstructing cell development trajectory. Applying scTIM to the large-scale mouse cell atlas data identifies critical markers for 15 tissues as 'mouse cell marker atlas', which allows us to investigate identities of different tissues and subtle cell types within a tissue. scTIM will serve as a useful method for single cell RNA-seq data mining. AVAILABILITY AND IMPLEMENTATION: scTIM is freely available at https://github.com/Frank-Orwell/scTIM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Optimization of SAW Devices with LGS/Pt Structure for Sensing Temperature.

Research has shown that SAW (surface acoustic wave) devices with an LGS/Pt (langasite La3Ga5SiO14/platinum) structure are useful in high-temperature sensor applications. Extreme high temperature brings great acoustic attenuation because of the thermal radiation loss, which requires that the sensing device offer a sufficiently high quality factor (Q) and a low loss. Therefore, it is necessary to improve the performance of the quality factor as much as possible so as to better meet the application of high-temperature sensors. Based on these reasons, the main work of this paper was to extract accurate simulation parameters to optimize the Pt/LGS device and obtain Q-value device parameters. Optimization of SAW devices with LGS/Pt structure for sensing extreme high temperature was addressed by employing a typical coupling of modes (COM) model in this work. Using the short pulse method, the reflection coefficient of Pt electrodes on LGS substrate was extracted accurately by characterizing the prepared SAW device with strategic design. Other relevant parameters for COM simulation were determined by finite element analysis. To determine the optimal design parameters, the COM simulation was conducted on the SAW sensing device with a one-port resonator pattern for sensing extreme temperature, which allows for a larger Q-value and low insertion loss. Experimental results validate the theoretical simulation. In addition, the corresponding high-temperature characteristics of the prepared sensing device were investigated.