BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework

Motivation: Removal of batch effect between multiple datasets from different experimental platforms has become an urgent problem, since single-cell RNA sequencing (scRNA-seq) techniques developed rapidly. Although there have been some methods for this problem, most of them still face the challenge of under-correction or over-correction. Specifically, handling batch effect in highly nonlinear scRNA-seq data requires a more powerful model to address under-correction. In the meantime, some previous methods focus too much on removing difference between batches, which may disturb the biological signal heterogeneity of datasets generated from different experiments, thereby leading to over-correction. Results: In this article, we propose a novel multi-layer adaptation autoencoder with dual-channel framework to address the under-correction and over-correction problems in batch effect removal, which is called BERMAD and can achieve better results of scRNA-seq data integration and joint analysis. First, we design a multi-layer adaptation architecture to model distribution difference between batches from different feature granularities. The distribution matching on various layers of autoencoder with different feature dimensions can result in more accurate batch correction outcome. Second, we propose a dual-channel framework, where the deep autoencoder processing each single dataset is independently trained. Hence, the heterogeneous information that is not shared between different batches can be retained more completely, which can alleviate over-correction. Comprehensive experiments on multiple scRNA-seq datasets demonstrate the effectiveness and superiority of our method over the state-of-the-art methods

Improving the Robustness of Electromyogram-Pattern Recognition for Prosthetic Control by a Postprocessing Strategy

Electromyogram (EMG) contains rich information for motion decoding. As one of its major applications, EMG-pattern recognition (PR)-based control of prostheses has been proposed and investigated in the field of rehabilitation robotics for decades. These prostheses can offer a higher level of dexterity compared to the commercially available ones. However, limited progress has been made toward clinical application of EMG-PR-based prostheses, due to their unsatisfactory robustness against various interferences during daily use. These interferences may lead to misclassifications of motion intentions, which damage the control performance of EMG-PR-based prostheses. A number of studies have applied methods that undergo a postprocessing stage to determine the current motion outputs, based on previous outputs or other information, which have proved effective in reducing erroneous outputs. In this study, we proposed a postprocessing strategy that locks the outputs during the constant contraction to block out occasional misclassifications, upon detecting the motion onset using a threshold. The strategy was investigated using three different motion onset detectors, namely mean absolute value, Teager–Kaiser energy operator, or mechanomyogram (MMG). Our results indicate that the proposed strategy could suppress erroneous outputs, during rest and constant contractions in particular. In addition, with MMG as the motion onset detector, the strategy was found to produce the most significant improvement in the performance, reducing the total errors up to around 50% (from 22.9 to 11.5%) in comparison to the original classification output in the online test, and it is the most robust against threshold value changes. We speculate that motion onset detectors that are both smooth and responsive would further enhance the efficacy of the proposed postprocessing strategy, which would facilitate the clinical application of EMG-PR-based prosthetic control

Mouse Embryonic Fibroblasts-Derived Extracellular Matrix Facilitates Expansion of Inner Ear-Derived Cells

Objective: Previous reports showed that mouse embryonic fibroblasts (MEFs) could support pluripotent stem cell selfrenewaland maintain their pluripotency. The goal of this study was to reveal whether the decellularized extracellularmatrix derived from MEFs (MEF-ECM) is beneficial to promote the proliferation of inner ear-derived cells.Materials and Methods: In this experimental study, we prepared a cell-free MEF-ECM through decellularization.Scanning electron microscope (SEM) and immunofluorescent staining were conducted for phenotype characterization.Organs of Corti were dissected from postnatal day 2 and the inner ear-derived cells were obtained. The identificationof inner ear-derived cells was conducted by using reverse transcription-polymerase chain reaction (RT-PCR). Cellcounting kit-8 (CCK-8) was used to evaluate the proliferation capability of inner ear-derived cells cultured on the MEFECMand tissue culture plate (TCP).Results: The MEF-ECM was clearly observed after decellularization via SEM, and the immunofluorescence stainingresults revealed that MEF-ECM was composed of three proteins, including collagen I, fibronectin and laminin. Mostimportantly, the results of CCK-8 showed that compared with TCP, MEF-ECM could effectively facilitate the proliferationof inner ear-derived cells.Conclusion: The discovery of the potential of MEF-ECM in promoting inner ear-derived cell proliferation indicatesthat the decellularized matrix microenvironment may play a vital role in keeping proliferation ability of these cells. Ourfindings indicate that the use of MEF-ECM may serve as a novel approach for expanding inner ear-derived cells andpotentially facilitating the clinical application of inner ear-derived cells for hearing loss in the future

The Effect of Temozolomide/Poly(lactide-co-glycolide) (PLGA)/Nano-Hydroxyapatite Microspheres on Glioma U87 Cells Behavior

In this study, we investigated the effects of temozolomide (TMZ)/Poly (lactide-co-glycolide)(PLGA)/nano-hydroxyapatite microspheres on the behavior of U87 glioma cells. The microspheres were fabricated by the “Solid/Water/Oil” method, and they were characterized by using X-Ray diffraction, scanning electron microscopy and differential scanning calorimetry. The proliferation, apoptosis and invasion of glioma cells were evaluated by MTT, flow cytometry assay and Transwell assay. The presence of the key invasive gene, αVβ3 integrin, was detected by the RT-PCR and Western blot method. It was found that the temozolomide/PLGA/nano-hydroxyapatite microspheres have a significantly diminished initial burst of drug release, compared to the TMZ laden PLGA microspheres. Our results suggest they can significantly inhibit the proliferation and invasion of glioma cells, and induce their apoptosis. Additionally, αVβ3 integrin was also reduced by the microspheres. These data suggest that by inhibiting the biological behavior of glioma cells in vitro, the newly designed temozolomide/PLGA/nano-hydroxyapatite microspheres, as controlled drug release carriers, have promising potential in treating glioma

Shape-related optical and catalytic properties of wurtzite-type CoO nanoplates and nanorods

National Basic Research Program of China [2012CB933103]; National Outstanding Youth Science Foundation of China [50825101]; National Natural Science Foundation of China [51171157, 51171158]In this paper, we report the anisotropic optical and catalytic properties of wurtzite-type hexagonal CoO (h-CoO) nanocrystals, an unusual nanosized indirect semiconductor material. h-CoO nanoplates and nanorods with a divided morphology have been synthesized via facile solution methods. The employment of flash-heating and surfactant tri-n-octylphosphine favors the formation of plate-like morphology, whereas the utilization of cobalt stearate as a precursor is critical for the synthesis of nanorods. Structural analyses indicate that the basal plane of the nanoplates is (001) face and the growth direction of the nanorods is along the c axis. Moreover, the UV-vis absorption spectra, the corresponding energy gap and the catalytic properties are found to vary with the crystal shape and the dimensions of the as-prepared h-CoO nanocrystals. Furthermore, remarkable catalytic activities for H-2 generation from the hydrolysis of alkaline NaBH4 solutions have been observed for the as-prepared h-CoO nanocrystals. The calculated Arrhenius activation energies show a decreasing trend with increasing extension degree along the direction, which is in agreement with the variation of the charge-transfer energy gap. Finally the maximum hydrogen generation rate of the h-CoO nanoplates exceeds most of the reported values of transition metal or noble metal containing catalysts performing in the same reaction system, which makes them a low-cost alternative to commonly used noble metal catalysts in H-2 generation from the hydrolysis of borohydrides, and might find potential applications in the field of green energy

A facile approach to fabrication of well-dispersed NiO-ZnO composite hollow microspheres

A novel, facile and template-free approach was developed for the fabrication of amorphous zinc-nickel citrate hollow microspheres and crystalline well-dispersed NiO-ZnO composite hollow microspheres. In this approach, amorphous zinc-nickel citrate hollow microspheres were prepared through a simple chemical reaction and with room temperature ageing at nickel nitrate solution. The zinc-nickel citrate hollow microspheres have an average size of about 1.4 μm. The average thickness of the shell is about 300 nm. The content of Ni in the zinc-nickel citrate can be simply adjusted by changing the ageing time. The well-dispersed NiO-ZnO composite hollow microspheres can be prepared via the perfect morphology inheritance of the zinc-nickel citrate hollow microspheres, by calcination at 500 °C for 2 h. The optical absorption of the samples can extend into the visible region after the loading of NiO. The NiO-ZnO composite hollow microspheres with the high content of NiO exhibit the highest photocatalytic activity for the degradation of different organic dyes including Rhodamine-B, methylene blue and methyl orange under UV irradiation, which might be ascribed to their highest separation efficiency of photogenerated electron-hole pairs. In addition, these NiO-ZnO composite photocatalysts can be used repeatedly without a significant decrease of the photocatalytic activity under UV irradiation. ? 2013 The Royal Society of Chemistry

An Improved Analytical Tuning Rule of a Robust PID Controller for Integrating Systems with Time Delay Based on the Multiple Dominant Pole-Placement Method

An improved analytical tuning rule of a Proportional-Integral-Derivative (PID) controller for integrating systems with time delay is proposed using the direct synthesis method and multiple dominant pole-placement approach. Different from the traditional multiple dominant pole-placement method, the desired characteristic equation is obtained by placing the third-order dominant poles at −1/λ and placing the second-order non-dominant poles at −5/λ (λ is the tuning parameter). According to root locus theory, the third-order dominant poles and the second-order non-dominant poles are nearly symmetrically located at the two sides of the fifth-order dominant poles. This makes the third-order dominant poles closer to the imaginary axis than the fifth-order dominant poles, which means that, possibly, better performances can be achieved. Analytical formulas of a PID controller with a lead-lag filter are derived. Simple tuning rules are also given to achieve the desired robustness, which is measured by the maximum sensitivity (Ms) value. The proposed method can achieve better performances and maintain better performances when there exist parameters’ perturbation compared with other methods. Simulations for various integrating processes as well as the nonlinear continuous stirred tank reactor (CSTR) model illustrate the applicability and effectiveness of the proposed method