Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference

The normalization of RNA sequencing data is a primary step for downstream analysis. The most popular method used for the normalization is the trimmed mean of M values (TMM) and DESeq. The TMM tries to trim away extreme log fold changes of the data to normalize the raw read counts based on the remaining non-deferentially expressed genes. However, the major problem with the TMM is that the values of trimming factor M are heuristic. This paper tries to estimate the adaptive value of M in TMM based on Jaeckel's Estimator, and each sample acts as a reference to find the scale factor of each sample. The presented approach is validated on SEQC, MAQC2, MAQC3, PICKRELL and two simulated datasets with two-group and three-group conditions by varying the percentage of differential expression and the number of replicates. The performance of the present approach is compared with various state-of-the-art methods, and it is better in terms of area under the receiver operating characteristic curve and differential expression.

Integrated drug response prediction models pinpoint repurposed drugs with effectiveness against rhabdomyosarcoma

Targeted therapies for inhibiting the growth of cancer cells or inducing apoptosis are urgently needed for effective rhabdomyosarcoma (RMS) treatment. However, identifying cancer-targeting compounds with few side effects, among the many potential compounds, is expensive and time-consuming. A computational approach to reduce the number of potential candidate drugs can facilitate the discovery of attractive lead compounds. To address this and obtain reliable predictions of novel cell-line-specific drugs, we apply prediction models that have the potential to improve drug discovery approaches for RMS treatment. The results of two prediction models were ensemble and validated via in vitro experiments. The computational models were trained using data extracted from the Genomics of Drug Sensitivity in Cancer database and tested on two RMS cell lines to select potential RMS drug candidates. Among 235 candidate drugs, 22 were selected following the result of the computational approach, and three candidate drugs were identified (NSC207895, vorinostat, and belinostat) that showed selective effectiveness in RMS cell lines in vitro via the induction of apoptosis. Our in vitro experiments have demonstrated that our proposed methods can effectively identify and repurpose drugs for treating RMS.

Organometal Halide Perovskite-Based Photoelectrochemical Module Systems for Scalable Unassisted Solar Water Splitting

Despite achievements in the remarkable photoelectrochemical (PEC) performance of photoelectrodes based on organometal halide perovskites (OHPs), the scaling up of small-scale OHP-based PEC systems to large-scale systems remains a great challenge for their practical application in solar water splitting. Significant resistive losses and intrinsic defects are major obstacles to the scaling up of OHP-based PEC systems, leading to the PEC performance degradation of large-scale OHP photoelectrodes. Herein, a scalable design of the OHP-based PEC systems by modularization of the optimized OHP photoelectrodes exhibiting a high solar-to-hydrogen conversion efficiency of 10.4% is suggested. As a proof-of-concept, the OHP-based PEC module achieves an optimal PEC performance by avoiding major obstacles in the scaling up of the OHP photoelectrodes. The constructed OHP module is composed of a total of 16 OHP photoelectrodes, and a photocurrent of 11.52 mA is achieved under natural sunlight without external bias. The successful operation of unassisted solar water splitting using the OHP module without external bias can provide insights into the design of scalable OHP-based PEC systems for future practical application and commercialization.

Terahertz Optical Properties and Carrier Behaviors of Graphene Oxide Quantum Dot and Reduced Graphene Oxide Quantum Dot via Terahertz Time-Domain Spectroscopy

Graphene quantum dots (GQDs) with a band gap have been widely applied in many fields owing to their unique optical properties. To better utilize the optical advantages of GQDs, it is important to understand their optical characteristics. Our study demonstrates the optical properties and carrier behaviors of synthesized graphene oxide quantum dot (GOQD) and reduced graphene oxide quantum dot (rGOQD) pellets via Terahertz time-domain spectroscopy (THz-TDS). The complex permittivity and optical conductivity are obtained in the terahertz region, indicating that the optical conductivity of the GOQD is higher than that of the rGOQD. Although rGOQD has a higher carrier density, approximately 1.5-times than that of GOQD, the lower charge carrier mobility of the rGOQD, which is obtained using Drude-Lorentz oscillator model fitting contributes to a decrease in optical conductivity. This lower mobility can be attributed to the more significant number of defect states within the rGOQD compared to GOQD. To the best of our knowledge, our study initially demonstrates the optical property and carrier behaviors of GOQD and rGOQD in the THz region. Moreover, this study provides important information on factors influencing carrier behavior to various fields in which carrier behavior plays an important role.

Intracellular Adhesion Molecule-1 Improves Responsiveness to Immune Checkpoint Inhibitor by Activating CD8+ T Cells

Immune checkpoint inhibitor (ICI) clinically benefits cancer treatment. However, the ICI responses are only achieved in a subset of patients, and the underlying mechanisms of the limited response remain unclear. 160 patients with non-small cell lung cancer treated with anti-programmed cell death protein-1 (anti-PD-1) or anti-programmed death ligand-1 (anti-PD-L1) are analyzed to understand the early determinants of response to ICI. It is observed that high levels of intracellular adhesion molecule-1 (ICAM-1) in tumors and plasma of patients are associated with prolonged survival. Further reverse translational studies using murine syngeneic tumor models reveal that soluble ICAM-1 (sICAM-1) is a key molecule that increases the efficacy of anti-PD-1 via activation of cytotoxic T cells. Moreover, chemokine (CXC motif) ligand 13 (CXCL13) in tumors and plasma is correlated with the level of ICAM-1 and ICI efficacy, suggesting that CXCL13 might be involved in the ICAM-1-mediated anti-tumor pathway. Using sICAM-1 alone and in combination with anti-PD-1 enhances anti-tumor efficacy in anti-PD-1-responsive tumors in murine models. Notably, combinatorial therapy with sICAM-1 and anti-PD-1 converts anti-PD-1-resistant tumors to responsive ones in a preclinical study. These findings provide a new immunotherapeutic strategy for treating cancers using ICAM-1.

Novel Mg- and Ga-doped ZnO/Li-Doped Graphene Oxide Transparent Electrode/Electron-Transporting Layer Combinations for High-Performance Thin-Film Solar Cells

Herein, a novel combination of Mg- and Ga-co-doped ZnO (MGZO)/Li-doped graphene oxide (LGO) transparent electrode (TE)/electron-transporting layer (ETL) has been applied for the first time in Cu₂ ZnSn(S,Se)₄ (CZTSSe) thin-film solar cells (TFSCs). MGZO has a wide optical spectrum with high transmittance compared to that with conventional Al-doped ZnO (AZO), enabling additional photon harvesting, and has a low electrical resistance that increases electron collection rate. These excellent optoelectronic properties significantly improved the short-circuit current density and fill factor of the TFSCs. Additionally, the solution-processable alternative LGO ETL prevented plasma-induced damage to chemical bath deposited cadmium sulfide (CdS) buffer, thereby enabling the maintenance of high-quality junctions using a thin CdS buffer layer (≈30 nm). Interfacial engineering with LGO improved the V_oc of the CZTSSe TFSCs from 466 to 502 mV. Furthermore, the tunable work function obtained through Li doping generated a more favorable band offset in CdS/LGO/MGZO interfaces, thereby, improving the electron collection. The MGZO/LGO TE/ETL combination achieved a power conversion efficiency of 10.67%, which is considerably higher than that of conventional AZO/intrinsic ZnO (8.33%).

Highly efficient graphene terahertz modulator with tunable electromagnetically induced transparency-like transmission

Graphene-based optical modulators have been extensively studied owing to the high mobility and tunable permittivity of graphene. However, weak graphene-light interactions make it difficult to achieve a high modulation depth with low energy consumption. Here, we propose a high-performance graphene-based optical modulator consisting of a photonic crystal structure and a waveguide with graphene that exhibits an electromagnetically-induced-transparency-like (EIT-like) transmission spectrum at terahertz frequency. The high quality-factor guiding mode to generate the EIT-like transmission enhances light-graphene interaction, and the designed modulator achieves a high modulation depth of 98% with a significantly small Fermi level shift of 0.05 eV. The proposed scheme can be utilized in active optical devices that require low power consumption.

Apelin as a new therapeutic target for COVID-19 treatment

BACKGROUND

Apelin is an endogenous neuropeptide that binds to the G-protein-coupled receptor (APJ) and participates in a variety of physiological processes in the heart, lungs and other peripheral organs. Intriguingly, [Pyr1]-Apelin-13, a highly potent pyroglutamic form of apelin, has the potential to bind to and be degraded by angiotensin-converting enzyme 2 (ACE2). ACE2 is known to operate as a viral receptor in the early stages of severe acute respiratory coronavirus (SARS-CoV-2) infection.

AIM

This study aimed to determine if apelin protects against SARS-CoV-2 infection by inhibiting ACE2 binding to SARS-CoV-2 spike protein.

DESIGN AND METHODS

To determine whether [Pyr1]-Apelin-13 inhibits ACE2 binding to the SARS-CoV-2 spike protein (S protein), we performed a cell-to-cell fusion assay using ACE2-expressing cells and S protein-expressing cells and a pseudovirus-based inhibition assay. We then analyzed publicly available transcriptome data while focusing on the beneficial effects of apelin on the lungs.

RESULTS

We found that [Pyr1]-Apelin-13 inhibits cell-to-cell fusion mediated by ACE2 binding to the S protein. In this experiment, [Pyr1]-Apelin-13 protected human bronchial epithelial cells, infected with pseudo-typed lentivirus-producing S protein, against viral infection. In the presence of [Pyr1]-Apelin-13, the level of viral spike protein expression was also reduced in a concentration-dependent manner. Transcriptome analysis revealed that apelin may control inflammatory responses to viral infection by inhibiting the nuclear factor kappa B pathway.

CONCLUSION

Apelin is a potential therapeutic candidate against SARS-CoV-2 infection.

In-Situ Spectro-Electrochemistry of Conductive Polymers Using Plasmonics to Reveal Doping Mechanisms

Conducting polymers are a key component for developing wearable organic electronics, but tracking their redox processes at the nanoscale to understand their doping mechanism remains challenging. Here we present an in-situ spectro-electrochemical technique to observe redox dynamics of conductive polymers in an extremely localized volume (<100 nm³). Plasmonic nanoparticles encapsulated by thin shells of different conductive polymers provide actively tuned scattering color through switching their refractive index. Surface-enhanced Raman scattering in combination with cyclic voltammetry enables detailed studies of the redox/doping process. Our data intriguingly show that the doping mechanism varies with polymer conductivity: a disproportionation mechanism dominates in more conductive polymers, while sequential electron transfer prevails in less conductive polymers.

Differential plastic responses to temperature and nitrogen deposition in the subalpine plant species, Primula farinosa subsp. modesta

Future environmental changes are projected to threaten plant populations near mountaintops, but plastic responses of plant traits that are related to demographic parameters may reduce the detrimental effects of altered environments. Despite its ecological significance, little is known about the intraspecific variation of plasticity in alpine plant species such as Primula farinosa subsp. modesta. In this study, we investigated the plastic responses of plants at the early developmental stage from four P. farinosa natural populations in response to temperature and nitrogen deposition under laboratory conditions. Measured traits included plant survival, leaf number, rosette diameter, carbon assimilation rate and leaf chlorophyll content. In addition, we conducted a demographic survey of the natural populations to assess the plant's performance at the early developmental stage in the field and evaluate the ecological implications of our experimental treatments. The seedling stage contributed to the projected population growth rate in natural conditions, and the growth and survival of seedlings in the field were comparable to those grown in the control treatment. In response to high temperature, plants exhibited lower survival but produced larger rosettes with more leaves. Nitrogen deposition had little effect on plant survival and plant size; however, it increased plant survival in one population and altered the effect of temperature on the carbon assimilation rate. Populations exhibited differential plasticity indexes of measured traits in response to environmental treatments. These results suggest that even though the plants suffer from high early mortality under increasing temperature, stimulated growth at a high temperature potentially contributes to the persistence of P. farinosa natural populations. Natural populations might face differential extinction risks due to distinctive plastic responses to altered environments.

Nanoscale Soft Wetting Observed in Co/Sapphire during Pulsed Laser Irradiation

Liquid drops on deformable soft substrates exhibit quite complicated wetting behavior as compared to those on rigid solid substrates. We report on a soft wetting behavior of Co nanoparticles (NPs) on a sapphire substrate during pulsed laser-induced dewetting (PLID). Co NPs produced by PLID wetted the sapphire substrate with a contact angle near 70°, which is in contrast to typical dewetting behavior of metal thin films exhibiting contact angles greater than 90°. In addition, a nanoscale γ-Al2O3 wetting ridge about 15 nm in size and a thin amorphous Al2O3 interlayer were observed around and beneath the Co NP, respectively. The observed soft wetting behavior strongly indicates that the sapphire substrate became soft and deformable during PLID. Moreover, the soft wetting was augmented under PLID in air due to the formation of a CoO shell, resulting in a smaller contact angle near 30°.