Sparse deconvolution for background noise suppression with total variation regularization in light field microscopy.

In this Letter, we present a method aiming at background noise removal in the 3D reconstruction of light field microscopy (LFM). Sparsity and Hessian regularization are taken as two prior knowledges to process the original light field image before 3D deconvolution. Due to the noise suppression function of total variation (TV) regularization, we add the TV regularization term to the 3D Richardson-Lucy (RL) deconvolution. By comparing the light field reconstruction results of our method with another state-of-the-art method that is also based on RL deconvolution, the proposed method shows improved performance in terms of removing background noise and detail enhancement. This method will be beneficial to the application of LFM in biological high-quality imaging.

Geometric Nonlinear Model for Prediction of Frequency-Temperature Behavior of SAW Devices for Nanosensor Applications.

Surface acoustic wave (SAW)-based sensors have become highly valued for their use as nanosensors in industrial applications. Accurate prediction of the thermal stability is a key problem for sensor design. In this work, a numerical tool based on the finite element method combined with piezoelectric Lagrangian equations has been developed to accurately predict the thermal sensitivity characteristics of surface acoustic wave devices. Theoretical analysis for the geometric nonlinearity contributing to the frequency-temperature characteristic and material constants' dependency on temperature were taken into consideration. The thermomechanical equilibrium equation built on the three-dimensional finite element method (3D-FEM) mesh node took mesh movement into account because thermal expansion was employed. The frequency-temperature characteristics of different SAW modes, including Rayleigh waves and leaky waves excited on a piezoelectric substrate of quartz or lithium tantalate, respectively, were calculated. The theoretical accuracy of the proposed numerical tool was verified by experiments.

Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have.

BACKGROUND: Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results. RESULTS: When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes. CONCLUSIONS: The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.

The role of the globular heads of the C1q receptor in HPV-16 E2-induced human cervical squamous carcinoma cell apoptosis via a mitochondria-dependent pathway.

BACKGROUND: Human papillomavirus type-16 (HPV-16) E2 protein acts as a transcriptional modulator and plays a key role in regulating many biological responses. The purpose of this study was to investigate the relationship between HPV-16 E2, the receptor for the globular heads of human C1q (gC1qR) gene expression, mitochondrial dysfunction and apoptosis regulation in human cervical squamous carcinoma cells (C33a and SiHa). METHODS: HPV-16 E2 and gC1qR expression was examined using real-time PCR and western blot analysis. Apoptosis in C33a and SiHa cells was assessed by flow cytometry. Mitochondrial function was detected via ROS generation, the amount of cytosolic Ca2+, and changes in the mitochondrial membrane potential (Δψm). RESULTS: The expression of the HPV-16 E2 and gC1qR gene significantly decreased in human cervical squamous carcinoma samples relative to the non-cancerous cervix samples. C33a and SiHa cells that were transfected with a vector encoding HPV-16 E2 displayed significantly increased gC1qR gene expression and mitochondrial dysfunction as well as an up-regulation of cellular apoptosis, which was abrogated by the addition of gC1qR small-interfering RNA (siRNA). CONCLUSIONS: These data support a mechanism whereby gC1qR plays an important role in HPV-16 E2-induced human cervical squamous carcinoma cell apoptosis via a mitochondria-dependent pathway.

Towards carbon neutrality: Sustainable recycling and upcycling strategies and mechanisms for polyethylene terephthalate via biotic/abiotic pathways.

Polyethylene terephthalate (PET), one of the most ubiquitous engineering plastics, presents both environmental challenges and opportunities for carbon neutrality and a circular economy. This review comprehensively addressed the latest developments in biotic and abiotic approaches for PET recycling/upcycling. Biotically, microbial depolymerization of PET, along with the biosynthesis of reclaimed monomers [terephthalic acid (TPA), ethylene glycol (EG)] to value-added products, presents an alternative for managing PET waste and enables CO2 reduction. Abiotically, thermal treatments (i.e., hydrolysis, glycolysis, methanolysis, etc.) and photo/electrocatalysis, enabled by catalysis advances, can depolymerize or convert PET/PET monomers in a more flexible, simple, fast, and controllable manner. Tandem abiotic/biotic catalysis offers great potential for PET upcycling to generate commodity chemicals and alternative materials, ideally at lower energy inputs, greenhouse gas emissions, and costs, compared to virgin polymer fabrication. Remarkably, over 25 types of upgraded PET products (e.g., adipic acid, muconic acid, catechol, vanillin, and glycolic acid, etc.) have been identified, underscoring the potential of PET upcycling in diverse applications. Efforts can be made to develop chemo-catalytic depolymerization of PET, improve microbial depolymerization of PET (e.g., hydrolysis efficiency, enzymatic activity, thermal and pH level stability, etc.), as well as identify new microorganisms or hydrolases capable of degrading PET through computational and machine learning algorithms. Consequently, this review provides a roadmap for advancing PET recycling and upcycling technologies, which hold the potential to shape the future of PET waste management and contribute to the preservation of our ecosystems.

Unleashing the potential of tungsten disulfide: Current trends in biosensing and nanomedicine applications.

The discovery of graphene ignites a great deal of interest in the research and advancement of two-dimensional (2D) layered materials. Within it, semiconducting transition metal dichalcogenides (TMDCs) are highly regarded due to their exceptional electrical and optoelectronic properties. Tungsten disulfide (WS2) is a TMDC with intriguing properties, such as biocompatibility, tunable bandgap, and outstanding photoelectric characteristics. These features make it a potential candidate for chemical sensing, biosensing, and tumor therapy. Despite the numerous reviews on the synthesis and application of TMDCs in the biomedical field, no comprehensive study still summarizes and unifies the research trends of WS2 from synthesis to biomedical applications. Therefore, this review aims to present a complete and thorough analysis of the current research trends in WS2 across several biomedical domains, including biosensing and nanomedicine, covering antibacterial applications, tissue engineering, drug delivery, and anticancer treatments. Finally, this review also discusses the potential opportunities and obstacles associated with WS2 to deliver a new outlook for advancing its progress in biomedical research.

Converting formaldehyde in methanol with MoO2 under irradiation: A pollution-free strategy for cleaning air.

Direct photocatalytic reduction of toxic formaldehyde (HCHO) in value-added chemicals and fuels is promising because that not only abates the environmental pollution, but also solves the energy shortage. Herein, self-supported MoO2 and MoO3 nanoparticles growing on Mo meshes were comparatively applied to the photocatalytic conversion of HCHO. Under UV-visble lights, MoO2 reduces HCHO in methanol (CH3OH) while MoO3 oxidizes HCHO in carbon oxide and water. Their contrary photocatalytic capacities were revealed. Compared with MoO3, the lower work function of MoO2 enables an electron-rich interface, realizing a complete reduction of 30 ppm HCHO to CH3OH in 30 min. Theoretical calculations clarify that a large number of delocalized electrons on MoO2 attracts HCHO molecule and activates its CO bond, facilitating subsequent hydrogenation and reduction of HCHO to CH3OH. As for MoO3, the wider bandgap and higher potential of valence band govern the photocatalytic oxidation of HCHO.

Band 40/41 Surface Acoustic Wave Filters on 42°YX-Lithium Tantalate Substrate with Suppression of Transverse Leakage.

The transverse leakage of leaky surface acoustic waves (LSAWs) occurs on 42°YX-lithium tantalate substrates (42LT), which increases the insertion loss, narrows the bandwidth and flattens the roll-off of band 40/41 SAW filters and duplexers. In this work, LSAW characteristics with different metal materials and thicknesses are calculated by the finite element method (FEM), which determines the IDT material and thickness used for band 40/41 SAW filter design. To deeply understand transverse leakage and suppress it, the effects of different gap and dummy lengths on transverse leakage are simulated and discussed. Then, a new technique of using a wider dummy without any additional lithographic or depositing processes is proposed to suppress the leakage. Its effectiveness is validated by both simulations and experiments. Then, the technique is extended to applications of band 40 and 41 SAW filters. The experimental results show that with the wider dummy structure, the band 40 and 41 SAW filters achieve a more than 0.2 dB improvement in the insertion loss, a wider bandwidth and a steeper roll-off characteristic. This technique may also be extended to the other band SAW filter applications.

Upregulation of MED7 was associated with progression in hepatocellular carcinoma.

OBJECTIVE: MED subunits have been reported to be associated with various types of tumors, however, the potential role of MED7 in hepatocellular carcinoma (HCC) was still unclear. The aim of the study was to explore the role of MED7 in HCC. METHODS: In this study, MED7 mRNA expression levels between HCC and adjacent normal tissues were first analyzed by several public datasets. Then we utilized a tissue microarray (TMA) to investigate the clinical role of MED7 in HCC by immunohistochemistry (IHC). Meanwhile, the potential mechanisms of MED7 based on gene-gene correlation analyses were also explored. RESULTS: High mRNA level of MED7 correlated with advanced stage and worse grade of differentiation. IHC results showed that MED7 protein level was upregulated in HCC and associated with Edmondson grade and Microvascular invasion in 330 cases of HCC. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that MED7 co-expressed genes participate primarily in ribonucleoprotein complex biogenesis, protein targeting, mRNA processing and nucleoside triphosphate metabolic process et cetera. Further analysis also revealed that MED7 mRNA level has significant correlation with immune cells infiltration levels. CONCLUSION: MED7 was upregulated in HCC and correlated with progression of HCC. Meanwhile, MED7 may promote HCC through participating in multiple gene networks to influence tumorigenesis as well as immune response in HCC microenvironment.

Effect of 2'-Fucosyllactose on Beige Adipocyte Formation in 3T3-L1 Adipocytes and C3H10T1/2 Cells.

2'-Fucosyllactose (2'-FL), the functional oligosaccharide naturally present in milk, has been shown to exert health benefits. This study was aimed to investigate the effect of 2'-fucosyllactose (2'-FL) on the browning of white adipose tissue in 3T3-L1 adipocytes and C3H10T1/2 cells. The results revealed that 2'-FL decreased lipid accumulations with reduced intracellular triglyceride contents in vitro. 2'-FL intervention increased the mitochondria density and the proportion of UCP1-positive cells. The mRNA expressions of the mitochondrial biogenesis-related and browning markers (Cox7a, Cyto C, Tfam, Ucp1, Pgc1α, Prdm16, Cidea, Elovl3, Pparα, CD137, and Tmem26) were increased after 2'-FL intervention to some extent. Similarly, the protein expression of the browning markers, including UCP1, PGC1α, and PRDM16, was up-regulated in the 2'-FL group. Additionally, an adenosine monophosphate-activated protein kinase (AMPK) inhibitor, compound C (1 µM), significantly decreased the induction of thermogenic proteins expressions mediated by 2'-FL, indicating that the 2'-FL-enhanced beige cell formation was partially dependent on the AMPK pathway. In conclusion, 2'-FL effectively promoted the browning of white adipose in vitro.

Optimization of Surface Acoustic Wave Resonators on 42°Y-X LiTaO3/SiO2/Poly-Si/Si Substrate for Improved Performance and Transverse Mode Suppression.

SAW devices with a multi-layered piezoelectric substrate have excellent performance due to advantages such as a high quality factor, Q, low loss insertion, large bandwidth, etc. Prior to manufacturing, a comprehensive analysis and proper design are essential to evaluating the device's key performance indicators, including the Bode Q value, bandwidth, and transverse mode suppression. This study explored the performance of SAW resonators employing a 42°Y-X LiTaO3 (LT) thin-plate-based multi-layered piezoelectric substrate. The thicknesses for each layer of the 42°Y-X LT/SiO2/poly-Si/Si substrate were optimized according to the index of phase velocity, Bode Q value, and bandwidth. The effect of the device structure parameters on the dispersion curve and slowness curve was studied, and a flat slowness curve was found to be favorable for transverse mode suppression. In addition, the design of the dummy configuration was also optimized for the suppression of spurious waves. Based on the optimized design, a one-port resonator on the 42°Y-X LT/SiO2/poly-Si/Si substrate was fabricated. The simulation results and measurements are presented and compared, which provides guidelines for the design of new types of SAW devices configured with complex structures.

The globular heads of the C1q receptor regulate apoptosis in human cervical squamous carcinoma cells via a p53-dependent pathway.

BACKGROUND: The globular heads of the human C1q receptor (gC1qR) localize predominantly to the mitochondrial matrix. gC1qR mediates many biological responses, including growth perturbation, morphological abnormalities and the initiation of apoptosis. The purpose of this study was to investigate the relationship between mitochondrial dysfunction, p53 status and gC1qR expression and the regulation of apoptosis in human cervical squamous carcinoma cells (C33a and SiHa). METHODS: Here, gC1qR expression was examined in human cervical tissues using real-time PCR and Western blot analysis. Apoptotic death of C33a and SiHa cells was assessed by flow cytometric analysis that detected the subG1 population. Mitochondrial function was assessed via ROS generation, the content of cytosolic Ca2+, and the change in mitochondrial membrane potential (Δψm). The viability and migration of C33a and SiHa cells were detected via the water-soluble tetrazolium salt (WST-1) assay and the transwell assay, respectively. RESULTS: gC1qR expression was decreased in cervical squamous cell carcinoma tissues compared with normal tissues. C33a and SiHa cells transfected with a vector encoding gC1qR displayed mitochondrial dysfunction and apoptosis, which was abrogated by the addition of a mutant form of p53 or p53 small interference RNA (siRNA). Furthermore, upon overexpression of gC1qR, cell viability and migration were significantly enhanced, and the apoptosis of C33a and SiHa cells were decreased when cells were treated with mutant p53 or p53 siRNA. CONCLUSIONS: These data support a mechanism whereby gC1qR induces apoptosis through the mitochondrial and p53-dependent pathways in cervical squamous cell carcinoma.

An Up-To-Date Overview of Dental Tissue Regeneration Using Dental Origin Mesenchymal Stem Cells: Challenges and Road Ahead.

Stem cells (SCs) research has experienced exponential growth in recent years. SC-based treatments can enhance the lives of people suffering from cardiac ischemia, Alzheimer's disease, and regenerative drug conditions, like bone or loss of teeth. Numerous kinds of progenitor/SCs have been hypothesized to depend on their potential to regain and/or heal wounded tissue and partly recover organ function. Growing data suggest that SCs (SCs) are concentrated in functions and that particular tissues have more SCs. Dental tissues, in particular, are considered a significant cause of mesenchymal stem cells (MSCs) cells appropriate for tissue regeneration uses. Tissue regeneration and SCs biology have particular attention in dentistry because they may give a novel method for creating clinical material and/or tissue redevelopment. Dental pulp, dental papilla, periodontal ligament, and dental follicle contain mesenchymal SCs. Such SCs, which must be identified and cultivated in specific tissue culture environments, may be used in tissue engineering applications such as tooth tissue, nerve regeneration, and bone redevelopment. A new cause of SCs, induced pluripotent SCs, was successfully made from human somatic cells, enabling the generation of the patient and disease-specific SCs. The dental SC's (DSCs) multipotency, rapid proliferation rate, and accessibility make it an ideal basis of MSC for tissue redevelopment. This article discusses current advances in tooth SC investigation and its possible application in tissue redevelopment.

Angiotensin-Converting Enzyme 2-Based Biosensing Modalities and Devices for Coronavirus Detection.

Rapid and cost-effective diagnostic tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are a critical and valuable weapon for the coronavirus disease 2019 (COVID-19) pandemic response. SARS-CoV-2 invasion is primarily mediated by human angiotensin-converting enzyme 2 (hACE2). Recent developments in ACE2-based SARS-CoV-2 detection modalities accentuate the potential of this natural host-virus interaction for developing point-of-care (POC) COVID-19 diagnostic systems. Although research on harnessing ACE2 for SARS-CoV-2 detection is in its infancy, some interesting biosensing devices have been developed, showing the commercial viability of this intriguing new approach. The exquisite performance of the reported ACE2-based COVID-19 biosensors provides opportunities for researchers to develop rapid detection tools suitable for virus detection at points of entry, workplaces, or congregate scenarios in order to effectively implement pandemic control and management plans. However, to be considered as an emerging approach, the rationale for ACE2-based biosensing needs to be critically and comprehensively surveyed and discussed. Herein, we review the recent status of ACE2-based detection methods, the signal transduction principles in ACE2 biosensors and the development trend in the future. We discuss the challenges to development of ACE2-biosensors and delineate prospects for their use, along with recommended solutions and suggestions.

N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana.

BACKGROUND: Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6-methyladenosine (m6A)/N6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored. RESULTS: Here, we demonstrate the existence of N4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry. CONCLUSIONS: Our findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.

Periodic Analysis of Surface Acoustic Wave Resonator with Dimensionally Reduced PDE Model Using COMSOL Code.

Radio-frequency (RF) surface acoustic wave (SAW) resonators used as filters and duplexers are mass-produced and widely used in current mobile phones. With the numerous emergences of the diverse device structure, a universal method used for the accurate and fast simulation of the SAW resonator calls for urgent demand. However, there are too many instances where the behavior of the entire acoustic resonator cannot be characterized rapidly and efficiently due to limitations in the current computer memory and speed. This is especially true for SAW resonators configured with long arrays of inter-digital transducers (IDTs), and we have to resort to a periodic analysis. In this paper, the previously reported generalized partial differential equations (PDE) based on the two-dimensional finite element method (2D-FEM) model is extended to analysis for the periodic structure of the SAW resonator. We present model order reduction (MOR) techniques based on FEM and periodic boundary conditions to achieve a dimensionally reduced PDE model without decreasing the accuracy of computations. Examples of different SAW devices, including the regular SAW, IHP-SAW and TC-SAW resonators, are provided which shows the results of the periodic analysis compared with the experimental results of the actual resonators. The investigation results demonstrate the properties of the proposed methodology and prove its effectiveness and accuracy.

Hybrid Full-Wave Analysis of Surface Acoustic Wave Devices for Accuracy and Fast Performance Prediction.

In this paper, a hybrid full-wave analysis of surface acoustic wave (SAW) devices is proposed to achieve accurate and fast simulation. The partial differential equation (PDE) models of the physical system in question and graphics processing unit (GPU)-assisted hierarchical cascading technology (HCT) are used to calculate acoustic-electric characteristics of a SAW filter. The practical solid model of the radio frequency (RF) filter package is constructed in High Frequency Structure Simulator (HFSS) software and the parasitic electromagnetics of the entire package is considered in the design process. The PDE-based models of the two-dimensional finite element method (2D-FEM) are derived in detail and solved by the PDE module embedded in COMSOL Multiphysics. Due to the advantages of PDE-based 2D-FEM, it is universal, efficient and not restricted to handling arbitrary materials and crystal cuts, electrode shapes, and multi-layered substrate. Combining COMSOL Multiphysics with a user-friendly interface, a flexible way of modeling and mesh generation, it can greatly reduce the complicated process of modeling and physical properties definition. Based on a hybrid full-wave analysis, we present an example application of this approach on a TC-SAW ladder filter with 5° YX-cut LiNbO3 substrate. Numerical results and measurements were calculated for comparison, and the accuracy and efficiency of the proposed method were verified.

Enhanced Performance of ZnO/SiO2/Al2O3 Surface Acoustic Wave Devices with Embedded Electrodes.

With the advent of the 5G era, surface acoustic wave (SAW) devices with a larger bandwidth and better temperature stability are strongly required, meanwhile the dimensions of devices are continuously scaling down. In this work, a new layout of ZnO/SiO2/Al2O3 SAW devices with embedded electrodes was developed, and with the help of the finite element method (FEM), the propagation characteristics were simulated. Through adopting embedded electrodes, a large electromechanical coupling coefficient (K2) of 6.6% for the Rayleigh mode can be achieved (5 times larger than that of the conventional ZnO/Al2O3 structure), feasible for wideband SAW devices, and a low acoustic velocity (Vp) of 2960 m/s is exhibited simultaneously, which benefits the miniaturization of SAW devices. The dramatic enhancement of K2 is mainly attributed to the more efficient excitation of SAW in piezoelectric films. Furthermore, a SiO2 overlay is added on the top of the structure to gain an excellent zero temperature coefficient of frequency (TCF). Experimentally, we successfully fabricated SAW one-port resonators based on the proposed structure and good characteristics of high K2, low Vp, and small TCF as simulated were confirmed. Our results show that the proposed structure provides a viable route to design SAW devices with a large bandwidth, small size, and robust temperature compensation for practical use.

Characteristics of self-guided laser plasma channels generated by femtosecond laser pulses in air.

With ultrashort laser pulses (25 fs) and low energy (E=15 mJ), we observe laser plasma channels with a length over 5 m in air. The diameter of the plasma channel is measured to be 120 microm. The average electron density in the channel is inferred to be about 10(18) W/cm(3) with an interferometric method. At the same time, the temporal evolution of the electron density in the plasma channel is investigated. The resistivity in the plasma channel is measured to be less than 1 Omega cm. It is suggested that the lifetime of the plasma channel can be greatly prolonged by launching another long laser pulse along the plasma channel.