PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses.

Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method conducted as a "repetition of time leaps in parallel worlds", comprising cycles of multiple molecular dynamics (MD) simulations performed in parallel and selection of the initial structures of MDs for the next cycle. We developed PaCS-Toolkit, an optimized software utility enabling the use of different MD software and trajectory analysis tools to facilitate the execution of the PaCS-MD simulation and analyze the obtained trajectories, including the preparation for the subsequent construction of the Markov state model. PaCS-Toolkit is coded with Python, is compatible with various computing environments, and allows for easy customization by editing the configuration file and specifying the MD software and analysis tools to be used. We present the software design of PaCS-Toolkit and demonstrate applications of PaCS-MD variations: original targeted PaCS-MD to peptide folding; rmsdPaCS-MD to protein domain motion; and dissociation PaCS-MD to ligand dissociation from adenosine A2A receptor.

A Coupled Calibration Method for Dual Cameras-Projector System with Sub-Pixel Accuracy Feature Extraction.

Binocular structured light systems are widely used in 3D measurements. In the condition of complex and local highly reflective scenes, to obtain more 3D information, binocular systems are usually divided into two pairs of devices, each having a Single Camera and a Projector (SCP). In this case, the binocular system can be seen as Dual Cameras-Projector (DCP) system. In the DCP calibration, the Left-SCP and Right-SCP need to be calibrated separately, which leads to inconsistent parameters for the same projector, thus reducing the measurement accuracy. To solve this problem and improve manoeuvrability, a coupled calibration method using an orthogonal phase target is proposed. The 3D coordinates on a phase target are uniquely determined by the binocular camera in DCP, rather than being calculated separately in each SCP. This ensures the consistency of the projector parameters. The coordinates of the projector image plane are calculated through the unwrapped phase, while the parameters are calibrated by the plane calibration method. In order to extract sub-pixel accuracy feature points, a method based on polynomial fitting using an orthogonal phase target is exploited. The experimental results show that the reprojection error of our method is less than 0.033 pixels, which improves the calibration accuracy.

Sustainable Recycling of Selenium-Based Optoelectronic Devices.

Selenium (Se), the world's oldest optoelectronic material, has been widely applied in various optoelectronic devices such as commercial X-ray flat-panel detectors and photovoltaics. However, despite the rare and widely-dispersed nature of Se element, a sustainable recycling of Se and other valuable materials from spent Se-based devices has not been developed so far. Here a sustainable strategy is reported that makes use of the significantly higher vapor pressure of volatile Se compared to other functional layers to recycle all of them from end-of-life Se-based devices through a closed-space evaporation process, utilizing Se photovoltaic devices as a case study. This strategy results in high recycling yields of ≈ 98% for Se and 100% for other functional materials including valuable gold electrodes and glass/FTO/TiO2 substrates. The refabricated photovoltaic devices based on these recycled materials achieve an efficiency of 12.33% under 1000-lux indoor illumination, comparable to devices fabricated using commercially sourced materials and surpassing the current indoor photovoltaic industry standard of amorphous silicon cells.

Structure of Amorphous Selenium: Small Ring, Big Controversy.

Selenium (Se) discovered in 1817 belongs to the family of chalcogens. Surprisingly, despite the long history of over two centuries and the chemical simplicity of Se, the structure of amorphous Se (a-Se) remains controversial to date regarding the dominance of chains versus rings. Here, we find that vapor-deposited a-Se is composed of disordered rings rather than chains in melt-quenched a-Se. We further reveal that the main origin of this controversy is the facile transition of rings to chains arising from the inherent instability of rings. This transition can be inadvertently triggered by certain characterization techniques themselves containing above-bandgap illumination (above 2.1 eV) or heating (above 50 °C). We finally build a roadmap for obtaining accurate Raman spectra by using above-bandgap excitation lasers with low photon flux (below 1017 phs m-2 s-1) and below-bandgap excitation lasers measured at low temperatures (below -40 °C) to minimize the photoexcitation- and heat-induced ring-to-chain transitions.

Synthesis of uniformly dispersed Fe2TiO5 nanodisks: a sensitive photoelectrochemical sensor for glucose monitoring in human blood serum.

A novel photoelectrochemical (PEC) sensor was constructed, using Fe2TiO5 nanodisks under visible-light irradiation, for the determination of glucose in human blood serum. The uniformly dispersed Fe2TiO5 nanodisks were synthesized for the first time by an ion exchange method and subsequent heat treatment. As excellent catalysts, the Fe2TiO5 nanodisks can directly catalyze the oxidation of glucose to produce current in the absence of glucose oxidase. Compared with commercial TiO2, the Fe2TiO5 nanodisks exhibit better activity in the electrocatalytic oxidation of glucose and can generate a photocurrent as a signal for glucose detection. The PEC sensor shows a wide linear range (4 µM-10 mM), a low limit of detection (0.588 µM) and a super sensitivity of 2653 µA mM-1 cm-2, which are much better than similar configurations reported previously. This PEC sensor has been successfully used to monitor glucose in human blood serum. Moreover, this PEC glucose sensor based on Fe2TiO5 nanodisks possesses great potential for application in point-of-care clinical diagnosis.

A polyaniline functionalized NiFeP nanosheet array-based electrochemical immunosensor using Au/Cu2O nanocubes as a signal amplifier for the detection of SARS-CoV-2 nucleocapsid protein.

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged as a novel pathogen in 2019. The virus is responsible for a severe acute respiratory syndrome outbreak, affecting the respiratory system of infected individuals. COVID-19 is a super amplifier of basic diseases, and the disease with basic diseases is often more serious. Controlling the spread of the COVID-19 pandemic relies heavily on the timely and accurate detection of the virus. To resolve the problem, a polyaniline functionalized NiFeP nanosheet array-based electrochemical immunosensor using Au/Cu2O nanocubes as a signal amplifier is fabricated for the detection of SARS-CoV-2 nucleocapsid protein (SARS-CoV-2 NP). Polyaniline (PANI) functionalized NiFeP nanosheet arrays are synthesized as an ideal sensing platform for the first time. PANI is coated on the surface of NiFeP by electropolymerization to enhance biocompatibility, beneficial for the efficient loading of the capture antibody (Ab1). Significantly, Au/Cu2O nanocubes possess excellent peroxidase-like activity and exhibit outstanding catalytic activity for the reduction of H2O2. Therefore, Au/Cu2O nanocubes combine with a labeled antibody (Ab2) through the Au-N bond to form labeled probes, which can effectively amplify current signals. Under optimal conditions, the immunosensor for the detection of SARS-CoV-2 NP shows a wide linear range of 10 fg mL-1-20 ng mL-1 and a low detection limit of 1.12 fg mL-1 (S/N = 3). It also exhibits desirable selectivity, repeatability, and stability. Meanwhile, the excellent analytical performance in human serum samples confirms the practicality of the PANI functionalized NiFeP nanosheet array-based immunosensor. The electrochemical immunosensor based on the Au/Cu2O nanocubes as a signal amplifier demonstrates great potential for application in the personalized point-of-care (POC) clinical diagnosis.

A SERS Biosensor Based on Functionalized Au-SiNCA Integrated with a Dual Signal Amplification Strategy for Sensitive Detection of Telomerase Activity During EMT in Laryngeal Carcinoma.

Purpose: This paper aims to construct a surface-enhanced Raman spectroscopy (SERS) biosensor based on functionalized Au-Si nanocone arrays (Au-SiNCA) using a dual signal amplification strategy (SDA-CHA) to evaluate telomerase activity during epithelial-mesenchymal transition (EMT) in laryngeal carcinoma (LC). Methods: A SERS biosensor based on functionalized Au-SiNCA was designed with an integrated dual-signal amplification strategy to achieve ultrasensitive detection of telomerase activity during EMT in LC patients. Results: Labeled probes (Au-AgNRs@4-MBA@H1) and capture substrates (Au-SiNCA@H2) were prepared by modifying hairpin DNA and Raman signal molecules. Using this scheme, telomerase activity in peripheral mononuclear cells (PMNC) could be successfully detected with a limit of detection (LOD) as low as 10-6 IU/mL. In addition, biological experiments using BLM treatment of TU686 effectively mimicked the EMT process. The results of this scheme were highly consistent with the ELISA scheme, confirming its accuracy. Conclusion: This scheme provides a reproducible, selective, and ultrasensitive assay for telomerase activity, which is expected to be a potential tool for the early screening of LC in future clinical applications.

A Study of the Mechanisms and Characteristics of Fluorescence Enhancement for the Detection of Formononetin and Ononin.

In this work, the origins for the spectral difference between two isoflavones, formononetin (F) and ononin (FG), are revealed via a comparison study of the fluorescence molecular structure. The fluorescence enhancement of FG in hot alkaline conditions is reported for the first time. For F, there is almost no fluorescence under acidic conditions, but when the pH is >4.8, its fluorescence begins to increase due to the deprotonation of 7-OH. Under a pH between 9.3 and 12.0, the anionic form of F produces a strong and stable fluorescence. The fluorescence quantum yield (Yf) of F is measured to be 0.042. FG shows only weak fluorescence in aqueous solutions under a wide range of pH until it is placed in hot alkaline solutions, which is attributed to the cleavage reaction of the γ-pyrone ring in FG. The Yf of FG is determined to be 0.020. Based on the fluorescence sensitization methods of F and FG, the quantitative analysis and detection of two substances can be realized. The limit of the detections for F and FG are 2.60 ng·mL-1 and 9.30 ng·mL-1, respectively. The linear detection ranges of F and FG are 11.7~1860 ng·mL-1 and 14.6~2920 ng·mL-1, respectively. Although the structural relationship between F and FG is glycoside and aglycone, under hot alkaline conditions, the final products after the cleavage and hydrolysis reactions are essentially different. The different fluorescence characteristics between F and FG pave a way for further identification and a quantitative analysis of the corresponding components in Chinese herbal medicine.

Indoor photovoltaics awaken the world's first solar cells.

Selenium (Se) solar cells were the world's first solid-state photovoltaics reported in 1883, opening the modern photovoltaics. However, its wide bandgap (~1.9 eV) limits sunlight harvesting. Here, we revisit the world's oldest but long-ignored photovoltaic material with the emergence of indoor photovoltaics (IPVs); the absorption spectrum of Se perfectly matches the emission spectra of commonly used indoor light sources in the 400 to 700 nm range. We find that the widely used Te adhesion layer also passivates defects at the nonbonded Se/TiO2 interface. By optimizing the Te coverage from 6.9 to 70.4%, the resulting Se cells exhibit an efficiency of 15.1% under 1000 lux indoor illumination and show no efficiency loss after 1000 hours of continuous indoor illumination without encapsulation, outperforming the present IPV industry standard of amorphous silicon cells in both efficiency and stability. We further fabricate Se modules (6.75 cm2) that produce 232.6 µW output power under indoor illumination, powering a radio-frequency identification-based localization tag.

Rapid determination of SARS-CoV-2 nucleocapsid proteins based on 2D/2D MXene/P-BiOCl/Ru(bpy)32+ heterojunction composites to enhance electrochemiluminescence performance.

At the end of 2019, the novel coronavirus disease 2019 (COVID-19), a cluster of atypical pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been known as a highly contagious disease. Herein, we report the MXene/P-BiOCl/Ru(bpy)32+ heterojunction composite to construct an electrochemiluminescence (ECL) immunosensor for SARS-CoV-2 nucleocapsid protein (CoVNP) determination. Two-dimensional (2D) material ultrathin phosphorus-doped bismuth oxychloride (P-BiOCl) is exploited and first applied in ECL. 2D architectures MXene not only act as "soft substrate" to improve the properties of P-BiOCl, but also synergistically work with P-BiOCl. Owing to the inimitable set of bulk and interfacial properties, intrinsic high electrochemical conductivity, hydrophilicity and good biocompatible of 2D/2D MXene/P-BiOCl/Ru(bpy)32+, this as-exploited heterojunction composite is an efficient signal amplifier and co-reaction accelerator in the presence of tri-n-propylamine (TPA) as a coreactant. The proposed MXene/P-BiOCl/Ru(bpy)32+-TPA system exhibits a high and stable ECL signal and achieves ECL emission quenching for "signal on-off" recognition of CoVNP. Fascinatingly, the constructed ECL biosensor towards CoVNP allows a wide linear concentration range from 1 fg/mL to 10 ng/mL and a low limit of detection (LOD) of 0.49 fg/mL (S/N = 3). Furthermore, this presented strategy sheds light on designing a highly efficient ECL nanostructure through the combination of 2D MXene architectures with 2D semiconductor materials in the field of nanomedicine. This ECL biosensor can successfully detect CoVNP in human serum, which can promote the prosperity and development of diagnostic methods of SARS-CoV-2.

Highly sensitive and simultaneous detection of ctDNAs related to non-small cell lung cancer in serum using a catalytic hairpin assembly strategy in a SERS microfluidic chip.

Circulating tumor DNA (ctDNA) is an ideal biomarker for cancer diagnosis based on liquid biopsy, so there is an urgent need for developing an efficient, rapid, and ultrasensitive detection method to meet clinical needs. In this paper, a novel surface-enhanced Raman scattering (SERS) microfluidic chip combined with a catalytic hairpin assembly (CHA) was proposed to detect two non-small cell lung cancer (NSCLC)-related ctDNA (TP53 and PIK3CA-Q546K) simultaneously. The chip consists of six channels for parallel detection. In the reaction region, the CHA reaction between HP1 of the SERS probe and HP2 of the capture substrate was triggered by ctDNAs to form HP1-HP2 duplexes. As the reaction proceeds, more and more SERS probes are captured on the substrate. The gathered reaction products continuously form a lot of hot spots, which greatly enhance the SERS signal. This reaction was completed within 5 minutes. Through this method, the detection limits of TP53 and PIK3CA-Q546K in human serum were as low as 2.26 aM and 2.34 aM, respectively. The microfluidic chip also exhibited high specificity, reproducibility and stability. The clinical feasibility of the SERS microfluidic chip was verified by analyzing the serum samples of healthy subjects and NSCLC patients. The reliability of the experimental results was verified by the qRT-PCR test. The constructed SERS-based analytical micro-platform has great potential in dynamic monitoring of cancer staging and could be used as a clinical tool for early cancer screening.

Remifentanil alleviates hypoxic-ischemic brain damage-induced cognitive impairment via BACH1.

Hypoxia-ischemia (HI) is among the most frequent causes of death and disability in neonates. We aimed here to examine the neuroprotective effects of Remifentanil (RE) and the underlying mechanisms in a rat model of hypoxic-ischemic brain damage (HIBD). We found that RE improved the learning memory ability, reduced neuronal cell damage and apoptosis, reduced inflammation induced by suppressing the expression of BTB domain and CNC homolog 1 (BACH1) in rats with HIBD. BACH1 attenuated the alleviating effect of RE on cognitive impairment in HIBD rats. Moreover, RE inhibited TRAF3 expression by downregulating BACH1, and TRAF3 attenuated the therapeutic effect of RE on cognitive impairment by activating the NF-κB signaling. In conclusion, our findings demonstrated that RE inhibits the expression of BACH1, which in turn inhibits the NF-κB signaling pathway by suppressing TRAF3. RE may be a promising therapeutic agent to attenuate HIBD-induced cognitive impairment.

Self-Assembly of a Triphenylene-Based Electron Donor Molecule on Graphene: Structural and Electronic Properties.

In this study, we report on the self-assembly of the organic electron donor 2,3,6,7,10,11-hexamethoxytriphenylene (HAT) on graphene grown epitaxially on Ir(111). Using scanning tunneling microscopy and low-energy electron diffraction, we find that a monolayer of HAT assembles in a commensurate close-packed hexagonal network on graphene/Ir(111). X-ray and ultraviolet photoelectron spectroscopy measurements indicate that no charge transfer between the HAT molecules and the graphene/Ir(111) substrate takes place, while the work function decreases slightly. This demonstrates that the HAT/graphene interface is weakly interacting. The fact that the molecules nonetheless form a commensurate network deviates from what is established for adsorption of organic molecules on metallic substrates where commensurate overlayers are mainly observed for strongly interacting systems.

A pump-free and high-throughput microfluidic chip for highly sensitive SERS assay of gastric cancer-related circulating tumor DNA via a cascade signal amplification strategy.

Circulating tumour DNA (ctDNA) has emerged as an ideal biomarker for the early diagnosis and prognosis of gastric cancer (GC). In this work, a pump-free, high-throughput microfluidic chip coupled with catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) as the signal cascade amplification strategy (CHA-HCR) was developed for surface-enhanced Raman scattering (SERS) assays of PIK3CA E542K and TP53 (two GC-related ctDNAs). The chip consisted of six parallel functional units, enabling the simultaneous analysis of multiple samples. The pump-free design and hydrophilic treatment with polyethylene glycol (PEG) realized the automatic flow of reaction solutions in microchannels, eliminating the dependence on external heavy-duty pumps and significantly improving portability. In the reaction region of the chip, products generated by target-triggered CHA initiated the HCR, forming long nicked double-stranded DNA (dsDNA) on the Au nanobowl (AuNB) array surface, to which numerous SERS probes (Raman reporters and hairpin DNA-modified Cu2O octahedra) were attached. This CHA-HCR strategy generated numerous active "hot spots" around the Cu2O octahedra and AuNB surface, significantly enhancing the SERS signal intensity. Using this chip, an ultralow limit of detection (LOD) for PIK3CA E542K (1.26 aM) and TP53 (2.04 aM) was achieved, and the whole process was completed within 13 min. Finally, a tumour-bearing mouse model was established, and ctDNA levels in mouse serum at different stages were determined. To verify the experimental accuracy, the gold-standard qRT-PCR assay was utilized, and the results showed a high degree of consistency. Thus, this rapid, sensitive and cost-effective SERS microfluidic chip has potential as an ideal detection platform for ctDNA monitoring.

Solution-processed Ge(ii)-based chalcogenide thin films with tunable bandgaps for photovoltaics.

Solution processes have been widely used to construct chalcogenide-based thin-film optoelectronic and electronic devices that combine high performance with low-cost manufacturing. However, Ge(ii)-based chalcogenide thin films possessing great potential for optoelectronic devices have not been reported using solution-based processes; this is mainly attributed to the easy oxidation of intermediate Ge(ii) to Ge(iv) in the precursor solution. Here we report solution-processed deposition of Ge(ii)-based chalcogenide thin films in the case of GeSe and GeS films by introducing hypophosphorous acid as a suitable reducing agent and strong acid. This enables the generation of Ge(ii) from low-cost and stable GeO2 powders while suppressing the oxidation of Ge(ii) to Ge(iv) in the precursor solution. We further show that such solution processes can also be used to deposit GeSe1-x S x alloy films with continuously tunable bandgaps ranging from 1.71 eV (GeS) to 1.14 eV (GeSe) by adjusting the atomic ratio of S- to Se-precursors in solution, thus allowing the realization of optimal-bandgap single-junction photovoltaic devices and multi-junction devices.

Fixed Point Attractor Theory Bridges Structure and Function in C. elegans Neuronal Network.

Understanding the structure-function relationship in a neuronal network is one of the major challenges in neuroscience research. Despite increasing researches at circuit connectivity and neural network structure, their structure-based biological interpretability remains unclear. Based on the attractor theory, here we develop an analytical framework that links neural circuit structures and their functions together through fixed point attractor in Caenorhabditis elegans. In this framework, we successfully established the structural condition for the emergence of multiple fixed points in C. elegans connectome. Then we construct a finite state machine to explain how functions related to bistable phenomena at the neural activity and behavioral levels are encoded. By applying the proposed framework to the command circuit in C. elegans, we provide a circuit level interpretation for the forward-reverse switching behaviors. Interestingly, network properties of the command circuit and first layer amphid interneuron circuit can also be inferred from their functions in this framework. Our research indicates the reliability of the fixed point attractor bridging circuit structure and functions, suggesting its potential applicability to more complex neuronal circuits in other species.

Risk assessment of COVID-19 infection for subway commuters integrating dynamic changes in passenger numbers.

The COVID-19 global pandemic has had a significant impact on mass travel. We examined the risk of transmission of COVID-19 infection between subway commuters using the Susceptible Exposed Infected Recovered (SEIR) model. The model considered factors that may influence virus transmission, namely subway disinfection, ventilation capacity, average commuter spacing, single subway journey time, COVID-19 transmission capacity, and dynamic changes in passenger numbers. Based on these parameters, above a certain threshold (25 min), the risk of infection for susceptible people increased significantly as journey time increased. Average distance between commuters and levels of ventilation and disinfection were also important influencing factors. Meanwhile, the model also indicated that the risk of infection varied at different times of the day. Therefore, this paper recommends strengthening ventilation and disinfection in the carriages and limiting the time of single journeys, with an average distance of at least 1 m between passengers. In this light, subway commuters need to take proactive precautions to reduce their risk of COVID-19 infection. Also, the results show the importance of managing subway stations efficiently during epidemic and post-epidemic eras.

A two-dimensional G-CoP/N,P-co-doped carbon nanowire electrode for the simultaneous determination of hydroquinone and catechol in domestic wastewater.

Hydroquinone (HQ) and catechol (CC) are important chemical raw materials in the modern industry, unfortunately, which are also high toxic phenolic pollutants. So how to achieve highly sensitive and selective determination HQ and CC is the challenge we face. In the present work, we report a facile strategy to obtain nitrogen and phosphorous co-doped glucose-derived carbon coated CoP nanowires (G-CoP/N,P-C NWs), in which nitrilotriacetic acid (NTA) was as the chelating reagent, glucose was as carbon source, and the precursors were subsequently experienced carbonization and phosphorization process. G-CoP/N,P-C NWs can shorten the distance of the electron transport and expand the reaction area, showing the intriguing electronic conductivity and electrocatalytic abilities. An electrochemical phenolic sensor based on G-CoP/N,P-C NWs is fabricated. The as-prepared sensor showcases the good sensing performance for HQ and CC with comparative linearity ranges of 0.8-900 µM (HQ) and 0.6-800 µM (CC), low limits of detections (LODs) of 0.18 µM (S/N = 3) and 0.12 µM (S/N = 3) for HQ and CC, respectively. Notably, it also displays excellent practical application for the recognition of HQ and CC in the rain water, the tap water, the domestic wastewater and the lake water, which may be a promising candidate in environmental water monitoring and drinking water safety.