CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses.

Coronaviruses have threatened humans repeatedly, especially COVID-19 caused by SARS-CoV-2, which has posed a substantial threat to global public health. SARS-CoV-2 continuously evolves through random mutation, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is critical to assess immune escape caused by viral mutations and develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes. Thus, we constructed CovEpiAb, a comprehensive database and analysis resource of human coronavirus (HCoVs) immune epitopes and antibodies. CovEpiAb contains information on over 60 000 experimentally validated epitopes and over 12 000 antibodies for HCoVs and SARS-CoV-2 variants. The database is unique in (1) classifying and annotating cross-reactive epitopes from different viruses and variants; (2) providing molecular and experimental interaction profiles of antibodies, including structure-based binding sites and around 70 000 data on binding affinity and neutralizing activity; (3) providing virological characteristics of current and past circulating SARS-CoV-2 variants and in vitro activity of various therapeutics; and (4) offering site-level annotations of key functional features, including antibody binding, immunological epitopes, SARS-CoV-2 mutations and conservation across HCoVs. In addition, we developed an integrated pipeline for epitope prediction named COVEP, which is available from the webpage of CovEpiAb. CovEpiAb is freely accessible at https://pgx.zju.edu.cn/covepiab/.

Suppressing the dephasing of optically trapped atoms inside a hollow-core fiber.

We demonstrate the suppression of inhomogeneous dephasing of cold 87Rb atoms optically trapped inside a hollow-core fiber. The differential light shift (DLS) for the clock transition caused by the trapping beam is reduced by one order of magnitude through the use of a weak compensation laser beam that is spatially mode-matched to the trapping beam. The coherence of the DLS-compensated system is characterized by microwave Ramsey interferometry, which shows Ramsey fringes with a contrast of over 0.6 at a separation time of 10 ms. The dephasing time, measured by Ramsey spectroscopy at different separation times, reaches tens of milliseconds after DLS cancellation, limited by the residual DLS caused by mode mismatching between the two laser beams. This work paves the way for compact and portable fiber-guided atom interferometers.

ROS mediated by TrPLD3 of Trichothecium roseum participated cell membrane integrity of apple fruit by influencing phosphatidic acid metabolism.

Trichothecium roseum is a typical necrotrophic fungal pathogen that not only bring about postharvest disease, but contribute to trichothecenes contamination in fruit and vegetables. Phospholipase D (PLD), as an important membrane lipid degrading enzyme, can produce phosphatidic acid (PA) by hydrolyzing phosphatidylcholine (PC) and phosphatidylinositol (PI). PA can promote the production of reactive oxygen species (ROS) by activating the activity of NADPH oxidase (NOX), thereby increasing the pathogenicity to fruit. However, the ROS mediated by TrPLD3 how to influence T. roseum infection to fruit by modulating phosphatidic acid metabolism, which has not been reported. In this study, the knockout mutant and complement strain of TrPLD3 were constructed through homologous recombination, TrPLD3 was tested for its effect on the colony growth and pathogenicity of T. roseum. The experimental results showed that the knockout of TrPLD3 inhibited the colony growth of T. roseum, altered the mycelial morphology, completely inhibited the sporulation, and reduced the accumulation of T-2 toxin. Moreover, the knockout of TrPLD3 significantly decreased pathogenicity of T. roseum on apple fruit. Compared to inoculated apple fruit with the wide type (WT), the production of ROS in apple infected with ΔTrPLD3 was slowed down, the relative expression and enzymatic activity of NOX, and PA content decreased, and the enzymatic activity and gene expression of superoxide dismutase (SOD) increased. In addition, PLD, lipoxygenase (LOX) and lipase activities were considerably decreased in apple fruit infected with ΔTrPLD3, the changes of membrane lipid components were slowed down, the decrease of unsaturated fatty acid content was alleviated, and the accumulation of saturated fatty acid content was reduced, thereby maintaining the cell membrane integrity of the inoculated apple fruit. We speculated that the decreased PA accumulation in ΔTrPLD3-inoculated apple fruit further weakened the interaction between PA and NOX on fruit, resulting in the reduction of ROS accumulation of fruits, which decreased the damage to the cell membrane and maintained the cell membrane integrity, thus reducing the pathogenicity to apple. Therefore, TrPLD3-mediated ROS plays a critical regulatory role in reducing the pathogenicity of T. roseum on apple fruit by influencing phosphatidic acid metabolism.

Influence of meteorological factors on open biomass burning at a background site in Northeast China.

Biomass burning (BB) is a very important emission source that significantly adversely impacts regional air quality. BB produces a large number of primary organic aerosol (POA) and black carbon (BC). Besides, BB also provides many precursors for secondary organic aerosol (SOA) generation. In this work, the ratio of levoglucosan (LG) to organic carbon (OC) and the fire hotspots map was used to identify the open biomass burning (OBB) events, which occurred in two representative episodes, October 13 to November 30, 2020, and April 1 to April 30, 2021. The ratio of organic aerosol (OA) to reconstructed PM2.5 concentration (PM2.5*) increased with the increase of LG/OC. When LG/OC ratio is higher than 0.03, the highest OA/PM2.5* ratio can reach 80%, which means the contribution of OBB to OA is crucial. According to the ratio of LG to K+, LG to mannosan (MN) and the regional characteristics of Longfengshan, it can be determined that the crop residuals are the main fuel. The occurrence of OBB coincides with farmers' preferred choices, i.e., burning biomass in "bright weather". The "bright weather" refers to the meteorological conditions with high temperature, low humidity, and without rain. Meteorological factors indirectly affect regional biomass combustion pollution by influencing farmers' active choices.

Hollow-conical atomic beam from a low-velocity intense source.

We demonstrate, for the first time, a hollow-conical atomic beam from a standard low-velocity intense source. Experimental results and numerical simulations indicate that the hollow-conical feature is caused by the converging-diverging extraction process. The degree of hollowness can be reduced by using a weaker push beam and extending the length of transverse cooling. Analytical models are proposed to quantitatively describe the hollowness of the atomic beam. This study can find applications where a compact and solid atomic beam is needed, such as coupling cold atoms into matter waveguides or continuous cold atomic beam interferometers.

Polarization-maintaining photonic crystal fiber with high Brillouin gain coefficient for Brillouin lasers.

Stimulated Brillouin scattering (SBS) is effective for realizing a laser with an ultra-narrow linewidth. Although photonic crystal fiber (PCF) is considered an excellent medium to achieve SBS, it does not meet the requirements of low loss, large birefringence, and ease of fabrication. We propose a polarization-maintaining PCF (PM-PCF) structure and theoretically analyze the effects of the geometric structural parameters of the PM-PCF on various optical properties. Our theoretical analysis and experimental results contribute to the advancement of the field of ultra-narrow linewidth fiber lasers, distributed fiber sensing, and fiber-optic gyroscopes related to SBS.

Shape recovery from fusion of polarization binocular vision and shading.

The shape from polarization can recover the fine texture of the target surface. However, the gradient field for shape recovery by polarization is ambiguous, which is caused by the multi-value of the azimuth angle. In response to the problem, a method of correcting the ambiguity by the fusion of polarization binocular vision and shading information is proposed in this paper. An iterative optimization algorithm is designed to estimate the direction of the light source, which provides the basis for the shading method to calculate the depth map. Additionally. the low-frequency depth map generated by binocular matching is used to correct the polarization gradient field. The polarization gradient field of the holes and small zenith angle regions in the binocular are corrected by the improved shading method. In the experiment, four different material target objects were used for shape recovery and compared with other methods. The results of the fusion method proposed are better in terms of fine texture. At the camera working distance of  700 mm, the resolving power performs well and demonstrates that changes in the depth of at least 0.1 mm can be distinguished from that recovery result.

MAX-DOAS Measurements of Tropospheric NO2 and HCHO Vertical Profiles at the Longfengshan Regional Background Station in Northeastern China.

The vertical profiles of nitrogen dioxide (NO2) and formaldehyde (HCHO) in the troposphere at the Longfengshan (LFS) regional atmospheric background station (127°36' E, 44°44' N, 330.5 m above sea level) from 24 October 2020 to 13 October 2021 were retrieved from solar scattering spectra by multi-axis differential optical absorption spectroscopy (MAX-DOAS). We analyzed the temporal variations of NO2 and HCHO as well as the sensitivity of ozone (O3) production to the concentration ratio of HCHO to NO2. The largest NO2 volume mixing ratios (VMRs) occur in the near-surface layer for each month, with high values concentrated in the morning and evening. HCHO has an elevated layer around the altitude of 1.4 km consistently. The means ± standard deviations of vertical column densities (VCDs) and near-surface VMRs were 4.69 ± 3.72 ×1015 molecule·cm-2 and 1.22 ± 1.09 ppb for NO2, and they were 1.19 ± 8.35 × 1016 molecule·cm-2 and 2.41 ± 3.26 ppb for HCHO. The VCDs and near-surface VMRs for NO2 were high in the cold months and low in the warm months, while HCHO presented the opposite. The larger near-surface NO2 VMRs appeared in the condition associated with lower temperature and higher humidity, but this relationship was not found between HCHO and temperature. We also found the O3 production at the Longfengshan station was mainly in the NOx-limited regime. This is the first study presenting the vertical distributions of NO2 and HCHO in the regional background atmosphere of northeastern China, which are significant to enhancing the understanding of background atmospheric chemistry and regional ozone pollution processes.

Valorisation of food waste for valuable by-products generation with economic assessment.

This study assessed the techno-economic feasibility of a biorefinery for valuable by-products (mainly hydrogen, ethanol and fertilizer) generation from food waste. The plant was designed to be built in Zhejiang province (China) with a processing capacity of 100 t food waste per day. It was found that the total capital investment (TCI) and annual operation cost (AOC) of the plant were US$ 7625549 and US$ 2432290.7 year-1, respectively. After the tax, US$ 3141867.6 year-1 of net profit could be reached. The payback period (PBP) was 3.5 years at a 7% discount rate. The internal rate of return (IRR) and return on investment (ROI) were 45.54% and 43.88%, respectively. Shutdown condition could happen with the feed of food waste less than 7.84 t day-1 (2587.2 t year-1) for the plant. This work was beneficial for attracting interests and even investment for valuable by-products generation from food waste in large scale.

Low pKa of Lys promotes glycation at one complementarity-determining region of a bispecific antibody.

Protein glycation is a common, normally innocuous, post-translational modification in therapeutic monoclonal antibodies. However, when glycation occurs on complementarity-determining regions (CDRs) of a therapeutic monoclonal antibody, its biological activities (e.g., potency) may be impacted. Here, we present a comprehensive approach to understanding the mechanism of protein glycation using a bispecific antibody. Cation exchange chromatography and liquid chromatography-mass spectrometry were used to characterize glycation at a lysine residue within a heavy chain (HC) CDR (HC-CDR3-Lys98) of a bispecific antibody. Thermodynamic analysis revealed that this reaction is reversible and can occur under physiological conditions with an apparent affinity of 8-10 mM for a glucose binding to HC-CDR3-Lys98. Results from kinetic analysis demonstrated that this reaction follows Arrhenius behavior in the temperature range of 5°C-45°C and can be well predicted in vitro and in a non-human primate. In addition, this glycation reaction was found to be driven by an unusually low pKa on the ε-amino group of HC-CDR3-Lys98. Van't Hoff analysis and homology modeling suggested that this reaction is enthalpically driven, with this lysine residue surrounded by a microenvironment with low polarity. This study provides, to our knowledge, new insights toward a mechanistic understanding of protein glycation and strategies to mitigate the impact of protein glycation during pharmaceutical development.

The pH signalling transcription factor PacC modulate growth, development, stress response and pathogenicity of Trichothecium roseum.

pH is one of the important environmental factors that affect the growth, development and pathogenicity of postharvest pathogen. The transcription factor PacC dominates the pH signal pathway. PacC in Trichothecium roseum showed three typical conserved zinc finger domains and closest homology to Fusarium graminearum. T. roseum increased the environmental pH both in vitro and in vivo. Expression patterns of TrpacC under different pH showed that at increasing pH from 3 to 5, the wild-type (WT) strain induced the expression of TrPacC in parallel to increased fungal growth; however, TrPacC expression decline at higer pH than 5, while fungal growth continued to increase. Development of a ΔTrPacC mutant down-regulated the expression of TrbrlA, TrabaA and TrwetA, reduced sporulation and delayed spore germination, resulting in smaller spores and sparse hyphae. ΔTrPacC mutant was sensitive to ionic stress, oxidative stress and cell wall integrity stress compared to the WT strain, especially the ionic stress. In addition, ∆TrPacC mutant showed reduced pathogenicity to muskmelon and tomato fruits. Taken together, T. roseum is an alkalinizing fungus, and the acidic environment could induce TrPacC expression. TrPacC positively regulates fungal growth and development as well as pathogenicity showing effect on fungal response to different stresses.

High-Performance Zinc-Air Batteries Based on Bifunctional Hierarchically Porous Nitrogen-Doped Carbon.

Active and durable bifunctional electrocatalysts for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) on the cathode are required for high-performance rechargeable metal-air batteries. Herein, the synthesis of hierarchically porous nitrogen-doped carbon (HPNC) with bifunctional oxygen electrocatalysis for Zn-air batteries is reported. The HPNC catalyst possesses a large surface area of 1459 m2 g-1 and exhibits superior electrocatalytic activity toward ORR and OER simultaneously with a low OER/ORR overpotential of 0.62 V, taking the difference between the potential at 10 mA cm-2 for OER and half-wave potential for ORR in 0.1 m KOH. Adopting HPNC as the air cathode, primary and rechargeable Zn-air batteries are fabricated. The primary batteries demonstrate a high open-circuit potential of 1.616 V, a specific capacity of 782.7 mAh gZn -1 and a superb peak power density of 201 mW cm-2 . The rechargeable batteries can be cycled stably for over 360 cycles or 120 h at the current density of 5 mA cm-2 . As elucidated by density functional theory, N-doping is preferred on defective sites with pentagon configuration and on the edge in the form of pyridinic-N-type. The high content of these two motifs in HPNC leads to the superior ORR and OER activities, respectively.

Small-core hollow-core nested antiresonant nodeless fiber with semi-circular tubes.

Hollow-core nested anti-resonant nodeless fibers (HC-NANFs) exhibit great performance in low loss and large bandwidth. Large core sizes are usually used to reduce confinement losses, but meanwhile, bring side effects such as high bending and coupling losses. This study proposes a small-core HC-NANF with a relatively low confinement loss. Semi-circular tubes (SCTs) are added to constitute the core boundary and reduce the fiber-core radius (R). Double NANFs tubes and single-ring tubes are added inside the SCTs to reduce loss. Simulation results show that the optimized structure with R of 5 µm has confinement loss and total loss of 0.687 dB/km and 4.27 dB/km at 1.55 µm, respectively. The bending loss is less than 10 dB/km at 1.4 ∼ 1.6 µm with a bending radius of 10 mm. The direct coupling loss with standard single mode fiber is greatly reduced to ∼ 0.125 dB compared to other HC-NANFs. The modified structure of HC-NANFs also shows a large bandwidth, effective single-mode operation, potentially high birefringence performance, and remarkable robustness of the optimized structure parameters, making it suitable for short-haul applications in laser-based gas sensing, miniaturized fiber sensing, etc.

Hybrid photonic bandgap effect in twisted hollow-core photonic bandgap fibers.

A hybrid photonic bandgap effect in twisted hollow-core photonic bandgap fibers (HC-PBFs) is theoretically investigated for the first time, to the best of our knowledge. Due to the topological effect, twisting of the fibers changes the effective refractive index and lifts the degeneracy of the photonic bandgap ranges of the cladding layers. This twist-induced hybrid photonic bandgap effect shifts up the center wavelength and narrows the bandwidth of the transmission spectrum. A quasi-single-mode low-loss transmission is achieved in the twisted 7-cell HC-PBFs with a twisting rate α = 7-8 rad/mm, which has a loss < 30 dB/km and higher-order mode extinction ratio > 15 dB. The twisted HC-PBFs could be suitable for applications such as spectral and mode filters.

A multi-feature deep learning system to enhance glaucoma severity diagnosis with high accuracy and fast speed.

Glaucoma is the leading cause of irreversible blindness, and the early detection and timely treatment are essential for glaucoma management. However, due to the interindividual variability in the characteristics of glaucoma onset, a single feature is not yet sufficient for monitoring glaucoma progression in isolation. There is an urgent need to develop more comprehensive diagnostic methods with higher accuracy. In this study, we proposed a multi- feature deep learning (MFDL) system based on intraocular pressure (IOP), color fundus photograph (CFP) and visual field (VF) to classify the glaucoma into four severity levels. We designed a three-phase framework for glaucoma severity diagnosis from coarse to fine, which contains screening, detection and classification. We trained it on 6,131 samples from 3,324 patients and tested it on independent 240 samples from 185 patients. Our results show that MFDL achieved a higher accuracy of 0.842 (95 % CI, 0.795-0.888) than the direct four classification deep learning (DFC-DL, accuracy of 0.513 [0.449-0.576]), CFP-based single-feature deep learning (CFP-DL, accuracy of 0.483 [0.420-0.547]) and VF-based single-feature deep learning (VF-DL, accuracy of 0.725 [0.668-0.782]). Its performance was statistically significantly superior to that of 8 juniors. It also outperformed 3 seniors and 1 expert, and was comparable with 2 glaucoma experts (0.842 vs 0.854, p = 0.663; 0.842 vs 0.858, p = 0.580). With the assistance of MFDL, junior ophthalmologists achieved statistically significantly higher accuracy performance, with the increased accuracy ranged from 7.50 % to 17.9 %, and that of seniors and experts were 6.30 % to 7.50 % and 5.40 % to 7.50 %. The mean diagnosis time per patient of MFDL was 5.96 s. The proposed model can potentially assist ophthalmologists in efficient and accurate glaucoma diagnosis that could aid the clinical management of glaucoma.

Tandem Electrochemical Oxidative Azidation/Heterocyclization of Tryptophan-Containing Peptides under Buffer Conditions.

As the aromatic tryptophan (Trp) side chain plays a pivotal role in influencing the structure and function of peptides and proteins, it has become an attractive target for the late-stage modification of these important biomolecules. Herein, we report an electrochemical approach for late-stage functionalization of peptides containing a Trp side chain through manganese-catalyzed tandem radical azidation/heterocyclization. This electrochemical oxidative strategy provides access to azide-substituted tetrazolo[1,5-a]indole-containing peptides with broad functional group tolerance, high site selectivity, and good yields of products (up to 87 %) under mild buffer conditions. Moreover, the modified Trp-containing peptides bearing an azide functionality are promising building blocks, paving the way for the construction of various derivatives, such as "click" chemistry products.

Site-Specific Quantitation of Drug Conjugations on Antibody-Drug Conjugates (ADCs) Using a Protease-Assisted Drug Deconjugation and Linker-like Labeling (PADDLL) Method.

Antibody-drug conjugates (ADCs) are biopharmaceuticals for the targeted delivery of antitumor agents. ADCs can be highly heterogeneous with various drug-to-antibody ratio (DAR) species, conjugation sites, and occupancy levels. The conjugation site can modulate the ADC stability and efficacy and therefore can be considered to be a critical quality attribute (CQA) during development. Traditional mass spectrometry (MS)-based peptide mapping methods cannot accurately quantify site-specific conjugations due to a significant ionization discrepancy between unconjugated native peptides and conjugated peptides. Here, we developed a novel protease-assisted drug deconjugation and linker-like labeling (PADDLL) method to quantify the levels of linker payload at specific conjugation sites. We utilized optimized papain digestion to deconjugate the drug payload and labeled unoccupied conjugation sites with a linker-like structure to provide comparable ionization efficiency for MS-based quantitation. This method was successfully applied on two cysteine-linked, protease-cleavable ADCs, and the method demonstrated good linearity and reliability, reaching a limit of quantitation of below 1%. The calculated DARs were comparable with the results from intact mass analysis. The lot-to-lot variation in conjugation distribution and inferior conjugation stability at HC Cys225 to other interchain cysteines were observed. This method provides a valuable tool for ADC design and product development. To the best of our knowledge, this is the first analytical method developed to accurately quantify site-specific linker-drug payload conjugations for ADCs.

Supramolecular Nanosubstrate-Mediated Delivery for CRISPR/Cas9 Gene Disruption and Deletion.

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) is an efficient and precise gene-editing technology that offers a versatile solution for establishing treatments directed at genetic diseases. Currently, CRISPR/Cas9 delivery into cells relies primarily on viral vectors, which suffer from limitations in packaging capacity and safety concerns. These issues with a nonviral delivery strategy are addressed, where Cas9•sgRNA ribonucleoprotein (RNP) complexes can be encapsulated into supramolecular nanoparticles (SMNP) to form RNP⊂SMNPs, which can then be delivered into targeted cells via supramolecular nanosubstrate-mediated delivery. Utilizing the U87 glioblastoma cell line as a model system, a variety of parameters for cellular-uptake of the RNP-laden nanoparticles are examined. Dose- and time-dependent CRISPR/Cas9-mediated gene disruption is further examined in a green fluorescent protein (GFP)-expressing U87 cell line (GFP-U87). The utility of an optimized SMNP formulation in co-delivering Cas9 protein and two sgRNAs that target deletion of exons 45-55 (708 kb) of the dystrophin gene is demonstrated. Mutations in this region lead to Duchenne muscular dystrophy, a severe genetic muscle wasting disease. Efficient delivery of these gene deletion cargoes is observed in a human cardiomyocyte cell line (AC16), induced pluripotent stem cells, and mesenchymal stem cells.

Single-polarization single-mode hollow-core photonic-bandgap fiber with thin slab waveguide.

A novel single-polarization single-mode hollow-core photonic bandgap fiber with thin slab waveguide (TSW) was designed and simulated. Single-polarization guidance is achieved by the high loss of a polarized fundamental mode (FM) induced by mode coupling with a higher-order TE/TM mode of TSW and low loss of another polarized FM. We achieve a polarization loss ratio ∼ 46.9 dB, birefringence Δn ∼ 2.4 × 10-4, loss ∼ 35.9 dB/km and minimum higher-order mode extinction ratio > 15 dB. Moreover, the performance could be maintained when the guidance wavelength λ = 1.44 ∼ 1.56 µm and bending radius rc > 9 mm. The proposed model will be suitable for application as resonator sensing paths of miniaturized resonator fiber optic gyroscopes, high-performance interferometers, fiber lasers, frequency metrology, quantum communications, and laser-based gas sensing, etc.

Low loss hollow-core antiresonant fiber with nested supporting rings.

A hollow-core antiresonant fiber (HC-ARF) with nested supporting rings (NSRs) is designed and simulated. The HC-ARF with NSRs has advantages and benefits of low loss, large bandwidth, simple structure and a well bending characteristic, in which confinement loss (CL) is ∼ 0.15 dB/km @ 1.55 µm and the bandwidth is ∼ 220 nm @ CL < 1 dB/km. The bending loss (BL) is lower than ∼ 1 dB/km @ bend radius rc > 24 mm at 1.55 µm. Therefore, the HC-ARF with NSRs has potential applications of data transmission, sensing, high power delivery and so on.