Molecular basis of receptor binding and antibody neutralization of Omicron.

The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading rapidly worldwide. Understanding the structural basis of the high transmissibility and enhanced immune evasion of Omicron is of high importance. Here, using cryo-electron microscopy, we present both the closed and the open states of the Omicron spike (S) protein, which appear more compact than the counterparts of the G614 strain1, potentially related to enhanced inter-protomer and S1-S2 interactions induced by Omicron residue substitution. The closed state showing dominant population may indicate a conformational masking mechanism for the immune evasion of Omicron. Moreover, we captured three states for the Omicron S-ACE2 complex, revealing that the substitutions on the Omicron RBM result in new salt bridges and hydrogen bonds, more favourable electrostatic surface properties, and an overall strengthened S-ACE2 interaction, in line with the observed higher ACE2 affinity of Omicron S than of G614. Furthermore, we determined the structures of Omicron S in complex with the Fab of S3H3, an antibody that is able to cross-neutralize major variants of concern including Omicron, elucidating the structural basis for S3H3-mediated broad-spectrum neutralization. Our findings shed light on the receptor engagement and antibody neutralization or evasion of Omicron and may also inform the design of broadly effective vaccines against SARS-CoV-2.

Plasma membrane repair empowers the necrotic survivors as innate immune modulators.

The plasma membrane is crucial to the survival of animal cells, and damage to it can be lethal, often resulting in necrosis. However, cells possess multiple mechanisms for repairing the membrane, which allows them to maintain their integrity to some extent, and sometimes even survive. Interestingly, cells that survive a near-necrosis experience can recognize sub-lethal membrane damage and use it as a signal to secrete chemokines and cytokines, which activate the immune response. This review will present evidence of necrotic cell survival in both in vitro and in vivo systems, including in C. elegans, mouse models, and humans. We will also summarize the various membrane repair mechanisms cells use to maintain membrane integrity. Finally, we will propose a mathematical model to illustrate how near-death experiences can transform dying cells into innate immune modulators for their microenvironment. By utilizing their membrane repair activity, the biological effects of cell death can extend beyond the mere elimination of the cells.

Genome-wide association study reveals the genetic basis for petal-size formation in rapeseed (Brassica napus) and CRISPR-Cas9-mediated mutagenesis of BnFHY3 for petal-size reduction.

Petals in rapeseed (Brassica napus) serve multiple functions, including protection of reproductive organs, nutrient acquisition, and attraction of pollinators. However, they also cluster densely at the top, forming a thick layer that absorbs and reflects a considerable amount of photosynthetically active radiation. Breeding genotypes with large, small, or even petal-less varieties, requires knowledge of primary genes for allelic selection and manipulation. However, our current understanding of petal-size regulation is limited, and the lack of markers and pre-breeding materials hinders targeted petal-size breeding. Here, we conducted a genome-wide association study on petal size using 295 diverse accessions. We identified 20 significant single nucleotide polymorphisms and 236 genes associated with petal-size variation. Through a cross-analysis of genomic and transcriptomic data, we focused on 14 specific genes, from which molecular markers for diverging petal-size features can be developed. Leveraging CRISPR-Cas9 technology, we successfully generated a quadruple mutant of Far-Red Elongated Hypocotyl 3 (q-bnfhy3), which exhibited smaller petals compared to the wild type. Our study provides insights into the genetic basis of petal-size regulation in rapeseed and offers abundant potential molecular markers for breeding. The q-bnfhy3 mutant unveiled a novel role of FHY3 orthologues in regulating petal size in addition to previously reported functions.

Ultrahigh-Efficiency Superior Energy Storage in Lead-Free Films with a Simple Composition.

Dielectric capacitors are highly desired in modern electronic devices and power systems to store and recycle electric energy. However, achieving simultaneous high energy density and efficiency remains a challenge. Here, guided by theoretical and phase-field simulations, we are able to achieve a superior comprehensive property of ultrahigh efficiency of 90-94% and high energy density of 85-90 J cm-3 remarkably in strontium titanate (SrTiO3), a linear dielectric of a simple chemical composition, by manipulating local symmetry breaking through introducing Ti/O defects. Atomic-scale characterizations confirm that these Ti/O defects lead to local symmetry breaking and local lattice strains, thus leading to the formation of the isolated ultrafine polar nanoclusters with varying sizes from 2 to 8 nm. These nanoclusters account for both considerable dielectric polarization and negligible polarization hysteresis. The present study opens a new realm of designing high-performance dielectric capacitors utilizing a large family of readily available linear dielectrics with very simple chemistry.

Long-term monitoring chlorophyll-a concentration using HJ-1 A/B imagery and machine learning algorithms in typical lakes, a cold semi-arid region.

Chlorophyll a (Chl-a) in lakes serves as an effective marker for assessing algal biomass and the nutritional level of lakes, and its observation is feasible through remote sensing methods. HJ-1 (Huanjing-1) satellite, deployed in 2008, incorporates a CCD capable of a 30 m resolution and has a revisit interval of 2 days, rendering it a superb choice or supplemental sensor for monitoring trophic state of lakes. For effective long-term and regional-scale mapping, both the imagery and the evaluation of machine learning algorithms are essential. The several typical machine learning algorithms, i.e., Support Vector Regression (SVR), Gradient Boosting Decision Trees (GBDT), XGBoost (XGB), Random Forest (RF), K-Nearest Neighbor (KNN), Kernel Ridge Regression (KRR), and Multi-Layer Perception Network (MLP), were developed using our in-situ measured Chl-a. A cross-validation grid to identify the most effective hyperparameter combinations for each algorithm was used, as well as the selected optimal superparameter combinations. In Chl-a mapping of three typical lakes, the R2 of GBDT, XGB, RF, and KRR all reached 0.90, while XGB algorithm also exhibited stable performance with the smallest error (RMSE = 3.11 µg/L). Adjustments were made to align the Chl-a spatial-temporal patterns with past data, utilizing HJ1-A/B CCD images mapping through XGB algorithm, which demonstrates its stability. Our results highlight the considerable effectiveness and utility of HJ-1 A/B CCD imagery for evaluation and monitoring trophic state of lakes in a cold arid region, providing the application cases contribute to the ongoing efforts to monitor water qualities.

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus).

KEY MESSAGE: Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.

The association between brominated flame retardants exposure with bone mineral density in US adults: A cross-sectional study of the national health and nutrition examination survey (NHANES) 2005-2014.

BACKGROUND AND AIMS: Exposure to brominated flame retardants (BFRs) has been widely confirmed to impair the normal functioning of the human body system. However, there is a paucity of study on the effects of serum BFRs on bone mineral density (BMD). This study aims to investigate the relationship between exposure to BFRs and BMD in a nationally representative sample of U.S. adults. METHODS: 3079 participants aged between 20 and 80 years with complete data were included in the study. Serum levels of BFRs were measured using automated liquid-liquid extraction and subsequent sample clean-up. The BMD of all participants were assessed by DXA examinations. Generalize linear model, Restricted cubic spline (RCS), subgroup, weighted quantile sum (WQS) and bayesian kernel machine regression (BKMR) were used to estimate the association between serum BFRs and BMD. RESULTS: Multivariate linear regression analyses revealed that, after adjusting for covariates, PBB153 was significantly associated with TF-BMD (ß = 0.0177, 95%CI: 0.0103-0.0252), FN-BMD (ß = 0.009, 95%CI: 0.0036-0.0145), TS-BMD (ß = 0.0081, 95%CI: 0.0013-0.015) and L1-BMD (ß = 0.0144, 95%CI: 0.0075-0.0213). However, the associations lose their statistical significance after further adjustment for sex. BFRs exhibited S-shaped or line-plateau dose-response curves with BMD. In subgroup analyses, BFRs were significantly associated with BMD in participants who were younger than 55 years, female, overweight (BMI >25 kg/m2), and less alcohol consumption. In WQS and BKMR analyses, the effects of BFRs mixtures on BMD differed by sex, and PBDE153, PBDE209 and PBB153 had the highest weights in the WQS regression model. CONCLUSION: This study showed that serum BFRs negatively predicted BMD in men, but not in women or the general population. PBDE153, PBDE209, and PBB153 were significant BMD factors, especially in younger, overweight, and less alcohol consumption individuals.

The impact of the combat method on radiomics feature compensation and analysis of scanners from different manufacturers.

BACKGROUND: This study investigated whether the Combat compensation method can remove the variability of radiomic features extracted from different scanners, while also examining its impact on the subsequent predictive performance of machine learning models. MATERIALS AND METHODS: 135 CT images of Credence Cartridge Radiomic phantoms were collected and screened from three scanners manufactured by Siemens, Philips, and GE. 100 radiomic features were extracted and 20 radiomic features were screened according to the Lasso regression method. The radiomic features extracted from the rubber and resin-filled regions in the cartridges were labeled into different categories for evaluating the performance of the machine learning model. Radiomics features were divided into three groups based on the different scanner manufacturers. The radiomic features were randomly divided into training and test sets with a ratio of 8:2. Five machine learning models (lasso, logistic regression, random forest, support vector machine, neural network) were employed to evaluate the impact of Combat on radiomic features. The variability among radiomic features were assessed using analysis of variance (ANOVA) and principal component analysis (PCA). Accuracy, precision, recall, and area under the receiver curve (AUC) were used as evaluation metrics for model classification. RESULTS: The principal component and ANOVA analysis results show that the variability of different scanner manufacturers in radiomic features was removed (P˃0.05). After harmonization with the Combat algorithm, the distributions of radiomic features were aligned in terms of location and scale. The performance of machine learning models for classification improved, with the Random Forest model showing the most significant enhancement. The AUC value increased from 0.88 to 0.92. CONCLUSIONS: The Combat algorithm has reduced variability in radiomic features from different scanners. In the phantom CT dataset, it appears that the machine learning model's classification performance may have improved after Combat harmonization. However, further investigation and validation are required to fully comprehend Combat's impact on radiomic features in medical imaging.

Concentration-Dependent Enrichment Identifies Primary Protein Targets of Multitarget Bioactive Molecules.

Multitarget bioactive molecules (MBMs) are of increasing importance in drug discovery as they could produce high efficacy and a low chance of resistance. Several advanced approaches of quantitative proteomics were developed to accurately identify the protein targets of MBMs, but little study has been carried out in a sequential manner to identify primary protein targets (PPTs) of MBMs. This set of proteins will first interact with MBMs in the temporal order and play an important role in the mode of action of MBMs, especially when MBMs are at low concentrations. Herein, we describe a valuable observation that the result of the enrichment process is highly dependent on concentrations of the probe and the proteome. Interestingly, high concentrations of probe and low concentrations of incubated proteome will readily miss the hyper-reactive protein targets and thereby increase the probability of rendering PPTs with false-negative results, while low concentrations of probe and high concentrations of incubated proteome more than likely will capture the PPTs. Based on this enlightening observation, we developed a proof-of-concept approach to identify the PPTs of iodoacetamide, a thiol-reactive MBM. This study will deepen our understanding of the enrichment process and improve the accuracy of pull-down-guided target identification.

Multi-modal imaging using a cascaded microscope design.

We present a multi-modal fiber array snapshot technique (M-FAST) based on an array of 96 compact cameras placed behind a primary objective lens and a fiber bundle array. Our technique is capable of large-area, high-resolution, multi-channel video acquisition. The proposed design provides two key improvements to prior cascaded imaging system approaches: a novel optical arrangement that accommodates the use of planar camera arrays, and a new ability to acquire multi-modal image data acquisition. M-FAST is a multi-modal, scalable imaging system that can acquire snapshot dual-channel fluorescence images as well as differential phase contrast measurements over a large 6.59 mm × 9.74 mm field-of-view at 2.2-µm center full-pitch resolution.

Stereochemistry and antimalarial activity of C-10 carba analogues of artemisinin.

Artemisinin is an endoperoxide bond-containing sesquiterpene lactone showing potent antimalarial effect as well as antitumor and antivirus activities. Inspired by this unique pharmacorphore, researchers around the world developed numerous Artemisinin derivatives. Among these derivatives, the C-10 carba analogues of artemisinin are frequently reported. However, the stereochemistry of C-10 carba analogues of artemisinin is overlooked and the corresponding mixture of stereoisomers are used. Herein, we reported for the first time stereochemistry and antimalarial activity of C-10 carba analogues of artemisinin. We employed two approaches to obtain the pure isomer of C-10 carba analogues and presented an interesting observation about their antimalarial activities. The minor isomer with large-sized substitute and S configuration at C-10 position had much lower antimalarial effect than the major isomer with R configuration. The study will shed light on the development of effective antimalarial drugs based on ART.

Evaluating the feasibility and outcomes of a resident-led school-based pediatric clinic.

Objective: A resident-led school-based clinic to serve low-income populations was established in 2019 and served as a continuity clinic for pediatric residents at a single university. Our aim was to assess the feasibility, clinic outcomes, and resident experience of a resident-led school-based clinic (RLSBC), established in an elementary school that serves an underserved population. Methods: A retrospective chart review for the first 6 months (October 2019 to March 2020) of clinic operations was conducted. Feasibility metrics included the number of patients, visits and planned follow-ups; clinic outcomes included the number and type of presenting complaint, new diagnoses and interventions. Residents were also surveyed to assess their satisfaction and perceived learning in training at the school-based clinic. Results: Over the first 19 clinic days, 48 children were seen at the school-based clinic. Of the clinic users, 60% did not have a primary care physician, 46% received a new diagnosis, 46% received an intervention in the form of medication prescription, laboratory/imaging requisitions or referrals, and 96% received a treatment plan. Residents positively rated the experience of staffing the school-based clinic in all aspects, including learning environment, clinic and team environment, teaching obtained, practice management, and overall experience. Conclusion: A RLSBC is feasible and our outcomes suggest that such clinics may address health care needs of low-income families and children, while being a positively rated educational experience for pediatric residents.

Increasing a microscope's effective field of view via overlapped imaging and machine learning.

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.

Exploring the impact of new particle formation events on PM2.5 pollution during winter in the Yangtze River Delta, China.

New particle formation (NPF) events are an increasingly interesting topic in air quality and climate science. In this study, the particle number size distributions, and the frequency of NPF events over Hefei were investigated from November 2018 to February 2019. The proportions of the nucleation mode, Aitken mode, and accumulation mode were 24.59%, 53.10%, and 22.30%, respectively, which indicates the presence of abundant ultrafine particles in Hefei. Forty-six NPF events occurred during the observation days, accounting for 41.82% of the entire observation period. Moreover, the favorable meteorological conditions, potential precursor gases, and PM2.5 range of the NPF events were analyzed. Compared to non-NPF days, the NPF events preferentially occurred on days with lower relative humidity, higher wind speeds, and higher temperatures. When the PM2.5 was 15-20, 70-80, and 105-115 µg/m3, the frequency of the NPF events was higher. Nucleation mode particles were positively related to atmospheric oxidation indicated by ozone when PM2.5 ranged from 15 to 20 µg/m3, and related to gaseous precursors like SO2 and NO2 when PM2.5 was located at 70-80 and 105-115 µg/m3. On pollution days, NPF events did not directly contribute to the increase in the PM2.5 in the daytime, however, NPF events would occur during the night and the growth of particulate matter contributes to the nighttime PM2.5 contents. This could lead to pollution that lasted into the next day. These findings are significant to the improvement of our understanding of the effects of aerosols on air quality.

Characteristic analysis of continuous new particle formation events in Hefei: A case study of the May Day holiday in China.

Studying the characteristics of new particle formation (NPF) is conducive to exploring the impact of atmospheric particulate matter on the climate, environment, and human health. The particle number size distributions (5.6-560 nm) of aerosols were measured using a fast mobility particle sizer (FMPS) from 1 to 11 May 2019. The clean atmosphere was one of the basic conditions for the occurrence of this continuous new particle formation events. It started between 9:00 and 12:00, and it mainly ended after 20:00. The growth rate (GR) and condensation sink (CS) values in Hefei were 2.98 ± 0.97 nm·h-1 and (3.0 ± 0.4) × 10-2 s-1, respectively. Back trajectory clustering analysis revealed that the mass concentration of the air masses from the southeastern part of Henan Province and the southern part of Anhui Province surrounding the study area were relatively high. The analysis results of the potential source contribution function (PSCF) and the concentration weighted trajectory (CWT) methods show that in addition to local pollution, the long-distance transport of pollutants in the Yangtze River Delta (YRD) greatly contributed to the accumulation modal particulate concentration in Hefei. Moreover, the population affected by PM2.5 during the observation period reached 8.19 × 104, accounting for 1.08% to the total population in Hefei. The premature death cases associated with PM2.5 reached 8.35 × 102. This study is helpful to understand the main influencing factors of consecutive NPF events and the health risks of fine particles.

Characterization of Key Odorants in Scallion Pancake and Investigation on Their Changes during Storage.

To characterize key odorants in scallion pancake (SP), volatiles were extracted by solvent extraction-solvent assisted flavor evaporation. A total of 51 odor-active compounds were identified by gas chromatography-olfactometry (GC-O) and chromatography-mass spectrometry (GC-MS). (Z/E)-3,6-Diethyl-1,2,4,5-tetrathiane was detected for the first time in scallion food. Application of aroma extract dilution analysis to extracts showed maltol, methyl propyl disulfide, dipropyl disulfide and 2-pentylfuran had the highest flavor dilution (FD) factor of 4096. Twenty-three odorants with FD factors ≥ 8 were quantitated, and their odor active values (OAVs) were calculated. Ten compounds with OAVs ≥ 1 were determined as the key odorants; a recombinate model prepared from the key odorants, including (E,E)-2,4-decadienal, dimethyl trisulfide, methyl propyl disulfide, hexanal, dipropyl trisulfide, maltol, acetoin, 2-methylnaphthalene, 2-pentylfuran and 2(5H)-furanone, successfully simulated the overall aroma profile of SP. The changes in odorants during storage were investigated further. With increasing concentrations and OAVs during storage, hexanal became an off-flavor compound.

TNFSF15 facilitates human umbilical cord blood haematopoietic stem cell expansion by activating Notch signal pathway.

The lack of efficient ex vivo expansion methods restricts clinical use of haematopoietic stem cells (HSC) for the treatment of haematological malignancies and degenerative diseases. Umbilical cord blood (UCB) serves as an alternative haematopoietic stem cell source. However, currently what limits the use of UCB-derived HSC is the very low numbers of haematopoietic stem and progenitor cells available for transplantation in a single umbilical cord blood unit. Here, we report that TNFSF15, a member of the tumour necrosis factor superfamily, promotes the expansion of human umbilical cord blood (UCB)-derived HSC. TNFSF15-treated UCB-HSC is capable of bone marrow engraftment as demonstrated with NOD/SCID or NOD/Shi-SCID/IL2Rgnull (NOG) mice in both primary and secondary transplantation. The frequency of repopulating cells occurring in the injected tibiae is markedly higher than that in vehicle-treated group. Additionally, signal proteins of the Notch pathway are highly up-regulated in TNFSF15-treated UCB-HSC. These findings indicate that TNFSF15 is useful for in vitro expansion of UCB-HSC for clinical applications. Furthermore, TNFSF15 may be a hopeful selection for further UCB-HSC application or study.

Fourier ptychography: current applications and future promises.

Traditional imaging systems exhibit a well-known trade-off between the resolution and the field of view of their captured images. Typical cameras and microscopes can either "zoom in" and image at high-resolution, or they can "zoom out" to see a larger area at lower resolution, but can rarely achieve both effects simultaneously. In this review, we present details about a relatively new procedure termed Fourier ptychography (FP), which addresses the above trade-off to produce gigapixel-scale images without requiring any moving parts. To accomplish this, FP captures multiple low-resolution, large field-of-view images and computationally combines them in the Fourier domain into a high-resolution, large field-of-view result. Here, we present details about the various implementations of FP and highlight its demonstrated advantages to date, such as aberration recovery, phase imaging, and 3D tomographic reconstruction, to name a few. After providing some basics about FP, we list important details for successful experimental implementation, discuss its relationship with other computational imaging techniques, and point to the latest advances in the field while highlighting persisting challenges.

Diverse families of antimicrobial peptides isolated from skin secretions of three species of East Asian frogs, Babina daunchina, Babina adenopleura, and Rana omeimontis (Ranidae).

Twenty-two novel cDNAs encoding 22 peptide precursors for 19 mature peptides including antimicrobial peptides (AMPs) were identified from East Asian frog species Babina daunchina, Babina adenopleura, and Rana omeimontis skin-derived cDNA libraries. Two atypical members of the brevinin-1 family AMPs, named brevinin-1AN1 (FLTGVLKLASKIPSVLCAVLKTC) and brevinin-1DN1(FLKGVINLASKIPSMLCAVLKTC), were purified from the skin secretions of B. adenopleura and B. daunchina, respectively. A member of the ranatuerin-2 family AMP named ranatuerin-2DN1 (GLFDSITQGLKDTAVKLLDKIKCKLSACPPA) was also purified from the skin secretion of B. daunchina. One AMP named japonicin-2OM1 (FIVPSIFLLKKAFCIALKKNC) was purified from the skin secretion of R. omeimontis. The antimicrobial tests showed that brevinin-1DN1, brevinin-1DN2, brevinin-1AN1, and japonicin-2OM1 possess higher antimicrobial activity against Gram-positive bacteria than Gram-negative bacteria.

Peptidomic analysis of antimicrobial peptides in skin secretions of Amolops mantzorum.

Amphibian skin secretions contain abundant bioactive peptides that are valuable natural resources for human beings. However, many amphibians are disappearing from the world, making relevant scientific studies even more important. In this study, 24 cDNA sequences encoding antimicrobial peptide (AMP) precursors were initially cloned by screening a cDNA library derived from the skin of the Sichuan torrent frog, Amolops mantzorum. Eighteen mature AMPs belonging to 11 different families were deduced from these cDNA clones. Biological function was confirmed in each family of these AMPs. Some of them were purified from the skin secretions, and their molecular structures were determined by Edman degradation. Liquid chromatography in conjunction with tandem mass spectrometry (LC-MS/MS)-based peptidomics was used to further confirm the actual presence and characteristics of mature AMPs in the skin secretions of A. mantzorum. Incomplete tryptic digestion and gas-phase fractionation (GPF) analysis were used to increase the peptidome coverage and reproducibility of peptide ion selection.