Iterative tomography with digital adaptive optics permits hour-long intravital observation of 3D subcellular dynamics at millisecond scale.

Long-term subcellular intravital imaging in mammals is vital to study diverse intercellular behaviors and organelle functions during native physiological processes. However, optical heterogeneity, tissue opacity, and phototoxicity pose great challenges. Here, we propose a computational imaging framework, termed digital adaptive optics scanning light-field mutual iterative tomography (DAOSLIMIT), featuring high-speed, high-resolution 3D imaging, tiled wavefront correction, and low phototoxicity with a compact system. By tomographic imaging of the entire volume simultaneously, we obtained volumetric imaging across 225 × 225 × 16 µm3, with a resolution of up to 220 nm laterally and 400 nm axially, at the millisecond scale, over hundreds of thousands of time points. To establish the capabilities, we investigated large-scale cell migration and neural activities in different species and observed various subcellular dynamics in mammals during neutrophil migration and tumor cell circulation.

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

eIF4EHP promotes Ldh mRNA translation in and fruit fly adaptation to hypoxia.

Hypoxia induces profound modifications in the gene expression program of eukaryotic cells due to lowered ATP supply resulting from the blockade of oxidative phosphorylation. One significant consequence of oxygen deprivation is the massive repression of protein synthesis, leaving a limited set of mRNAs to be translated. Drosophila melanogaster is strongly resistant to oxygen fluctuations; however, the mechanisms allowing specific mRNA to be translated into hypoxia are still unknown. Here, we show that Ldh mRNA encoding lactate dehydrogenase is highly translated into hypoxia by a mechanism involving a CA-rich motif present in its 3' untranslated region. Furthermore, we identified the cap-binding protein eIF4EHP as a main factor involved in 3'UTR-dependent translation under hypoxia. In accordance with this observation, we show that eIF4EHP is necessary for Drosophila development under low oxygen concentrations and contributes to Drosophila mobility after hypoxic challenge. Altogether, our data bring new insight into mechanisms contributing to LDH production and Drosophila adaptation to oxygen variations.

Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising.

Calcium imaging has transformed neuroscience research by providing a methodology for monitoring the activity of neural circuits with single-cell resolution. However, calcium imaging is inherently susceptible to detection noise, especially when imaging with high frame rate or under low excitation dosage. Here we developed DeepCAD, a self-supervised deep-learning method for spatiotemporal enhancement of calcium imaging data that does not require any high signal-to-noise ratio (SNR) observations. DeepCAD suppresses detection noise and improves the SNR more than tenfold, which reinforces the accuracy of neuron extraction and spike inference and facilitates the functional analysis of neural circuits.

Identifying novel acute pancreatitis sub-phenotypes using total serum calcium trajectories.

BACKGROUND: Acute pancreatitis (AP) has heterogeneous clinical features, and identifying clinically relevant sub-phenotypes is useful. We aimed to identify novel sub-phenotypes in hospitalized AP patients using longitudinal total serum calcium (TSC) trajectories. METHODS: AP patients had at least two TSC measurements during the first 24 h of hospitalization in the US-based critical care database (Medical Information Mart for Intensive Care-III (MIMIC-III) and MIMIC-IV were included. Group-based trajectory modeling was used to identify calcium trajectory phenotypes, and patient characteristics and treatment outcomes were compared between the phenotypes. RESULTS: A total of 4518 admissions were included in the analysis. Four TSC trajectory groups were identified: "Very low TSC, slow resolvers" (n = 65; 1.4% of the cohort); "Moderately low TSC" (n = 559; 12.4%); "Stable normal-calcium" (n = 3875; 85.8%); and "Fluctuating high TSC" (n = 19; 0.4%). The "Very low TSC, slow resolvers" had the lowest initial, maximum, minimum, and mean TSC, and highest SOFA score, creatinine and glucose level. In contrast, the "Stable normal-calcium" had the fewest ICU admission, antibiotic use, intubation and renal replace treatment. In adjusted analysis, significantly higher in-hospital mortality was noted among "Very low TSC, slow resolvers" (odds ratio [OR], 7.2; 95% CI, 3.7 to 14.0), "moderately low TSC" (OR, 5.0; 95% CI, 3.8 to 6.7), and "Fluctuating high TSC" (OR, 5.6; 95% CI, 1.5 to 20.6) compared with the "Stable normal-calcium" group. CONCLUSIONS: We identified four novel sub-phenotypes of patients with AP, with significant variability in clinical outcomes. Not only the absolute TSC levels but also their trajectories were significantly associated with in-hospital mortality.

Harmine inhibits the proliferation and migration and promotes the apoptosis of colon cancer cells via inhibition of the FAK/AKT and ERK1/2/CREB signaling pathways.

Harmine is present in a variety of medicinal plants, and its effects on colon cancer cells remain unclear. Here, we found that harmine exhibited significant inhibitory effects on the proliferation of colon cancer cells by inhibiting the phosphorylation levels of the FAK/AKT and ERK1/2/CREB. Furthermore, harmine also inhibited the migration of colon cancer cells and suppressed the expression levels of MMP-2, MMP-9, and VEGF. Additionally, harmine-induced apoptosis in colon cancer cells by regulating the expression of Bcl-2 and Bax. In conclusion, our findings suggest that harmine exerts a significant inhibitory effect on the development of colon cancer cells.

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region.

BACKGROUND: Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species. RESULTS: The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes. CONCLUSIONS: This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.

Accurate and complete genomes from metagenomes.

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

Optical neural ordinary differential equations.

Increasing the layer number of on-chip photonic neural networks (PNNs) is essential to improve its model performance. However, the successive cascading of network hidden layers results in larger integrated photonic chip areas. To address this issue, we propose the optical neural ordinary differential equations (ON-ODEs) architecture that parameterizes the continuous dynamics of hidden layers with optical ODE solvers. The ON-ODE comprises the PNNs followed by the photonic integrator and optical feedback loop, which can be configured to represent residual neural networks (ResNets) and implement the function of recurrent neural networks with effectively reduced chip area occupancy. For the interference-based optoelectronic nonlinear hidden layer, the numerical experiments demonstrate that the single hidden layer ON-ODE can achieve approximately the same accuracy as the two-layer optical ResNets in image classification tasks. In addition, the ON-ODE improves the model classification accuracy for the diffraction-based all-optical linear hidden layer. The time-dependent dynamics property of ON-ODE is further applied for trajectory prediction with high accuracy.

Catalyst- and solvent-free regioselective ring opening of aziridines with amines: application in the gram-scale synthesis of the α,ß-diamino propionic derivative, aspergillomarasmine A.

A green and efficient approach for synthesizing α,ß-diamino propionic derivatives was developed through the ring opening of α-C-alkyloxycarbonyl aziridine. This method features catalyst- and solvent-free conditions, high regioselectivity, and wide substrate scope including solid amines, and realizes the gram-scale synthesis of aspergillomarasmine A.

Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury.

Based on the multiomics analysis, this study is aimed at investigating the underlying mechanism of didymin against acute liver injury (ALI). The mice were administrated with didymin for 2 weeks, followed by injection with lipopolysaccharide (LPS) plus D-galactosamine (D-Gal) to induce ALI. The pathological examination revealed that didymin significantly ameliorated LPS/D-Gal-induced hepatic damage. Also, it markedly reduced proinflammatory cytokines release by inhibiting the TLR4/NF-κB pathway activation, alleviating inflammatory injury. A transcriptome analysis proved 2680 differently expressed genes (DEGs) between the model and didymin groups and suggested that the PI3K/Akt and metabolic pathways might be the most relevant targets. Meanwhile, the metabolome analysis revealed 67 differently expressed metabolites (DEMs) between the didymin and model groups that were mainly clustered into the glycerophospholipid metabolism, which was consistent with the transcriptome study. Importantly, a comprehensive analysis of both the omics indicated a strong correlation between the DEGs and DEMs, and an in-depth study demonstrated that didymin alleviated metabolic disorder and hepatocyte injury likely by inhibiting the glycerophospholipid metabolism pathway through the regulation of PLA2G4B, LPCAT3, and CEPT1 expression. In conclusion, this study demonstrates that didymin can ameliorate LPS/D-Gal-induced ALI by inhibiting the glycerophospholipid metabolism and PI3K/Akt and TLR4/NF-κB pathways.

Physician altruism under the change from pure payment system to mixed payment schemes: experimental evidence.

BACKGROUND: Mixed payment schemes have become one of the effective measures to balance medical costs and quality of medical services. However, altruism as an intrinsic motivation may influence the effect of switching from a pure payment system to mixed payment schemes. This study aimed to quantify physicians' altruism and analyze the effect of changes of payment system on physicians' altruism and thus proposed references for the reform of payment system. METHODS: We simulated an exogenous payment system in a controlled laboratory with five experimental groups and 150 medical student subjects. Physicians' altruism was measured by estimating altruistic parameter and marginal rate of substitution. The non-parametric test and the least square regression analysis were used to analyze the differences of altruistic parameters between pure payment systems and mixed payment schemes. Finally, we analyzed the effect of changes in payment system accompanied by changes in trade-off range on physicians' altruism. RESULTS: We find that the mean value of individual altruistic parameter is 0.78 and the marginal rate of substitution is 1.078. Their estimates at the individual level were significantly positively correlated (Spearman's ρ = 0.715, p < 0.01). The shift from pure payment system to mixed payment scheme reduced the altruistic parameter. However, the altruistic parameter increased with the increase of the trade-off range. Physicians who were more altruistic generated higher patients' health benefit. For each unit increase in altruistic parameter, the increase in patients' health benefit was lower in mixed payment scheme than in the pure payment system. CONCLUSION: The estimates of altruistic parameters are reliable. Physicians attach a higher weight to patients' benefit than to their own profit. Mixed payment schemes improve physicians' behavior and relate to lower altruistic parameters; physicians only need to sacrifice less personal profits to generate the same or even higher altruistic parameter as under the pure payment system. The design of mixed payment schemes that make the interests of physicians and patients close to each other by reducing the trade-off range can provide implication for the reform of payment system in which the physicians' interest and the patients' benefit are consistent.

The effect of internal salary incentives based on insurance payment on physicians' behavior: experimental evidence.

BACKGROUND: Understanding how physicians respond to payment methods is crucial for designing effective incentives and enhancing the insurance system. Previous theoretical research has explored the effects of payment methods on physician behavior based on a two-level incentive path; however, empirical evidence to validate these theoretical frameworks is lacking. To address this research gap, we conducted a laboratory experiment to investigate physicians' behavioral responses to three types of internal salary incentives based on diagnosis-related-group (DRG) and fee-for-service (FFS). METHODS: A total of 150 medical students from Capital Medical University were recruited as participants. These subjects played the role of physicians in choosing the quantity of medical services for nine types of patients under three types of salary incentives-fixed wage, constant fixed wage with variable performance wage, and variable fixed wage with variable performance wage, of which performance wage referred to the payment method balance under FFS or DRG. We collected data on the quantities of medical services provided by the participants and analyzed the results using the Friedman test and the fixed effects model. RESULTS: The results showed that a fixed wage level did not have a significant impact on physicians' behavior. However, the patients benefited more under the fixed wage compared to other salary incentives. In the case of a floating wage system, which consisted of a constant fixed wage and a variable performance wage from the payment method balance, an increase in performance wage led to a decrease in physicians' service provision under DRG but an increase under FFS. Consequently, this resulted in a decrease in patient benefit. When the salary level remained constant, but the composition of the salary varied, physicians' behavior changed slightly under FFS but not significantly under DRG. Additionally, patient benefits decreased as the ratio of performance wages increased under FFS. CONCLUSIONS: While using payment method balance as physicians' salary may be effective in transferring incentives of payment methods to physicians through internal compensation frameworks, it should be used with caution, particularly when the measurement standard of care is imperfect.

The impacts of altruism levels on the job preferences of medical students: a cross-sectional study in China.

BACKGROUND: Rational allocation of human resources for health is crucial for ensuring public welfare and equitable access to health services. Understanding medical students' job preferences could help develop effective strategies for the recruitment and retention of the health workforce. Most studies explore the relationship between extrinsic incentives and job choices through discrete choice experiments (DCEs). Little attention has been paid to the influence of intrinsic altruism on job choice. This study aimed to explore the heterogeneous preferences of medical students with different levels of altruism regarding extrinsic job attributes. METHODS: We conducted an online survey with 925 medical students from six hospitals in Beijing from July to September 2021. The survey combined job-choice scenarios through DCEs and a simulation of a laboratory experiment on medical decision-making behavior. Behavioral data were used to quantify altruism levels by estimating altruistic parameters based on a utility function. We fit mixed logit models to estimate the effects of altruism on job preference. RESULTS: All attribute levels had the expected effect on job preferences, among which monthly income (importance weight was 30.46%, 95% CI 29.25%-31.67%) and work location (importance weight was 22.39%, 95% CI 21.14%-23.64%) were the most salient factors. The mean altruistic parameter was 0.84 (s.d. 0.19), indicating that medical students' altruism was generally high. The subgroup analysis showed that individuals with higher altruism levels had a greater preference for non-financial incentives such as an excellent work environment, sufficient training and career development opportunities, and a light workload. The change in the rate of the uptake of a rural position by individuals with lower levels of altruism is sensitive to changes in financial incentives. CONCLUSIONS: Medical students' altruism was generally high, and those with higher altruism paid more attention to non-financial incentives. This suggests that policymakers and hospital managers should further focus on nonfinancial incentives to better motivate altruistic physicians, in addition to appropriate economic incentive when designing recruitment and retention interventions. Medical school administrations could attach importance to the promotion of altruistic values in medical education.

Double-Pulse Generation of Indistinguishable Single Photons with Optically Controlled Polarization.

Single-photon sources play a key role in photonic quantum technologies. Semiconductor quantum dots can emit indistinguishable single photons under resonant excitation. However, the resonance fluorescence technique typically requires cross-polarization filtering, which causes a loss of the unpolarized quantum dot emission by 50%. To solve this problem, we demonstrate a method for generating indistinguishable single photons with optically controlled polarization by two laser pulses off-resonant with neutral exciton states. This scheme is realized by exciting the quantum dot to the biexciton state and subsequently driving the quantum dot to an exciton eigenstate. By combining with a magnetic field, we demonstrated the generation of photons with optically controlled polarization (the degree of polarization is 101(2)%), laser-neutral exciton detuning up to 0.81 meV, high single-photon purity (99.6(1)%), and indistinguishability (85(4)%). Laser pulses can be blocked using polarization and spectral filtering. Our work makes an important step toward indistinguishable single-photon sources with near-unity collection efficiency.

A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) is the most common malignant tumor that seriously affects human health. Previous studies have indicated that abnormal levels of glycosylation promote progression and poor prognosis of lung cancer. Thus, the present study aimed to explore the prognostic signature related to glycosyltransferases (GTs) for LUAD. METHODS: The gene expression profiles were obtained from The Cancer Genome Atlas (TCGA) database, and GTs were obtained from the GlycomeDB database. Differentially expressed GTs-related genes (DGTs) were identified using edge package and Venn diagram. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and ingenuity pathway analysis (IPA) methods were used to investigate the biological processes of DGTs. Subsequently, Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses were performed to construct a prognostic model for LUAD. Kaplan-Meier (K-M) analysis was adopted to explore the overall survival (OS) of LUAD patients. The accuracy and specificity of the prognostic model were evaluated by receiver operating characteristic analysis (ROC). In addition, single-sample gene set enrichment analysis (ssGSEA) algorithm was used to analyze the infiltrating immune cells in the tumor environment. RESULTS: A total of 48 DGTs were mainly enriched in the processes of glycosylation, glycoprotein biosynthetic process, glycosphingolipid biosynthesis-lacto and neolacto series, and cell-mediated immune response. Furthermore, B3GNT3, MFNG, GYLTL1B, ALG3, and GALNT13 were screened as prognostic genes to construct a risk model for LUAD, and the LUAD patients were divided into high- and low-risk groups. K-M curve suggested that patients with a high-risk score had shorter OS than those with a low-risk score. The ROC analysis demonstrated that the risk model efficiently diagnoses LUAD. Additionally, the proportion of infiltrating aDCs (p < 0.05) and Tgds (p < 0.01) was higher in the high-risk group than in the low-risk group. Spearman's correlation analysis manifested that the prognostic genes (MFNG and ALG3) were significantly correlated with infiltrating immune cells. CONCLUSION: In summary, this study established a novel GTs-related risk model for the prognosis of LUAD patients, providing new therapeutic targets for LUAD. However, the biological role of glycosylation-related genes in LUAD needs to be explored further.

Imperfection-insensitivity quantum random number generator with untrusted daily illumination.

Quantum random number generators (QRNGs) promise secure randomness generation based on the foundational unpredictability of quantum mechanics. However, the unavoidable gaps between theoretical models and practical devices could lead to security invalidation. Recently, a source-independent quantum random number generator (SI-QRNG) has been proposed to solve the issue of uncharacteristic sources. However, in most current analyses of SI-QRNG protocols, the security proofs with imperfect measurements are individual for different factors and very sensitive to small deviations from theoretical models. Here, we establish a unified model for imperfect measurements in the SI-QRNG and provide a tight rate bound based on the uncertainty relation for smooth entropies. Then the performance with large device imperfections is evaluated and the randomness rate in our model can approach a similar order of magnitude of the rate upper bound in common discrete variable QRNGs. In addition, by utilizing the daily illumination and measurement devices with large imperfections, we experimentally demonstrate our scheme at the rate of the order of magnitude of Mbps.

Mode selection in InGaAs/InGaAsP quantum well photonic crystal lasers based on coupled double-heterostructure cavities.

Photonic crystal lasers with a high-Q factor and small mode volume are ideal light sources for on-chip nano-photonic integration. Due to the submicron size of their active region, it is usually difficult to achieve high output power and single-mode lasing at the same time. In this work, we demonstrate well-selected single-mode lasing in a line-defect photonic crystal cavity by coupling it to the high-Q modes of a short double-heterostructure photonic crystal cavity. One of the FP-like modes of the line-defect cavity can be selected to lase by thermo-optically tuning the high-Q mode of the short cavity into resonance. Six FP-like modes are successively tuned into lasing with side mode suppression ratios all exceeding 15 dB. Furthermore, we show a continuous wavelength tunability of about 10 nm from all the selected modes. The coupled cavity system provides a remarkable platform to explore the rich laser physics through the spatial modulation of vacuum electromagnetic field at submicron scale.

System to eliminate the graininess of an integral imaging 3D display by using a transmissive mirror device.

We propose a system to eliminate the graininess of an integral imaging 3D display by using a transmissive mirror device (TMD). The proposed system consists of a 2D display, a micro-lens array (MLA), and a TMD. The TMD comprises square apertures with mirror-reflective inner wall. The light rays pass through the square aperture to form a diffraction spot, and the diffraction light intensity has a Sinc-function distribution. Therefore, the TMD can be used as an optical low-pass filter. In a certain imaging range, the mainlobe of the Sinc-function distribution is almost unchanged. The TMD has the property of a volumetric optical low-pass filter. It can interpolate the interval between discrete 3D pixels. Therefore, the TMD can be used to eliminate the graininess. The resolution of the 3D image is improved by 2.12 times. The experimental results verify the feasibility of the proposed system.