Learning-based lens wavefront aberration recovery.

Wavefront aberration describes the deviation of a wavefront in an imaging system from a desired perfect shape, such as a plane or a sphere, which may be caused by a variety of factors, such as imperfections in optical equipment, atmospheric turbulence, and the physical properties of imaging subjects and medium. Measuring the wavefront aberration of an imaging system is a crucial part of modern optics and optical engineering, with a variety of applications such as adaptive optics, optical testing, microscopy, laser system design, and ophthalmology. While there are dedicated wavefront sensors that aim to measure the phase of light, they often exhibit some drawbacks, such as higher cost and limited spatial resolution compared to regular intensity measurement. In this paper, we introduce a lightweight and practical learning-based method, named LWNet, to recover the wavefront aberration for an imaging system from a single intensity measurement. Specifically, LWNet takes a measured point spread function (PSF) as input and recovers the wavefront aberration with a two-stage network. The first stage network estimates an initial wavefront aberration via supervised learning, and the second stage network further optimizes the wavefront aberration via self-supervised learning by enforcing the statistical priors and physical constraints of wavefront aberrations via Zernike decomposition. For supervised learning, we created a synthetic PSF-wavefront aberration dataset via ray tracing of 88 lenses. Experimental results show that even trained with simulated data, LWNet works well for wavefront aberration estimation of real imaging systems and consistently outperforms prior learning-based methods.

Low-frequency background estimation and noise separation from high-frequency for background and noise subtraction.

In fluorescence microscopy, background blur and noise are two main factors preventing the achievement of high-signal-to-noise ratio (SNR) imaging. Background blur primarily emanates from inherent factors including the spontaneous fluorescence of biological samples and out-of-focus backgrounds, while noise encompasses Gaussian and Poisson noise components. To achieve background blur subtraction and denoising simultaneously, a pioneering algorithm based on low-frequency background estimation and noise separation from high-frequency (LBNH-BNS) is presented, which effectively disentangles noise from the desired signal. Furthermore, it seamlessly integrates low-frequency features derived from background blur estimation, leading to the effective elimination of noise and background blur in wide-field fluorescence images. In comparisons with other state-of-the-art background removal algorithms, LBNH-BNS demonstrates significant advantages in key quantitative metrics such as peak signal-to-noise ratio (PSNR) and manifests substantial visual enhancements. LBNH-BNS holds immense potential for advancing the overall performance and quality of wide-field fluorescence imaging techniques.

Identification of the riboflavin cofactor-binding site in the Vibrio cholerae ion-pumping NQR complex: A novel structural motif in redox enzymes.

The ion-pumping NQR complex is an essential respiratory enzyme in the physiology of many pathogenic bacteria. This enzyme transfers electrons from NADH to ubiquinone through several cofactors, including riboflavin (vitamin B2). NQR is the only enzyme reported that is able to use riboflavin as a cofactor. Moreover, the riboflavin molecule is found as a stable neutral semiquinone radical. The otherwise highly reactive unpaired electron is stabilized via an unknown mechanism. Crystallographic data suggested that riboflavin might be found in a superficially located site in the interface of NQR subunits B and E. However, this location is highly problematic, as the site does not have the expected physiochemical properties. In this work, we have located the riboflavin-binding site in an amphipathic pocket in subunit B, previously proposed to be the entry site of sodium. Here, we show that this site contains absolutely conserved residues, including N200, N203, and D346. Mutations of these residues decrease enzymatic activity and specifically block the ability of NQR to bind riboflavin. Docking analysis and molecular dynamics simulations indicate that these residues participate directly in riboflavin binding, establishing hydrogen bonds that stabilize the cofactor in the site. We conclude that riboflavin is likely bound in the proposed pocket, which is consistent with enzymatic characterizations, thermodynamic studies, and distance between cofactors.

Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.

A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, without flagellum and designated ZYF765T, was isolated from seawater sampled at a depth of 4000 m in the Mariana Trench. Strain ZYF765T grew with 1-15 % (w/v) NaCl (optimum, 4 %), at 16-37 °C (28 °C) and at pH 6.0-10.0 (pH 7.0-8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYF765T formed a lineage within the family Hyphomonadaceae, and was distinct from the most closely related species Glycocaulis abyssi, Glycocaulis albus and Glycocaulis alkaliphilus with 16S rRNA gene sequences similarities ranging from 98.42 to 98.63 %. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids comprised three unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified aminolipid. The predominant fatty acids (more than 10 % of total fatty acids) were C18 : 1ω7c (46.2 %) and C18 : 0 (14.1 %). The DNA G+C content was 67.7 mol%. On the basis of the results of polyphasic taxonomic analysis, strain ZYF765T is considered to represent a novel species within the genus Glycocaulis, for which the name Glycocaulis profundi sp. nov. is proposed. The type strain is ZYF765T (=JCM 33028T=MCCC 1K03554T).

Marinobacter salinexigens sp. nov., a marine bacterium isolated from hadal seawater of the Mariana Trench.

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated ZYF650T, was isolated from the hadal seawater (9600 m) of the Mariana Trench. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ZYF650T formed a lineage within the family Alteromonadaceae that was distinct from the most closely related species Marinobacter mobilis and Marinobacter nitratireducens with 16S rRNA gene sequences similarities of 98.0 and 97.7 %, respectively. Strain ZYF650T showed average nucleotide identity values of 75.7 % with Marinobacter hydrocarbonoclasticus, 73.3 % with Marinobacter mobilis and 79.3 % with Marinobacter nitratireducens, and DNA-DNAhybridization values of 21.5, 21.3 and 22.0 % with M. hydrocarbonoclasticus, M. mobilis and M. nitratireducens, respectively, which were lower than the threshold for species delineation. Strain ZYF650T grew with 0-14 % (w/v) NaCl (optimum, 7-8 %) at a temperature range of 10-45 °C (optimum, 28 °C) and pH 6.0-9.5 (optimum, pH 7.0-8.0). The sole respiratory quinone was ubiquinone-9 (Q-9). The polar lipids in ZYF650T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified polar lipids, two unidentified aminolipids and two phospholipids. The predominant fatty acids (more than 10 % of total fatty acids) were C18 : 1 ω9c (21.9 %), C16 : 0 (21.7 %), C12 : 0 3-OH (14.0 %), C16 : 1 ω9c (13.2 %) and C12 : 0 (12.2 %). The DNA G+C content of strain ZYF650T was 55.6 %. On the basis of polyphasic taxonomic analysis, strain ZY650T is considered to represent a novel specie of the genus Marinobacter in the family Alteromonadaceae, for which the name Marinobacter salinexigens sp. nov. is proposed. The type strain is ZYF650T (=JCM 33013T=MCCC 1K03552T).

Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions.

Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world's health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3-4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.

Background-free wide-field fluorescence imaging using edge detection combined with HiLo.

Fluorescence microscopy has been widely used in the field of biological imaging, but the disturbance of background noise has always been an unavoidable phenomenon. To obtain a background free image, a virtual HiLo based on edge detection (V-HiLo-ED) method for background removing is proposed, which is different from the existing popular software algorithms that obtain the background-free image by subtracting the estimated background, but the background-free image is directly reconstructed by estimating the foreground. Compared with two other popular software-based methods, the wavelet-based background and noise subtraction algorithm (WBNS) and the rolling ball algorithm (RBA), the V-HiLo-ED owns a better quality on achieving background-free imaging. Compared with hardware-based method such as HiLo method, V-HiLo-ED exhibits almost the same performance but faster speed. In combination with light sheet microscopy, the V-HiLo-ED further improves the signal-to-noise ratio of images with thick light-sheet. These experiment results indicate that the V-HiLo-ED owns the potentiality in many other image applications such as endoscopy.

[Impact of provincial infrastructure investment on the vulnerability of social-ecological system in China]. / æˆ‘å›½çœåŸŸåŸºç¡€è®¾æ–½æŠ•å ¥å¯¹ç¤¾ä¼š-生态系统脆弱性的影响.

The impact of infrastructure investment on social-economic system or ecological system has been widely discussed, yet, the overall impact of infrastructure investment on social-ecological system (SES) is still unknown. This study summarized the impact mechanism of infrastructure investment on social ecosystem vulnerability. We first sorted out the impact mechanism of infrastructure investment on SES vulnerability, and then empirically analyzed the effect of provincial infrastructure investment on SES vulnerability by using spatial autocorrelation and spatial econometric models on the basis of accounting provincial per capita infrastructure capital stock and comprehensive evaluation of SES vulnerability. The results showed that the infrastructure capital stock per capita at provincial level increased significantly during 2004-2017, with a spatial pattern that the north was higher than the south and the east/west was higher than the middle in China. The provincial SES vulnerability was improved, with spatial distribution characteristics of gradually getting worse from east to west in China. There was positive spatial correlation between provincial infrastructure investment and SES vulnerability, with aggregation distribution characteristics. There was inverted U-shaped relationship between infrastructure investment and SES vulnerability in China, that was, the appropriate investment of infrastructure at early could decrease SES vulnerability, while over-investment would increase it. Our results revealed the overall impact mechanism and dynamic characteristics of infrastructure investment on SES vulnerability, and could provide theoretical and policy-making support for the coordination of infrastructure construction and SES vulnerability governance at the macro level for China.

Integrated Metabonomics and Network Pharmacology to Reveal the Action Mechanism Effect of Shaoyao Decoction on Ulcerative Colitis.

Background: Traditional Chinese medicine (TCM) has the advantage of multi-component and multi-target, which becomes a hot spot in the treatment of numerous diseases. Shaoyao decoction (SYD) is a TCM prescription, which is mainly used to treat damp-heat dysentery clinically, with small side effects and low cost. However, its mechanism remains elusive. The purpose of this study is to explore the mechanism of SYD in the treatment of mice with ulcerative colitis (UC) induced by dextran sulfate sodium (DSS) through metabolomics and network pharmacology, and verify through molecular docking and immunohistochemistry, so as to provide a scientific basis for the role of SYD in the treatment of UC. Materials and Methods: Firstly, DSS-induced UC models were established and then untargeted metabolomics analysis of feces, livers, serum and urine was performed to determine biomarkers and metabolic pathways closely related to the role of SYD. Besides, network pharmacology was applied to screen the active components and UC-related targets, which was verified by molecular docking. Finally, metabonomics and network pharmacology were combined to draw the metabolite-pathway-target network and verified by immunohistochemistry. Results: Metabolomics results showed that a total of 61 differential metabolites were discovered in SYD-treated UC with 3 main metabolic pathways containing glycerophospholipid metabolism, sphingolipid metabolism and biosynthesis of unsaturated fatty acids, as well as 8 core targets involving STAT3, IL1B, IL6, IL2, AKT1, IL4, ICAM1 and CCND1. Molecular docking demonstrated that the first five targets had strong affinity with quercetin, wogonin, kaempferol and baicalein. Combined with metabolomics and network pharmacology, sphingolipid signaling pathway, PI3K/AKT-mTOR signaling pathway and S1P3 pathway were identified as the main pathways. Conclusion: SYD can effectively ameliorate various symptoms and alleviate intestinal mucosal damage and metabolic disorder in DSS induced UC mice. Its effect is mainly related to sphingolipid metabolism, PI3K/AKT-mTOR signaling pathway and S1P3 pathway.

Distinctive gene expression patterns in pregnancy-associated breast cancer.

Pregnancy-associated breast cancer (PABC) is diagnosed during pregnancy or within 1 year postpartum, but the unique aspects of its etiology and pathogenesis have not been fully elucidated. This study aimed to ascertain the molecular mechanisms of PABC to facilitate diagnosis and therapeutic development. The Limma package was used to characterize the differentially expressed genes in PABC as compared to non-pregnancy-associated breast cancer (NPABC) and normal breast tissue. A total of 871 dysregulated genes were identified in the PABC versus NPABC groups and 917 in the PABC versus normal groups, with notable differences in the expression of MAGE and CXCL family genes. The dysregulated genes between the PABC and normal groups were mainly associated with signal transduction and immune response, while Kyoto Encyclopedia of Genes and Genomes analysis revealed that the dysregulated genes were enriched in immune-related pathways, including the major histocompatibility complex (MHC) class II protein complex, the type I interferon signaling pathway, regulation of α-ß T-cell proliferation, and the T-cell apoptotic process. Through protein-protein interaction network construction, CD44 and BRCA1 were identified as prominent hub genes with differential expression in PABC versus NPABC. Furthermore, a cluster with eleven hub genes was identified in PABC versus normal adjacent tissues, of which the expression of EGFR, IGF1, PTGS2, FGF1, CAV1, and PLCB1 were verified to be differentially expressed in an independent cohort of PABC patients. Notably, IGF1, PTGS2, and FGF1 were demonstrated to be significantly related to patient prognosis. Our study reveals a distinctive gene expression pattern in PABC and suggests that IGF1, PTGS2, and FGF1 might serve as biomarkers for diagnosis and prognosis of PABC.

Metabolomics Study of Shaoyao Plants Decoction on the Proximal and Distal Colon in Mice with Dextran Sulfate Sodium-Induced Colitis by UPLC-Q-TOF-MS.

Purpose: Shaoyao decoction (SYD) is a traditional Chinese medicine used to treat ulcerative colitis (UC). The exact mechanism of action of SYD in UC treatment is still unclear. Here, we examined the therapeutic effects of SYD in mice with dextran sulfate sodium (DSS)-induced colitis and explored the underlying mechanism. Methods: The experimental group was divided into normal control, UC, and SYD treatment groups. The UC model of C57BL/6 mice was induced using 3% (w/v) DSS for 7 days. SYD was orally administered for 7 days. The proximal and distal colonic metabolic profiles were detected using quadrupole-time-of-flight mass spectrometry-based untargeted metabolomics. Results: SYD significantly increased weight, reduced disease activity index scores, and ameliorated colon length shortening and pathological damage in mice. In the distal colon, SYD increased the abundance of phosphatidic acid and lysophosphatidylethanolamine and decreased the abundance of lactosylceramide, erythrodiol 3-palmitate, and lysophosphatidylcholine. In the proximal colon, SYD increased the abundance of palmitic acid, cyclonormammein, monoacylglyceride, 13S-hydroxyoctadecadienoic acid, and ceanothine C and decreased the abundance of tetracosahexaenoic acid, phosphatidylserine, and diglyceride. Conclusion: Our findings revealed that SYD could alleviate UC by regulating metabolic dysfunction, which provides a reference for further studies on SYD.

Sensitive fluorescence biosensor for SARS-CoV-2 nucleocapsid protein detection in cold-chain food products based on DNA circuit and g-CNQDs@Zn-MOF.

SARS-CoV-2 isolation from cold-chain food products confirms the possibility of outbreaks through cold-chain food products. RNA extraction combined with RT-PCR is the primary method currently utilized for the detection of SARS-CoV-2. However, the requirement of hours of analytical time and the high price of RT-PCR hinder its worldwide implementation in food supervision. Here, we report a fluorescence biosensor for detection of SARS-CoV-2 N protein. The fluorescence biosensor was fabricated by aptamer-based conformational entropy-driven circuit where molecular beacon strands were labeled with graphitic carbon nitrides quantum dots@Zn-metal-organic framework (g-CNQDs@Zn-MOF) and Dabcyl. The detection of the N protein was achieved via swabbing followed by competitive assay using a fixed amount of N-48 aptamers in the analytical system. A fluorescence emission spectrum was employed for the detection. The detection limit of our fluorescence biosensor was 1.0 pg/mL for SARS-CoV-2 N protein, indicating very excellent sensitivity. The fluorescence biosensor did not exhibit significant cross-reactivity with other N proteins. Finally, the biosensor was successfully applied for the detection of SARS-CoV-2 N protein in actual cold-chain food products showing same excellent accuracy as RT-PCR method. Thus, our fluorescence biosensor is a promising analytical tool for rapid and sensitive detection of SARS-CoV-2 N protein.

Effects of dietary iron level on growth performance, hematological status, and intestinal function in growing-finishing pigs.

This study investigated the different addition levels of iron (Fe) in growing-finishing pigs and the effect of different Fe levels on growth performance, hematological status, intestinal barrier function, and intestinal digestion. A total of 1,200 barrows and gilts ([Large White × Landrace] × Duroc) with average initial body weight (BW; 27.74 ± 0.28 kg) were housed in 40 pens of 30 pigs per pen (gilts and barrows in half), blocked by BW and gender, and fed five experimental diets (eight replicate pens per diet). The five experimental diets were control diet (basal diet with no FeSO4 supplementation), and the basal diet being supplemented with 150, 300, 450, or 600 mg/kg Fe as FeSO4 diets. The trial lasted for 100 d and was divided into the growing phase (27 to 60 kg of BW) for the first 50 d and the finishing phase (61 to 100 kg of BW) for the last 50 d. The basal diet was formulated with an Fe-free trace mineral premix and contained 203.36 mg/kg total dietary Fe in the growing phase and 216.71 mg/kg in the finishing phase based on ingredient contributions. And at the end of the experiment, eight pigs (four barrows and four gilts) were randomly selected from each treatment (selected one pig per pen) for digesta, blood, and intestinal samples collection. The results showed that the average daily feed intake (P = 0.025), average daily gain (P = 0.020), and BW (P = 0.019) increased linearly in the finishing phase of pigs fed with the diets containing Fe. On the other hand, supplementation with different Fe levels in the diet significantly increased serum iron and transferrin saturation concentrations (P < 0.05), goblet cell numbers of duodenal villous (P < 0.001), and MUC4 mRNA expression (P < 0.05). The apparent ileal digestibility (AID) of amino acids (AA) for pigs in the 450 and 600 mg/kg Fe groups was greater (P < 0.05) than for pigs in the control group. In conclusion, dietary supplementation with 450 to 600 mg/kg Fe improved the growth performance of pigs by changing hematological status and by enhancing intestinal goblet cell differentiation and AID of AA.

Endoscopic nasojejunal feeding tube placement in patients with severe hepatopancreatobiliary diseases: a retrospective study of 184 patients.

BACKGROUND: Total parenteral nutrition (TPN) has been recognized as the mainstay of nutritional support in patients with severe hepatopancreatobiliary (HPB) diseases for decades. However, recent studies advocate the utilization of endoscopic nasojejunal feeding tube placement (ENFTP), rather than the conventional approach. This study was designed to compare the clinical value of ENFTP and TPN in patients with severe HPB diseases. METHODS: Two groups of patients with severe HPB diseases were analyzed retrospectively. One group of 88 patients received ENFTP, and the other 96 received TPN. Routine blood levels, serum glucose and prealbumin, hepatic and renal function, serum lipid, and calcium were measured at baseline and after 1, 2, and 4 weeks of nutritional support. Also, complication rate, mortality, nutritional support time, mechanical ventilation time, mean length of time in intensive care unit, and duration of hospital stay were analyzed. RESULTS: After 4 weeks of nutritional support, the degree of recovery of red blood cells, prealbumin, and blood glucose was greater in the ENFTP than in the TPN group (P<0.05). Furthermore, the ENFTP group showed a lower incidence of septicemia, multiple organ dysfunction syndrome, peri-pancreatic infection, biliary infection, and nosocomial infection, in addition to shorter nutritional support time and hospital stay (P<0.05). CONCLUSIONS: ENFTP is much more effective than TPN in assisting patients with severe HPB diseases to recover from anemia, low prealbumin level, and high serum glucose, as well as in decreasing the rates of various infections (pulmonary infection excluded), multiple organ dysfunction syndrome rate, nutrition support time, and length of hospital stay. Therefore, ENFTP is safer and more economical for clinical application.

A Conserved Glycoside Hydrolase Family 7 Cellobiohydrolase PsGH7a of Phytophthora sojae Is Required for Full Virulence on Soybean.

Phytopathogens deploy glycoside hydrolases (GHs) to disintegrate plant cell walls for nutrition and invasion. However, the pathogenic mechanisms of the majority of GHs in virulence remain unknown, especially in oomycetes. In this study, a Phytophthora sojae gene encodes a GH7 family cellobiohydrolase, named PsGH7a, was identified. PsGH7a was highly induced during the cyst germination and infection stages. PsGH7a is conserved in oomycetes, and shares a high amino acid sequence identity (>85%) within Phytophthora genus. The recombinant PsGH7a catalyzes the hydrolysis of ß-1,4-glucan and avicel, which represent the major components of cellulose in plant cell wall. The mutation of catalytic residue Glu236 to alanine resulted in a lower catalytic activity. In addition, the PsGH7a promotes Phytophthora invasion, while the mutant can not. Notably, PsGH7a protein triggers hypersensitive cell death in diverse plants. PsGH7a knockout mutants were generated via CRISPR/Cas9 system, to investigate its biological function. Compared to wild-type strain P6497, the mutants showed reduced virulence on susceptible soybean, indicates PsGH7a is indispensable to P. sojae virulence.

The aerobic respiratory chain of Pseudomonas aeruginosa cultured in artificial urine media: Role of NQR and terminal oxidases.

Pseudomonas aeruginosa is a Gram-negative γ-proteobacterium that forms part of the normal human microbiota and it is also an opportunistic pathogen, responsible for 30% of all nosocomial urinary tract infections. P. aeruginosa carries a highly branched respiratory chain that allows the colonization of many environments, such as the urinary tract, catheters and other medical devices. P. aeruginosa respiratory chain contains three different NADH dehydrogenases (complex I, NQR and NDH-2), whose physiologic roles have not been elucidated, and up to five terminal oxidases: three cytochrome c oxidases (COx), a cytochrome bo3 oxidase (CYO) and a cyanide-insensitive cytochrome bd-like oxidase (CIO). In this work, we studied the composition of the respiratory chain of P. aeruginosa cells cultured in Luria Broth (LB) and modified artificial urine media (mAUM), to understand the metabolic adaptations of this microorganism to the growth in urine. Our results show that the COx oxidases play major roles in mAUM, while P. aeruginosa relies on CYO when growing in LB medium. Moreover, our data demonstrate that the proton-pumping NQR complex is the main NADH dehydrogenase in both LB and mAUM. This enzyme is resistant to HQNO, an inhibitory molecule produced by P. aeruginosa, and may provide an advantage against the natural antibacterial agents produced by this organism. This work offers a clear picture of the composition of this pathogen's aerobic respiratory chain and the main roles that NQR and terminal oxidases play in urine, which is essential to understand its physiology and could be used to develop new antibiotics against this notorious multidrug-resistant microorganism.