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BACKGROUND: With the rise of large-scale genome sequencing projects, genotyping of thousands of samples has produced immense variant call format (VCF) files. It is becoming increasingly challenging to store, transfer, and analyze these voluminous files. Compression methods have been used to tackle these issues, aiming for both high compression ratio and fast random access. However, existing methods have not yet achieved a satisfactory compromise between these 2 objectives. FINDINGS: To address the aforementioned issue, we introduce GSC (Genotype Sparse Compression), a specialized and refined lossless compression tool for VCF files. In benchmark tests conducted across various open-source datasets, GSC showcased exceptional performance in genotype data compression. Compared with the industry's most advanced tools (namely, GBC and GTC), GSC achieved compression ratios that were higher by 26.9% to 82.4% over GBC and GTC on the datasets, respectively. In lossless compression scenarios, GSC also demonstrated robust performance, with compression ratios 1.5× to 6.5× greater than general-purpose tools like gzip, zstd, and BCFtools-a mode not supported by either GBC or GTC. Achieving such high compression ratios did require some reasonable trade-offs, including longer decompression times, with GSC being 1.2× to 2× slower than GBC, yet 1.1× to 1.4× faster than GTC. Moreover, GSC maintained decompression query speeds that were equivalent to its competitors. In terms of RAM usage, GSC outperformed both counterparts. Overall, GSC's comprehensive performance surpasses that of the most advanced technologies. CONCLUSION: GSC balances high compression ratios with rapid data access, enhancing genomic data management. It supports seamless PLINK binary format conversion, simplifying downstream analysis.
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Compresión de Datos , Programas Informáticos , Compresión de Datos/métodos , Humanos , Genotipo , Biología Computacional/métodos , Algoritmos , Secuenciación de Nucleótidos de Alto Rendimiento/métodosRESUMEN
The inverted metamorphic multi-junction solar cell is anticipated to be widely applied in stratospheric flight because of its exceptional properties of flexibility and light weight. We propose an ipsilateral welding technology based on Ti/Au electrodes to simplify the fabrication process of GaInP/GaAs/InGaAs solar cells and encapsulate large-sized flexible solar cells. After annealing at 200°C for 2 h, the Ti/Au electrode achieved a low specific contact resistivity of 2.9×10-7 Ωâ c m 2. The performance of the ohmic contact remains stable after the thermal cycling tests. The Ti/Au electrode can require less heat input for welding to reduce the risk of microcrack formation of the solar cells. By employment of this electrode, a 24c m 2 solar cell achieved a conversion efficiency of 34.74%. A flexible solar cell module with an efficiency of 32.82% under AM 1.5G illumination was obtained by the ipsilateral electrode welding technology.
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This erratum corrects an error in Fig. 1 of the original paper, Appl. Opt.63, 2815 (2024)APOPAI0003-693510.1364/AO.518102.
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Oral mucositis (OM) is a severe complication of cancer therapies caused by off-target cytotoxicity. Palifermin, which is recombinant human keratinocyte growth factor (KGF), is currently the only mitigating treatment available to a subset of OM patients. This study used a previously established model of oral mucositis on a chip (OM-OC) comprised of a confluent human gingival keratinocytes (GIE) layer attached to a basement membrane-lined subepithelial layer consisting of human gingival fibroblasts (HGF) and human dermal microvascular endothelial cells (HMEC) on a stable collagen I gel. Cisplatin, radiation, and combined treatments are followed by a recovery period in the OM-OC to determine possible cellular and molecular mechanisms of OM under effects of KGF. Cancer treatments affected the keratinocyte layer, causing death and epithelial barrier loss. Both keratinocytes and subepithelial cells died rapidly, as evidenced by propidium iodide staining. In response to radiation exposure, cell death occurred in the apical epithelial layer, predominantly, within 24h. Cisplatin exposure predominantly promoted death of basal epithelial cells within 32-36h. Presence of KGF in OM-OC protected tissues from damage caused by cancer treatments in a dose-dependent manner, being more effective at 10 ng/mL. As verified by F-actin staining and the Alamar Blue assay, KGF contributed to epithelial survival and induced proliferation of GIE and HGF as well as HMEC within 120h. When the expression of eighty inflammatory cytokines is evaluated at OM induction (Day 12) and resolution (Day 18) stages in OM-OC, some cytokines are identified as potential novel therapeutic targets. In comparison with chemoradiation exposure, KGF treatment showed a trend to decrease IL-8 and TNF-a expression at Day 12 and 18, and TGF-ß1 at Day 18 in OM-OC. Taken together, these findings support the utility of OM-OC as a platform to model epithelial damage and evaluate molecular mechanisms following OM treatment.
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Factor 7 de Crecimiento de Fibroblastos , Queratinocitos , Proteínas Recombinantes , Estomatitis , Humanos , Estomatitis/tratamiento farmacológico , Estomatitis/patología , Factor 7 de Crecimiento de Fibroblastos/farmacología , Proteínas Recombinantes/farmacología , Queratinocitos/efectos de los fármacos , Queratinocitos/metabolismo , Cisplatino/farmacología , Neoplasias/tratamiento farmacológico , Encía , Fibroblastos/efectos de los fármacos , Fibroblastos/metabolismoRESUMEN
An ethynyl-modified interpenetrated MOF material with lvt topology, [Cu2(BTEB)(NMF)2]·NMF·8H2O (compound 1, H4BTEB = 4,4',4'',4'''-(benzene-1,2,4,5-tetrayltetrakis(ethyne-2,1-diyl))tetrabenzoic acid, NMF = N-Methylformamide), was successfully synthesized by using an alkynyl-functionalized H4BTEB organic ligand under solvothermal conditions. Structural analysis shows that compound 1, consisting of a tetradentate carboxylic acid ligand and classical [Cu2(CO2)4] paddle-wheel structure building units, has a rare 4-connected lvt topology with dual interpenetrating structure, which can improve the framework stability, as well as the gas adsorption capacity and selectivity due to the restricted pore channel. According to the study of gas adsorption performance, compound 1 with a larger surface area, boasts a superior adsorption capacity for small gas molecules. Also, ideal adsorption solution theory (IAST) computational simulation shows that compound 1 has good gas adsorption selectivity for C3H8/CH4, indicating its potential application in gas separation.
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This study evaluated the effects of defatted superworm (Zophobas atratus) larvae meal (DBWLM) as an alternative protein ingredient for juvenile Pacific white shrimp (Penaeus vannamei). Six isonitrogenous and isolipidic experimental diets were characterized by replacing 0%, 15%, 30%, 45%, 60%, and 75% fish meal (DBWLM0, DBWLM15, DBWLM30, DBWLM45, DBWLM60, and DBWLM75, respectively) with DBWLM on a w/w basis and feeding them to juvenile shrimp (0.34 ± 0.04 g) for 56 days. The results showed that the replacement of up to 75% fish meal by DBWLM had no negative effect on the growth performance of P. vannamei. The survival of shrimp in the DBWLM30 group was the highest, and the weight gain, specific growth rate, feed conversion ratio, condition factor, and apparent digestibility coefficients of dry matter in the DBWLM15 group were the highest. The substitution of DBWLM for fish meal significantly increased the elasticity of flesh, improved the total content of umami amino acids in flesh (aspartic acid, glutamic acid, glycine, and alanine), promoted lipid metabolism in shrimp, and reduced serum lipid levels. With the increase in DBWLM level, serum acid phosphatase, alkaline phosphatase activity, and intestinal inflammatory gene expression (IGF-1 and IL-6) were inhibited, malondialdehyde content decreased, and total antioxidant capacity level and superoxide dismutase activity increased significantly. Histological sections of the hepatopancreas showed that when 60% or more fish meal was replaced, the hepatopancreas atrophied and had irregular lumen distortion, but the cell membrane was not damaged. Microbiome analysis showed that the abundance of Bacteroidetes and Firmicutes increased and the abundance of Proteobacteria decreased in the DBWLM replacement group, and it was rich in "metabolism"-related functional pathways. It is worth mentioning that the expression of amino-acid-related enzymes was upregulated in the DBWLM15 and DBWLM30 groups, and the DBWLM75 group inhibited the biosynthesis of steroids and hormones. To conclude, the replacement of 15%-45% fish meal with DBWLM can result in better growth and immune status, improved meat elasticity, and reduced inflammation in P. vannamei. However, it is recommended that the replacement level should not exceed 60%, otherwise it will cause atrophy of hepatopancreas cells.
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Purpose: To develop a deep learning approach that enables ultra-low-dose, 1% of the standard clinical dosage (3 MBq/kg), ultrafast whole-body PET reconstruction in cancer imaging. Materials and Methods: In this Health Insurance Portability and Accountability Act-compliant study, serial fluorine 18-labeled fluorodeoxyglucose PET/MRI scans of pediatric patients with lymphoma were retrospectively collected from two cross-continental medical centers between July 2015 and March 2020. Global similarity between baseline and follow-up scans was used to develop Masked-LMCTrans, a longitudinal multimodality coattentional convolutional neural network (CNN) transformer that provides interaction and joint reasoning between serial PET/MRI scans from the same patient. Image quality of the reconstructed ultra-low-dose PET was evaluated in comparison with a simulated standard 1% PET image. The performance of Masked-LMCTrans was compared with that of CNNs with pure convolution operations (classic U-Net family), and the effect of different CNN encoders on feature representation was assessed. Statistical differences in the structural similarity index measure (SSIM), peak signal-to-noise ratio (PSNR), and visual information fidelity (VIF) were assessed by two-sample testing with the Wilcoxon signed rank t test. Results: The study included 21 patients (mean age, 15 years ± 7 [SD]; 12 female) in the primary cohort and 10 patients (mean age, 13 years ± 4; six female) in the external test cohort. Masked-LMCTrans-reconstructed follow-up PET images demonstrated significantly less noise and more detailed structure compared with simulated 1% extremely ultra-low-dose PET images. SSIM, PSNR, and VIF were significantly higher for Masked-LMCTrans-reconstructed PET (P < .001), with improvements of 15.8%, 23.4%, and 186%, respectively. Conclusion: Masked-LMCTrans achieved high image quality reconstruction of 1% low-dose whole-body PET images.Keywords: Pediatrics, PET, Convolutional Neural Network (CNN), Dose Reduction Supplemental material is available for this article. © RSNA, 2023.
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Aboveground transmission oil pipelines can cross debris flow-prone areas. Currently, there are no available methodologies to assess pipeline failure status with the different pipeline arrangements (location, direction, and segment lengths) and different operating conditions. For solving the research gap, this study proposes a novel methodology to simulate the cascade processes of debris flow propagation, the impact of debris flow on pipelines, and pipeline failure. With consideration of different pipeline arrangement and operating conditions. We introduce the polar coordinate system to set up locations and directions scenarios for the first time. Also, we use the 3-D debris flow simulation model (DebrisInterMixing solver in OpenFOAM) coupled with a modified pipeline mechanical model considering operating conditions for the first time. The proposed methodology shows the different trends of pipeline failure probability with the increase of pipeline segment length for the different pipeline locations and directions. The result shows, for the pipelines of 30° the tensile stress has a more moderate increase rate with the increase of pipeline segment length, and the pipeline failure probability keeps 0 at the 5-m location. At 5 m and 15 m locations, the failure probabilities of the pipelines of 60° and 90° start to increase when the segment length is 13-14 m, while for other pipelines the segment length is 17-19 m. The findings of this study can support the decisions of government authorities, stakeholders, and operators for risk assessment, prioritization of hazard mitigation measures and emergency planning, or concerning decisions regarding pipeline siting during the design, routing, construction, operation, and maintenance stage.
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The extended damp heat and thermal cycling tests were performed on unencapsulated flexible thin-film GaInP/GaAs/InGaAs solar cells to assess the long-term stability. The solar cells were subjected to 85 °C/85% damp heat test for more than 1000 h and 420 cycles of thermal cycling test between -60 °C and 75 °C, respectively. The performance attenuations of flexible solar cells were less than 2% in both cases, which were due to the slow decline of the open-circuit voltage with aging time. The slight decrease in open voltage was attributed to the increase in reverse saturation current due to the enhanced recombination, which was in good agreement with the calculation based on the two-diode model. The good performance of the unencapsulated flexible GaInP/GaAs/InGaAs solar cells in severe environment indicated the stable and reliable device fabrication art in the experiment.
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Microfluidic-integrated freestanding membranes with suitable biocompatibility and tunable physicochemical properties are in high demand for a wide range of life science and biological studies. However, there is a lack of facile and rapid methods to integrate such versatile membranes into microfluidics. A recently invented interfacial electrofabrication of chitosan membranes offers an in-situ membrane integration strategy that is flexible, controllable, simple, and biologically friendly. In this follow-up study, we explored the ability to program the physical properties of these chitosan membranes by varying the electrofabrication conditions (e.g., applied voltage and pH of alginate). We found a strong association between membrane growth rate, properties, and fabrication parameters: high electrical stimuli and pH of alginate resulted in high optical retardance and low permeability, and vice versa. This suggests that the molecular alignment and density of electrofabricated chitosan membranes could be actively tailored according to application needs. Lastly, we demonstrated that this interfacial electrofabrication could easily be expanded to produce chitosan membrane arrays with higher uniformity than the previously well-established flow assembly method. This study demonstrates the tunability of the electrofabricated membranes' properties and functionality, thus expanding the utility of such membranes for broader applications in the future.
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Biofilms are found in many infections in the forms of surface-adhering aggregates on medical devices, small clumps in tissues, or even in synovial fluid. Although antibiotic resistance genes are studied and monitored in the clinic, the structural and phenotypic changes that take place in biofilms can also lead to significant changes in how bacteria respond to antibiotics. Therefore, it is important to better understand the relationship between biofilm phenotypes and resistance and develop approaches that are compatible with clinical testing. Current methods for studying antimicrobial susceptibility are mostly planktonic or planar biofilm reactors. In this work, we develop a new type of biofilm reactor-three-dimensional (3D) microreactors-to recreate biofilms in a microenvironment that better mimics those in vivo where bacteria tend to form surface-independent biofilms in living tissues. The microreactors are formed on microplates, treated with antibiotics of 1000 times of the corresponding minimal inhibitory concentrations (1000 × MIC), and monitored spectroscopically with a microplate reader in a high-throughput manner. The hydrogels are dissolvable on demand without the need for manual scraping, thus enabling measurements of phenotypic changes. Bacteria inside the biofilm microreactors are found to survive exposure to 1000 × MIC of antibiotics, and subsequent comparison with plating results reveals no antibiotic resistance-associated phenotypes. The presented microreactor offers an attractive platform to study the tolerance and antibiotic resistance of surface-independent biofilms such as those found in tissues.
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Segmenting dental plaque from images of medical reagent staining provides valuable information for diagnosis and the determination of follow-up treatment plan. However, accurate dental plaque segmentation is a challenging task that requires identifying teeth and dental plaque subjected to semantic-blur regions (i.e., confused boundaries in border regions between teeth and dental plaque) and complex variations of instance shapes, which are not fully addressed by existing methods. Therefore, we propose a semantic decomposition network (SDNet) that introduces two single-task branches to separately address the segmentation of teeth and dental plaque and designs additional constraints to learn category-specific features for each branch, thus facilitating the semantic decomposition and improving the performance of dental plaque segmentation. Specifically, SDNet learns two separate segmentation branches for teeth and dental plaque in a divide-and-conquer manner to decouple the entangled relation between them. Each branch that specifies a category tends to yield accurate segmentation. To help these two branches better focus on category-specific features, two constraint modules are further proposed: 1) contrastive constraint module (CCM) to learn discriminative feature representations by maximizing the distance between different category representations, so as to reduce the negative impact of semantic-blur regions on feature extraction; 2) structural constraint module (SCM) to provide complete structural information for dental plaque of various shapes by the supervision of an boundary-aware geometric constraint. Besides, we construct a large-scale open-source Stained Dental Plaque Segmentation dataset (SDPSeg), which provides high-quality annotations for teeth and dental plaque. Experimental results on SDPSeg datasets show SDNet achieves state-of-the-art performance.
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Placa Dental , Humanos , Placa Dental/diagnóstico por imagen , Semántica , Coloración y EtiquetadoRESUMEN
Microbes are typically found in multi-species (polymicrobial) communities. Cooperative and competitive interactions between species, mediated by diffusible factors and physical contact, leads to highly dynamic communities that undergo changes in composition diversity and size. Infections can be more severe or more difficult to treat when caused by multiple species. Interactions between species can improve the ability of one or more species to tolerate anti-microbial treatments and host defenses. Pseudomonas aeruginosa (Pa), a ubiquitous bacterium, and the opportunistic pathogenic yeast, Candida albicans (Ca), are frequently found together in cystic fibrosis lung infections and wound infections. While significant progress has been made in determining interactions between Pa and Ca, there are still important questions that remain unanswered. Here, we probe the mutual interactions between Pa and Ca in a custom-made microfluidic device using biopolymer chitosan membranes that support cross-species communication. By assembling microbes in physically separated, chemically communicating populations or bringing into direct interactions in a mixed culture, in situ polymicrobial growth and biofilm morphology were qualitatively characterized and quantified. Our work reveals new dynamic details of their mutual interactions including cooperation, competition, invasion, and biofilm formation. The membrane-based microfluidic platform can be further developed to understand the polymicrobial interactions within a controlled interactive microenvironment to improve microbial infection prevention and treatment.
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Candida albicans , Pseudomonas aeruginosa , Microfluídica , BiopelículasRESUMEN
Oral mucositis (OM) is a debilitating complication affecting roughly 70% of head and neck cancer patients receiving chemotherapy and/or radiation treatment. No broadly effective preventative treatment for OM exists. Therefore, anin vitromodel of cancer treatment-induced OM would aid studies into possible origins of the pathology and future drug targets to ameliorate it. In this study, we present a microfluidic oral mucosa triculture tissue construct consisting of a keratinocyte layer attached to a subepithelial fibroblast and endothelial cell-embedded collagen gel. To address the typically low stability of mucosal constructs in microfluidics, ruthenium-catalyzed photocrosslinking was implemented to strengthen the collagen gel and prevent the invasion of keratinocytes, thus maintaining tissue construct geometry and oral mucosa barrier function for over 18 d of culture. Next, the OM chip was exposed to cisplatin (day 10) and damaging radiation (day 11, ± cisplatin at day 10), mimicking damage from cancer therapy. Damage to and then recovery of the tissue layers and function were observed over days 11-18. Therefore, several important features of OM induction and resolution were modeled in microfluidic culture. The OM model on a chip allows for more sophisticated studies into mechanisms of OM and potential treatments.
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Rutenio , Estomatitis , Humanos , Cisplatino/efectos adversos , Rutenio/efectos adversos , Dispositivos Laboratorio en un Chip , Estomatitis/inducido químicamente , Estomatitis/tratamiento farmacológico , Mucosa BucalRESUMEN
Chemotaxis is a fundamental bacterial response mechanism to changes in chemical gradients of specific molecules known as chemoattractant or chemorepellent. The advancement of biological platforms for bacterial chemotaxis research is of significant interest for a wide range of biological and environmental studies. Many microfluidic devices have been developed for its study, but challenges still remain that can obscure analysis. For example, cell migration can be compromised by flow-induced shear stress, and bacterial motility can be impaired by nonspecific cell adhesion to microchannels. Also, devices can be complicated, expensive, and hard to assemble. We address these issues with a three-channel microfluidic platform integrated with natural biopolymer membranes that are assembled in situ. This provides several unique attributes. First, a static, steady and robust chemoattractant gradient was generated and maintained. Second, because the assembly incorporates assembly pillars, the assembled membrane arrays connecting nearby pillars can be created longer than the viewing window, enabling a wide 2D area for study. Third, the in situ assembled biopolymer membranes minimize pressure and/or chemiosmotic gradients that could induce flow and obscure chemotaxis study. Finally, nonspecific cell adhesion is avoided by priming the polydimethylsiloxane (PDMS) microchannel surfaces with Pluronic F-127. We demonstrated chemotactic migration of Escherichia coli as well as Pseudomonas aeruginosa under well-controlled easy-to-assemble glucose gradients. We characterized motility using the chemotaxis partition coefficient (CPC) and chemotaxis migration coefficient (CMC) and found our results consistent with other reports. Further, random walk trajectories of individual cells in simple bright field images were conveniently tracked and presented in rose plots. Velocities were calculated, again in agreement with previous literature. We believe the biopolymer membrane-integrated platform represents a facile and convenient system for robust quantitative assessment of cellular motility in response to various chemical cues.
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Quimiotaxis , Técnicas Analíticas Microfluídicas , Biopolímeros , Factores Quimiotácticos , Quimiotaxis/fisiología , Escherichia coli/fisiología , MicrofluídicaRESUMEN
Purpose: DNA methylation heterogeneity is a type of tumor heterogeneity in the tumor microenvironment, but studies on the identification of the molecular heterogeneity of the lung adenocarcinoma genome with respect to DNA methylation sites and their roles in lung cancer progression and prognosis are scarce. Methods: Prognosis-associated DNA methylation subtypes were filtered by the Cox proportional hazards model and then established by unsupervised cluster analysis. Association analysis of these subtypes with clinical features and functional analysis of annotated genes potentially affected by methylation sites were performed. The robustness of the model was further tested by a Bayesian network classifier. Results: Over 7 thousand methylation sites were associated with lung adenocarcinoma prognosis. We identified seven molecular methylation subtypes, including 630 methylation sites. The subtypes yielded the most stable results for differentiating methylation profiles, prognosis, and gene expression patterns. The annotated genes potentially affected by these methylation sites are enriched in biological processes such as morphogenesis and cell adhesion, but their individual impact on the tumor microenvironment and prognosis is multifaceted. Discussion. We revealed that DNA methylation heterogeneity could be clustered and associated with the clinical features and prognosis of lung adenocarcinoma, which could lead to the development of a novel molecular tool for clinical evaluation.
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Adenocarcinoma del Pulmón , Neoplasias Pulmonares , Adenocarcinoma del Pulmón/genética , Teorema de Bayes , Biomarcadores de Tumor/genética , Metilación de ADN , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patología , Pronóstico , Microambiente Tumoral/genéticaRESUMEN
Phospholipids have an important antioxidant effect on animals. The effects of different dietary phospholipid sources on the growth, antioxidant activity, immunity, and gut microbiota of female broodstock of Pacific white shrimp Litopenaeus vannamei were investigated. Four isoproteic and isolipid semi-purified diets containing 4% soybean lecithin (SL), egg yolk lecithin (EL), or krill oil (KO) and a control diet without phospholipid supplementation were fed to female broodstock of L. vannamei (34.7 ± 4.2 g) for 28 days. The growth performance, antioxidative capacity, and innate immunity of the female broodstock fed phospholipid supplemented diets were improved regardless of sources compared with the control shrimp. The effects on growth and antioxidant capacity in female shrimp fed the KO diet were highest. The innate immunity of female shrimp fed the EL and KO diets were significantly higher than shrimp fed the SL diet. Dietary phospholipid supplementation increased gut microbiota diversity and richness, and the Chao1 and ACE values in the KO group were significantly higher than in the control group. The richness of Proteobacteria, Photobacterium, and Vibrio decreased, whereas the richness of Firmicutes and Bacteroidetes increased in the shrimp fed the KO diet compared with the shrimp fed the SL and EL diets. The interactions of gut microbiota in shrimp fed the KO diet were the most complex, and the positive interaction was the largest among all the treatments. The functional genes of gut microbiota in shrimp fed the KO diet were significantly enriched in lipid metabolism and terpenoid/polyketide metabolism pathways. Spearman correlation analysis showed that Fusibacter had significantly positive correlations with antioxidant activity (total antioxidant capacity, superoxide dismutase, glutathione peroxidase), immune enzyme activity (phenoloxidase and lysozyme), and immune gene expression (C-type lectin 3, Caspase-1). All findings suggest that dietary phospholipids supplementation can improve the growth and health status of female L. vananmei broodstock. Krill oil is more beneficial in improving the antioxidant capacity and innate immunity than other dietary phospholipid sources. Furthermore, krill oil can help establish the intestinal immune barrier by increasing the richness of Fusibacter and promote the growth of female shrimp. Fusibacter may be involved in iron metabolism to improve the antioxidant capacity of female shrimp.
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Optical phase and birefringence signals occur in cells and thin, semi-transparent biomaterials. A dual-modality quantitative phase and polarization microscope was designed to study the interaction of cells with extracellular matrix networks and to relate optical pathlength and birefringence signals within structurally anisotropic biomaterial constructs. The design was based on an existing, custom-built digital holographic microscope, to which was added a polarization microscope utilizing liquid crystal variable retarders. Phase and birefringence channels were calibrated, and data was acquired sequentially from cell-seeded collagen hydrogels and electrofabricated chitosan membranes. Computed phase height and retardance from standard targets were accurate within 99.7% and 99.8%, respectively. Phase height and retardance channel background standard deviations were 35â nm and 0.6â nm, respectively. Human fibroblasts, visible in the phase channel, aligned with collagen network microstructure, with retardance and azimuth visible in the polarization channel. Electrofabricated chitosan membranes formed in 40 µm tall microfluidic channels possessed optical retardance ranging from 7 to 11â nm, and phase height from 37 to 39 µm. These results demonstrate co-registered dual-channel acquisition of phase and birefringence parameter maps from microstructurally-complex biospecimens using a novel imaging system combining digital holographic microscopy with voltage-controlled polarization microscopy.
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Research on nutrition and feed development for the broodstock of the Pacific white shrimp, Litopenaeus vannamei, is rare, and a poor broodstock quality is a critical factor restricting the seed supply in shrimp farming. As an essential nutrient for the gonadal development of L. vannamei, one control diet (no phospholipid) and three typical phospholipids (soybean lecithin, egg yolk lecithin, and krill oil) were evaluated in a semipurified diet of 4% phospholipid for a 28-day trial (initial weight 34.7 ± 4.2 g). Dietary phospholipid supplementation significantly promoted the ovarian maturation of female L. vannamei. Compared with soybean lecithin and egg yolk lecithin, krill oil showed the best positive results. Shrimp fed with a diet krill oil has obtained a significantly higher gonadosomatic index, yolk particle deposition, lipid accumulation, and estrogen secretion than from other sources. Ovary lipidomic analysis showed that the krill oil enriched the lipid composition of the ovary. The "glycerophospholipid metabolism" and "sphingolipid metabolism" pathways were significantly varied via topological pathway analysis. Genes and hub genes, with significantly different expression levels, were significantly enriched in the "fatty acid metabolism pathway," "glycerophospholipid metabolism," and "arachidonic acid metabolism" pathways by transcriptomic analysis. Correlation analysis of the transcriptome and lipidomics showed that the differential gene "hormone-sensitive lipase-like" (HSL) was positively correlated with various lipids [triglycerides (TG), phosphatidic acid (PA), phosphatidylserine (P), phosphatidylethanolamine (PE), glucosylceramide (GlcCer), phosphatidylglycerol (PG), and phosphatidylinositol (PI)] but was negatively correlated with diacylglycerol (DG), lysophosphatidylethanolamine (LPE), and sphingomyelin (SM). In conclusion, the dietary phospholipids, especially krill oil as a phospholipid source, can promote the development of L. vannamei ovaries by increasing the accumulation of nutrients such as triglycerides and sterols, and the secretion of estrogen or related hormones, such as estradiol and methylfarneside, by affecting the metabolism of glycerol phospholipids and some key fatty acids.
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Recently, more and more cold flowing water aquaculture has been adopted, but its wastewater treatment is always ignored, which causes great pressure on the environment. In this study, a compound in-situ treatment system that applied hydroponic plants and biofilm was constructed to treat the wastewater produced by cold flowing water culture of sturgeon. The removal efficiency of the nutrients from culture and the microbial composition in water and biofilm were tested, the correlation between the water quality indexes and bacterium was analyzed, and the abundance of nitrogen and phosphorus cycling genes was quantified. The results show that the system respectively achieved 90%, 100%, 100%, 100% and 48% removal efficiency of NH4+-N, NO3--N, TN, TP and COD which were produced by experimental sturgeon culture. Chinese cabbage (Brassica rapa var. chinensis) and water dropwort (Oenanthe javanica) showed obvious growth in the four plants, which contributed to the removal of nutrients from wastewater. Besides, in the biofilm, Proteobacteria, Bacteroidetes and Verrucomicrobia became the top three dominant flora at the phylum level, and Flavobacterium, Rhodoferax, Sphaerotilus and Chitinimonas became the top four dominant flora at the genus level, which promoted the removal of nitrogen in the wastewater. The FAPROTAX analysis result shows that the highest functions within the carbon and nitrogen metabolisms were significantly identified in the biofilm, such as chemoheterotrophy, aerobic chemoheterotrophy and nitrate reduction. Further, the abundance of denitrifying genes (narG and napA) was higher than the nitrifying related genes (nxrB and amoA), indicating the more active denitrifying process. In summary, the compound in-situ treatment system efficiently removed nutrients from cold flowing water aquaculture. And the combined purification of hydroponic plants and biofilm which is rich in denitrifying bacterium plays an essential role in this process.