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Abstract To address the issues of high demand for efficiently recognizing fish species in marine scientific research, such as impact assessments on biodiversity and monitoring, an automated hierarchical image classification web‐based platform, named FishAI, was developed. Trained with marine fish images collected from the World Register of Marine Species, FishAI used the Vision Transformer (ViT) model, to classify fish. The model considers hierarchy levels, covering 3 classes, 38 orders, 154 families, 438 genera, and 808 species. The FishAI achieved accuracies of 0.975 (Class), 0.798 (Order), 0.743 (Family), 0.638 (Genus), and 0.626 (Species) on test images, respectively, by using the hyperparameter optimization. Comparison between ViT and other baseline backbones proves its superiority by capturing long‐distance dependency. In addition, FishAI yields the top‐5 prediction accuracies of 1.000 (Class), 0.887 (Order), 0.816 (Family), 0.729 (Genus), and 0.727 (Species), respectively. In order to further enhance the practicality of FishAI, the user‐friendly graphic interface (http://www.csbio.sjtu.edu.cn/bioinf/FishAI/) facilitates its easy‐to‐use application. Furthermore, interpretability analysis by Grad‐CAM provides a visual explanation of the highlighted regions on the images for FishAI's prediction among different hierarchies.

Most studies on the genesis of polymetallic nodules suggested that nodules in the South China Sea (SCS) are hydrogenetic; however, the complexity and the heterogeneity in hydrology and geochemistry of the SCS might cause different processes of nodule formation, impacting their application and economic value. Microbial-mediated ferromanganese deposition is an important process in nodule formation, but the related microbial potentials are still unclear in the SCS. In this study, we sampled in three typical regions (A, B, and C) of the SCS enriched with polymetallic nodules. Firstly, we investigated environmental and microbial characteristics of the water columns to determine the heterogeneity of upper seawater that directly influenced deep-sea environments. Then, microbial compositions and structures in sediment cores, overlying waters, and nodules (inside and outside) collected within the same region were analyzed for inferring features of nodule environments. Microbial interactions between nodules and surrounding environments were estimated with collinear network analysis. The microbial evidence indicated that geochemical characteristics in deep sea of the SCS that were key to the polymetallic nodule formation were severely affected by organic matter flux from upper water column. The sediment in region A was sub-oxic due to the large input of terrigenous and phytoplankton-derived organic matter, potentially enhancing the overflow of reduced metals from the porewater. The intense microbial interaction between nodules and surface sediment reinforced the origin of metals for the ferromanganese deposition from the sediment (diagenetic type). Contrarily, the sediments in regions B and C were relatively rich in oxygen, and metal ions could be majorly supplied from seawater (hydrogenetic type). The large discrepancy in microbial communities between nodule inside and remaining samples suggested that nodules experienced a long-term formation process, consistent with the feature of hydrogenetic nodules. Overall, distributions and interactions of microbial communities in nodules and surrounding environments significantly contributed to the nodule formation in the SCS by manipulating biogeochemical processes that eventually determined the source and the fate of metal ions.

ObjectiveIn this study, the impact of inhibiting the PI3K/AKT/NF-κB pathway on lung oxidative damage induced by Echinococcus granulosus cyst fluid was investigated.MethodsTwenty-four mice were randomly assigned to four groups. Three months after inoculation with hydatid cyst segments, mice in group A were treated with intraperitoneal and intratracheal saline injections; mice in group B were administered a caudal vein injection of a PI3K inhibitor, followed by cyst fluid sensitization; mice in group C received an AKT inhibitor via caudal vein, followed by cyst fluid sensitization; and mice in group D were subjected to cyst fluid sensitization without any inhibitor treatment. Cellular changes in lung tissues across all groups were evaluated, including pathological section analysis. Analysis of pulmonary tissue and serum from these mice included the assessment of PI3K/AKT/NF-κB pathway proteins, inflammatory factors, and related mRNA levels.ResultsMice in groups B and C exhibited a higher proportion of M2-type macrophages and significantly lower levels of PI3K/AKT/NF-κB pathway proteins, inflammatory factors (interleukin-6 [IL-6]/tumor necrosis factor-α [TNF-α]), and oxidative markers in lung tissues compared to mice in group D (P < 0.05).ConclusionOur results in this study indicate that activation of the PI3K/AKT/NF-κB pathway contributed to an increase in the M1 macrophage phenotype, leading to enhanced secretion of peroxidases and inflammatory factors. This mechanism plays a crucial role in the oxidative and inflammatory lung damage associated with allergic reactions to E. granulosus cyst fluid.

Abstract Objective To determine the pathogenesis and molecular targets of anaphylaxis caused by hydatid cyst fluid leakage. Methods First, Balb/c mice were infected with Echinococcus granulosus, and then the anaphylaxis model was developed. The mice were separated into: anaphylaxis caused by the cystic echinococcosis group (ANPC), the cystic echinococcosis without anaphylaxis group (CE group), and the normal control group (CTRL). Following this, the spleen tissue was collected for microRNA (miRNA) sequencing. Using bioinformatics analysis, differentially expressed miRNAs (DEMs) were identified. Then, through the use of protein–protein interaction (PPI) networks, the key target genes for miRNA regulation associated with echinococcosis‐induced anaphylaxis were identified. Results ANPC and CE groups have 29 and 39 DEMs compared to the CTRL group, respectively. Based on these 25 DEMs, interactions between miRNA and mRNA were screened, and 174 potential target genes were identified. We performed gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on these 174 target genes, and the results revealed that the three pathways with the highest enrichment were the PI3K‐Akt signaling pathway, FoxO signaling pathway, and Focal adhesion. The interaction analysis of PPI and miRNA‐hub gene networks revealed that interleukin 6 (IL‐6) was regulated by miR‐146a‐5p and miR‐149‐5p, while IL‐10 was regulated by miR‐29b‐3p and miR‐29c‐3. Using reverse transcription polymerase chain reaction, we found that the miRNAs regulating IL‐6 and IL‐10 were significantly upregulated in the ANPC group, and there are three pathways involved in that process: Pathways of PI3K‐Akt signaling, FoxO signaling, and Focal adhesion. IL‐6 and IL‐10 play an important role in cellular pyroptosis and apoptosis. Therefore, the aforementioned results provide significant reference value for elucidating the mechanism of cellular pyroptosis and apoptosis in echinococcosis‐induced anaphylaxis, and for formulating tissue and organ protection strategies for patients with cystic echinococcosis when anaphylaxis is triggered by hydatid cyst rupture.

IntroductionIn response to the need for automated classification in global marine biological studies, deep learning is applied to image-based classification of marine echinoderms.MethodsImages of marine echinoderms are collected and classified according to their systematic taxonomy. The images belong to 5 classes, 38 orders, 145 families, 459 genera, and 1021 species, respectively. The deep learning model, EfficientNetV2, outperforms the competing model and is chosen for developing the automated classification tool, EchoAI. Then, the EfficientNetV2-based tool, EchoAI is applied to each taxonomic level.ResultsThe accuracy for the test dataset was 0.980 (class), 0.876 (order), 0.738 (family), 0.612 (genus), and 0.469 (species), respectively. Online prediction service is provided.DiscussionThe EchoAI model and results are facilitated for investigating the diversity, abundance and distribution of species at the global scale, and the methodological strategy can also be applied to image classification of other categories of marine organisms, which is of great significance for global marine studies. EchoAI is freely available at http://www.csbio.sjtu.edu.cn/bioinf/EchoAI/ for academic use.

IntroductionSoil microorganisms are the key factors in elucidating the effects of thinning on tree growth performance, but the effects of vegetation and soil on the species composition and function of soil microorganisms after thinning are still not well elaborated.MethodsThe effects of thinning on understory vegetation diversity, soil physicochemical properties and soil microbial community composition were investigated in a thinning trial plantation of Cryptomeria japonica var. sinensis, including four thinning intensities (control: 0%, LIT: 20%, MIT: 30% and HIT: 40%), and the relationships of the microbial community structure with the understory vegetation diversity and soil properties were assessed.ResultsThe results showed that thinning had a greater effect on the diversity of the shrub layer than the herb layer. The soil bulk density and the contents of soil organic matter, total potassium and nitrogen increased with increasing thinning intensities. The Shannon and Chao indices of soil bacteria and fungi were significantly lower in the LIT, MIT and HIT treatments than in the control. Thinning can significantly increase the abundance of Proteobacteria and Actinobacteria, and higher thinning intensities led to a higher relative abundance of Ascomycota and a lower relative abundance of Basidiomycota, Rozellomycota, and Mortierellomycota. Redundancy analysis indicated that soil physicochemical properties rather than understory vegetation diversity were the main drivers of microbial communities, and fungi were more sensitive to soil properties than bacteria. Functional prediction showed that thinning significantly reduced the potential risk of human diseases and plant pathogens, and the nitrogen fixation capacity of bacteria was the highest in the HIT treatment. Thinning significantly increased the relative abundance of cellulolysis and soil saprotrophs in bacteria and fungi.ConclusionThe findings provide important insights into the effects of thinning on C. japonica var. sinensis plantation ecosystems, which is essential for developing thinning strategies to promote their ecological and economic benefits.

In order to explore the actual change in the particle size distribution of the dispersed phase water droplets of the water-in-oil emulsion in the electric field demulsification process, and obtain the optimal electric field parameters according to the change rules of the particle sizes, a dynamic test evaluation system for high-voltage electric field demulsification was set up with a self-developed compact tubular high-voltage electric field coalescer, a G600 focused beam reflectance measurement instrument and a high-frequency/high-voltage pulsed AC power supply. On the basis of testing and verifying the effectiveness of the evaluation system, tests of evaluation for the impact of the electric field intensity, frequency, duty cycle and water content on the performance of the compact tubular high-voltage electric field coalescer were conducted systematically. The test results indicate that: for the prepared white oil emulsion with a water content of 30%, the optimal combination of electric field parameters for demulsification comprises an electric field intensity of 1.2 kV/cm, a frequency of 1 500 Hz and a duty cycle of 45%. With the water content of the white oil emulsion changed to 20% and 40% successively, the optimal electric field intensities obtained are 1.65 kV/cm and 1.05 kV/cm, and the optimal frequencies are 2 000 Hz and 1 500 Hz respectively, which indicates that the optimal electric field intensity decreases gradually with the water content of the emulsion increasing. Meanwhile, the optimal frequency also presents a trend of decreasing. The self-developed test evaluation system and the evaluation method for high-voltage electric field demulsification can accurately and effectively characterize the change rules of the particles size distribution of the dispersed phase in the emulsion.

Objectives: Acute type A aortic dissection (aTAAD) is usually lethal without emergency surgery. Although veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is widely used in patients with cardiogenic shock following cardiac surgery, VA-ECMO support following aTAAD surgery has not been well-described. Based on our 6-year experience, we aimed to retrospectively analyze risk factors, application and timing of VA-ECMO, and outcomes in aTAAD patients.Methods: In this retrospective, single-center study, we enrolled adult patients who underwent aTAAD surgery from January 2014 to December 2019 and were supported with VA-ECMO. Patients were divided into two groups according to whether or not they were successfully weaned from VA-ECMO. Preoperative, intraoperative and postoperative variables were assessed and analyzed. Outcomes of the patients were followed up until discharge.Results: Twenty-seven patients who received aTAAD surgery with VA-ECMO support were included in the study. Nine patients (33.3%) were successfully weaned from VA-ECMO. The median VA-ECMO support time and length of hospital stay in the successfully weaned group were significantly longer than in the group could not be successfully weaned (192 [111–327] vs. 55 [23–95] h, p < 0.01; 29 [18–40] vs. 4 [3–8] days, p < 0.01). Overall in-hospital mortality was 81.5%. The main causes of death were bleeding (37%), neurological complications (15%), and multiple organ dysfunction syndrome (15%). Preoperative levels of creatine kinase-MB (CK-MB) were lower in patients who were successfully weaned from VA-ECMO than in the failed group (14 [6–30] vs. 55 [28–138] U/L, p < 0.01). Postoperative peak levels of CK-MB, cardiac troponin T, lactate dehydrogenase, and lactate were significantly lower in the successful group than in the failed group.Conclusion: Postoperative VA-ECMO support was rarely used in aTAAD patients. Our study showed that VA-ECMO can be considered as a salvage treatment in aTAAD patients, despite the high rate of complications and mortality.

Abstract Croceicoccus marinus E4A9Twas isolated from deep-sea sediment collected from the East Pacific polymetallic nodule area. The strain is able to produce esterase, which is widely used in the food, perfume, cosmetic, chemical, agricultural and pharmaceutical industries. Here we describe the characteristics of strain E4A9, including the genome sequence and annotation, presence of esterases, and metabolic pathways of the organism. The genome of strain E4A9T comprises 4,109,188 bp, with one chromosome (3,001,363 bp) and two large circular plasmids (761,621 bp and 346,204 bp, respectively). Complete genome contains 3653 coding sequences, 48 tRNAs, two operons of 16S–23S-5S rRNA gene and three ncRNAs. Strain E4A9T encodes 10 genes related to esterase, and three of the esterases (E3, E6 and E10) was successfully cloned and expressed in Escherichia coli Rosetta in a soluble form, revealing its potential application in biotechnological industry. Moreover, the genome provides clues of metabolic pathways of strain E4A9T, reflecting its adaptations to the ambient environment. The genome sequence of C. marinus E4A9T now provides the fundamental information for future studies.

Dorvilleids were collected from hydrothermal vents on the Southwest Indian Ridge by manned submersible Jiaolong. These represent a new species of Ophryotrocha that is here described as Ophryotrocha jiaolongi sp. n. This is the first dorvilleid described from vents on the Southwest Indian Ridge. It most closely resembles another vent species, Ophryotrocha akessoni Blake, 1985 from the Galapagos Rift, but can be distinguished by its antennae, palps, jaw structure. The new species has particularly distinctive mandibles, which allow it to be easily identified.

Abstract The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl a synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.

Background: In cardiac surgery, elevation of procalcitonin (PCT) could be observed postoperatively in the absence of any evidence of infection and also seems to be a prognostic marker. PCT levels measured in patients undergoing Type A aortic dissection (TAAD) were used to determine prognostic values for complications and surgical outcomes. Methods: Measurements of PCT, C-reactive protein (CRP), and leukocyte count were observed in TAAD surgery patients (n = 251; average age: 49.02 ± 12.83 years; 78.5% male) at presurgery (T0) and 24 h (T1), 48 h (T2), and 7 days (T3) postsurgery. PCT clearance (PCTc) on days 2 and 7 was calculated: (PCTday1− PCTday2/day7)/PCTday1 × 100%. Endotracheal intubation duration, length of stay (LOS) in the Intensive Care Unit (ICU)/hospital, and complications were recorded. Results: PCT peaked 24 h postsurgery (median 2.73 ng/ml) before decreasing. Correlation existed between PCT levels at T1 and duration of cardiopulmonary bypass (P = 0.001, r = 0.278). Serum PCT concentrations were significantly higher in nonsurvivor and multiple organ dysfunction syndrome groups on all postoperative days. PCT levels at T1 correlated with length of time of ventilation support and ICU/hospital LOS. Comparing PCT values of survivors versus nonsurvivors, a PCT cutoff level of 5.86 ng/ml at T2 had high sensitivity (70.6%) and specificity (74.3%) in predicting in-hospital death. PCTc-day 2 and 7 were significantly higher in survivor compared with nonsurvivor patients (38% vs. 8%, P= 0.012, 83% vs. −39%, P< 0.001). A PCTc-day 7 cutoff point of 48.7% predicted survival with high sensitivity (77.8%) and specificity (81.8%). Conclusions: PCT level and PCTc after TAAD surgery might serve as early prognostic markers to predict postoperative outcome. PCT measurement may help identify high-risk patients.

Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%), P. shioyasakiensis SE3T (97.8%), P. arabiensis JCM 17292T (97.3%), and P. gelatinilytica NH153T (97.1%). The 16S rRNA gene sequence similarity between JW1T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1T and type strains of the closely related Pseudoalteromonas species were 70.9-83.3% and 20.0-26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8). The principal fatty acids are summed feature 3 (C16:1ω7c and/or iso-C15:0 2OH), C18:1ω7c, and C16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1T = CGMCC 1.15681T = KCTC 52406T = MCCC 1K02162T) is proposed.

In China, snails Pomacea canaliculata and its new breed the gold snail, Achatina fulica and its new breeds the white jade snail, have been sold on the Internet in recent years. We concluded that 24,853 sales of P. canaliculata and A. fulica had been made through the Internet selling platform before 2019. Further surveys indicated that 51% sellers were located in endemic areas of Angiostrongylus cantonensis. However, no A. cantonensis-positive snails were found among Internet-sold snails. Laboratory animal infection experiments proved that all 4 breeds of snails could transmit A. cantonensis. Internet sales of the 4 snails are of bio-safty temporarily but still present a high risk to spread angiostrongyliasis in China; moreover. Internet sales of P. canaliculata and A. fulica should be brought to the attention of concerned administrations in China. [ABSTRACT FROM AUTHOR]

To perform transcriptional profiling of adult female Angiostrongylus cantonensis, three groups of adult female A. cantonensis were isolated and their mRNA was separated and sequenced through the nextgeneration sequencing (NGS) technology. Sequencing data were assembled into unigenes and transcripts. Finally, all unigenes and transcripts were annotated by querying the NR, Gene Ontology (GO), COG and KOG databases.A total of 71047 unigenes and 106652 transcripts were assembled. A. cantonensis was successfully annotated by the NR and GO databases, resulting in 8107 unigenes and 16105 transcripts. Meanwhile, 10422 unigenes and 20974 transcripts were annotated by the COG/KOG databases. ORF querying annotated 10531 unigenes and 28186 transcripts. It could be observed that the unigenes and transcripts associated with metabolism and parasitism of adult female A. cantonensis were highly expressed. In this study, the transcriptome of adult female Angiostrongylus cantonensis was analyzed and successfully annotated. Metabolism and parasitism related genes were highly expressed at adult female A. cantonensis. [ABSTRACT FROM AUTHOR]