The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification.

BACKGROUND: Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification. RESULTS: In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima. CONCLUSIONS: Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.

Hidden hyperchaotic attractors in a new 4D fractional order system and its synchronization.

The research of finding hidden attractors in nonlinear dynamical systems has attracted much consideration because of its practical and theoretical importance. A new fractional order four-dimensional system, which can exhibit some hidden hyperchaotic attractors, is proposed in this paper. The predictor-corrector method of the Adams-Bashforth-Moulton algorithm and the parameter switching algorithm are used to numerically study this system. It is interesting that three different kinds of hidden hyperchaotic attractors with two positive Lyapunov exponents are found, and the fractional order system can have a line of equilibria, no equilibrium point, or only one stable equilibrium point. Moreover, a self-excited attractor is also recognized with the change of its parameters. Finally, the synchronization behavior is studied by using a linear feedback control method.

Construction and validation of risk prediction models for pulmonary embolism in hospitalized patients based on different machine learning methods.

Objective: This study aims to apply different machine learning (ML) methods to construct risk prediction models for pulmonary embolism (PE) in hospitalized patients, and to evaluate and compare the predictive efficacy and clinical benefit of each model. Methods: We conducted a retrospective study involving 332 participants (172 PE positive cases and 160 PE negative cases) recruited from Guangdong Medical University. Participants were randomly divided into a training group (70%) and a validation group (30%). Baseline data were analyzed using univariate analysis, and potential independent risk factors associated with PE were further identified through univariate and multivariate logistic regression analysis. Six ML models, namely Logistic Regression (LR), Decision Tree (DT), Random Forest (RF), Naive Bayes (NB), Support Vector Machine (SVM), and AdaBoost were developed. The predictive efficacy of each model was compared using the receiver operating characteristic (ROC) curve analysis and the area under the curve (AUC). Clinical benefit was assessed using decision curve analysis (DCA). Results: Logistic regression analysis identified lower extremity deep venous thrombosis, elevated D-dimer, shortened activated partial prothrombin time, and increased red blood cell distribution width as potential independent risk factors for PE. Among the six ML models, the RF model achieved the highest AUC of 0.778. Additionally, DCA consistently indicated that the RF model offered the greatest clinical benefit. Conclusion: This study developed six ML models, with the RF model exhibiting the highest predictive efficacy and clinical benefit in the identification and prediction of PE occurrence in hospitalized patients.

Natural food preservation with ginger essential oil: Biological properties and delivery systems.

Recently, the increasing demand from consumers for preservative-free or naturally preserved foods has forced the food industry to turn to natural herbal and plant-derived preservatives rather than synthetic preservatives to produce safe foods. Essential oils derived from ginger (Zingiber officinale Roscoe) are widely known for their putative health-promoting bioactivities, and this paper covers their extraction methods, chemical composition, and antibacterial and antioxidant activities. Especially, the paper reviews their potential applications in food preservation, including nanoemulsions, emulsions, solid particle encapsulation, and biodegradable food packaging films/coatings. The conclusion drawn is that ginger essential oil can be used not only for direct food preservation but also encapsulated using various delivery forms such as nanoemulsions, Pickering emulsions, and solid particle encapsulation to improve its release control ability. The film of encapsulated ginger essential oil has been proven to be superior to traditional methods in preserving foods such as bread, meat, fish, and fruit.