K-Track-Covid: interactive web-based dashboard for analyzing geographical and temporal spread of COVID-19 in South Korea.

The COVID-19 pandemic has necessitated the development of robust tools for tracking and modeling the spread of the virus. We present 'K-Track-Covid,' an interactive web-based dashboard developed using the R Shiny framework, to offer users an intuitive dashboard for analyzing the geographical and temporal spread of COVID-19 in South Korea. Our dashboard employs dynamic user interface elements, employs validated epidemiological models, and integrates regional data to offer tailored visual displays. The dashboard allows users to customize their data views by selecting specific time frames, geographic regions, and demographic groups. This customization enables the generation of charts and statistical summaries pertinent to both daily fluctuations and cumulative counts of COVID-19 cases, as well as mortality statistics. Additionally, the dashboard offers a simulation model based on mathematical models, enabling users to make predictions under various parameter settings. The dashboard is designed to assist researchers, policymakers, and the public in understanding the spread and impact of COVID-19, thereby facilitating informed decision-making. All data and resources related to this study are publicly available to ensure transparency and facilitate further research.

Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E.

Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.

Ferrocene-modified half-sandwich iridium(III) and ruthenium(II) propionylhydrazone complexes and anticancer application.

Ferrocene, ruthenium(II) and iridium(III) organometallic complexes, potential substitutes for platinum-based drugs, have shown good application prospects in the field of cancer therapy. Therefore, in this paper, six ferrocene-modified half-sandwich ruthenium(II) and iridium(III) propionylhydrazone complexes were prepared, and the anticancer potential was evaluated and compared with cisplatin. These complexes showed potential in-vitro anti-proliferative activity against A549 cancer cells, especially for Ir-based complexes, and showing favorable synergistic anticancer effect. Meanwhile, these complexes showed little cytotoxicity and effective anti-migration activity. Ir3, the most active complex (ferrocene-appended iridium(III) complex), could accumulate in the intracellular mitochondria, disturb the cell cycle (S-phase), induce the accumulation of reactive oxygen species, and eventually cause the apoptosis of A549 cells. Then, the design of these complexes provides a good structural basis for the multi-active non­platinum organometallic anticancer complexes.

Evaluating Oral Probiotic Supplements as Complementary Treatment in Advanced Lung Cancer Patients Receiving ICIs: A Prospective Real-World Study.

OBJECTIVE: To evaluate the effectiveness of oral probiotic supplements in patients undergoing immune checkpoint inhibitors (ICIs) for the treatment of advanced lung cancer. METHODS: This prospective real-world study enrolled patients with advanced lung cancer who were receiving ICIs as part of their treatment. The patients were divided into 2 groups: Group OPS received oral probiotic supplements along with ICIs, while Group C did not. The primary endpoint was progression-free survival (PFS). The secondary outcome measure was the objective response rate (ORR). RESULTS: A total of 253 patients were included in the study, with 71 patients in Group OPS and 182 patients in the control group (Group C). No significant differences were observed in the median PFS between the 2 groups for all patients. However, for small cell lung cancer (SCLC) patients, the median PFS was significantly better in the Group OPS compared to the Group C (11.1 months vs 7.0 months, P = .049). No significant differences were observed in median PFS for the non-small cell lung cancer (NSCLC) cohort between the 2 groups, but a trend towards better median PFS in Group OPS was noticed (16.5 months vs 12.3 months, P = .56). The ORR for the entire cohort was 58.0%. CONCLUSION: Oral probiotics supplements in combination with ICIs included regimen may improve the outcome in patients with advanced SCLC. The above points should be proved by further study.

This study examined whether the addition of oral probiotic supplements to ICIs could enhance the treatment of advanced lung cancer. A total of 253 patients with advanced lung cancer were involved in the study, with some receiving probiotics in combination with ICIs and others not. The findings revealed that patients with SCLC who took probiotics had significantly better PFS compared to those who did not. Additionally, there was a tendency towards enhanced PFS in NSCLC patients who received probiotics. In conclusion, the study indicates that incorporating oral probiotics with ICIs may lead to better outcomes for patients with advanced SCLC, although further research is necessary to validate these results.This real world study explores whether oral probiotic supplements along with immune checkpoint inhibitors (ICIs) can help treat advanced lung cancer. The study included 253 patients with advanced lung cancer receiving ICIs treatment, part of them taking probiotics along with ICIs. The results showed that patients with small cell lung cancer (SCLC) who took probiotics had better progression-free survival (PFS) compared to those who didn't. There was also a trend towards better PFS in non-small cell lung cancer (NSCLC) patients who took probiotics. Overall, the study suggests that taking oral probiotics along with ICIs may improve outcomes for patients with advanced SCLC, but more research is needed to confirm these findings.

SARS-CoV-2 Omicron Variants Show Attenuated Neurovirulence Compared with the Wild-Type Strain in Elderly Human Brain Spheroids.

Infection with severe acute respiratory syndrome coronavirus 2 Omicron variants still causes neurological complications in elderly individuals. However, whether and how aging brains are affected by Omicron variants in terms of neuroinvasiveness and neurovirulence are unknown. Here, we utilize resected paracarcinoma brain tissue from elderly individuals to generate primary brain spheroids (BSs) for investigating the replication capability of live wild-type (WT) strain and Omicron (BA.1/BA.2), as well as the mechanisms underlying their neurobiological effects. We find that both WT and Omicron BA.1/BA.2 are able to enter BSs but weakly replicate. There is no difference between Omicron BA.1/BA.2 and WT strains in neurotropism in aging BSs. However, Omicron BA.1/BA.2 exhibits ameliorating neurological damage. Transcriptional profiling indicates that Omicron BA.1/BA.2 induces a lower neuroinflammatory response than WT strain in elderly BSs, suggesting a mechanistic explanation for their attenuated neuropathogenicity. Moreover, we find that both Omicron BA.1/BA.2 and WT strain infections disrupt neural network activity associated with neurodegenerative disorders by causing neuron degeneration and amyloid-ß deposition in elderly BSs. These results uncover Omicron-specific mechanisms and cellular immune responses associated with severe acute respiratory syndrome coronavirus 2-induced neurological complications.

A series of spontaneously blinking dyes for super-resolution microscopy.

Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.

Bouncing Dynamics of Drops' Successive Off-Center Impact.

Bouncing dynamics of a trailing drop off-center impacting a leading drop with varying time intervals and Weber numbers are investigated experimentally. Whether the trailing drop impacts during the spreading or receding process of the leading drop is determined by the time interval. For a short time interval of 0.15 ≤ Δt* ≤ 0.66, the trailing drop impacts during the spreading of the leading drop, and the drops completely coalesce and rebound; for a large time interval of 0.66 < Δt* ≤ 2.21, the trailing drop impacts during the receding process, and the drops partially coalesce and rebound. Whether the trailing drop directly impacts the surface or the liquid film of the leading drop is determined by the Weber number. The trailing drop impacts the surface directly at moderate Weber numbers of 16.22 ≤ We ≤ 45.42, while it impacts the liquid film at large Weber numbers of 45.42 < We ≤ 64.88. Intriguingly, when the trailing drop impacts the surface directly or the receding liquid film, the contact time increases linearly with the time interval but independent of the Weber number; when the trailing drop impacts the spreading liquid film, the contact time suddenly increases, showing that the force of the liquid film of the leading drop inhibits the receding of the trailing drop. Finally, a theoretical model of the contact time for the drops is established, which is suitable for different impact scenarios of the successive off-center impact. This study provides a quantitative relationship to calculate the contact time of drops successively impacting a superhydrophobic surface, facilitating the design of anti-icing surfaces.

Transcriptome analysis revealed SMURF2 as a prognostic biomarker for oral cancer.

BACKGROUND: The activation of TGF-ß pathway can facilitate tumorigenesis. Understanding the TGF-related genes (TRGs) in oral cancer and determining their prognostic value is of utmost importance. METHODS: The TRGs were selected to develop a prognostic model based on lasso regression. Oral cancer patients were classified into high-risk and low-risk groups based on the risk model. Subsequently, multivariate COX regression was employed to identify the prognostic marker. Additionally, the expression of SMURF2 was validated using quantitative real-time polymerase chain reaction (qRT-PCR) and the Human Protein Atlas (HPA) database. To investigate the relationship between SMURF2 expression and immune cell infiltrations, we conducted single-sample Gene Set Enrichment Analysis (ssGSEA) analyses. RESULTS: We identified 16 differentially expressed TRGs in oral cancer, all of which showed upregulation. From these, we selected eight TRGs as prognostic signatures. Furthermore, the high-risk group demonstrated lower infiltration levels of immune cells, immune score, and higher tumor purity. Interestingly, we also found that SMURF2 serves as an independent prognostic biomarker. SMURF2 was upregulated in oral cancer, as confirmed by public databases and qRT-PCR analysis. Importantly, our results indicate a close association between SMURF2 expression and the immune microenvironment. CONCLUSION: The 8-TRG signature prognosis model that we constructed has the ability to predict the survival rate and immune activity of oral cancer patients. SMURF2 could be effective in recognizing prognosis and evaluating immune efficacy for oral cancer.

Integrin αvß3-targeted self-assembled polypeptide nanomicelles for efficacious sonodynamic therapy against breast cancer.

Sonodynamic therapy (SDT) is an advanced non-invasive cancer treatment strategy with moderate tissue penetration, less invasiveness and a reliable curative effect. However, due to the low stability, potential bio-toxicity and lack of tumor targeting capability of most sonosensitizers, the vast clinical application of SDT has been challenging and limited. Therefore, it is desirable to develop a novel approach to implement sonosensitizers to SDT for cancer treatments. In this study, an amphiphilic polypeptide was designed to effectively encapsulate rose bengal (RB) as a model sonosensitizer to form peptido-nanomicelles (REPNs). The as-fabricated REPNs demonstrated satisfactory tumor targeting and fluorescence performances, which made them superb imaging tracers in vivo. In the meantime, they generated considerable amounts of reactive oxygen species (ROS) to promote tumor cell apoptosis under ultrasound irradiation and showed excellent anti-tumor performance without obvious side effects. These engineered nanomicelles in combination with medical ultrasound may be used to achieve integrin αvß3-targeted sonodynamic therapy against breast cancer, and it is also a promising non-invasive cancer treatment strategy for clinical translations.

Design and anticancer behaviour of cationic/neutral half-sandwich iridium(III) imidazole-phenanthroline/phenanthrene complexes.

Considerable attention has been devoted to the exploration of organometallic iridium(III) (IrIII) complexes for their potential as metallic anticancer drugs. In this study, twelve half-sandwich IrIII imidazole-phenanthroline/phenanthrene complexes were prepared and characterized. Complexes exhibited promising in-vitro anti-proliferative activity, and some are obviously superior to cisplatin towards A549 cells. These complexes possessed suitable fluorescence, and a non-energy-dependent uptake pathway was identified, subsequently leading to their accumulation in the lysosome and the lysosomal damage. Additionally, complexes could inhibit the cell cycle (G1-phase) and catalyze intracellular NADH oxidation, thus substantiating the elevation of intracellular reactive oxygen species (ROS) level, which confirming the oxidative mechanism. Western blotting further confirmed that complexes could induce A549 cell apoptosis through the lysosomal-mitochondrial anticancer pathway, which was inconsistent with cisplatin. In summary, these complexes offer fresh concepts for the development of organometallic non­platinum anticancer drugs.

Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.

Dietary supplementation of Chinese herbal medicines enhances the immune response and resistance of rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus.

Rainbow trout is a widely farmed economical cold-water fish worldwide, but the prevalence of infectious hematopoietic necrosis virus (IHNV) presents a severe risk to the aquaculture industry, resulting in high mortality and huge economic losses. In this study, the impacts of different concentrations (0, 10, 20, and 30 g/kg) of Chinese herbal medicine mixture (CHMM) on the immune response and resistance of rainbow trout to IHNV infection were evaluated. The results show that CHMM noticeably increased (P < 0.05) T-SOD, CAT, AST, ALT, ACP, and AKP activities and decreased MDA content. NF-κB, TNF-α, IFN-ß, IL-1ß, JAK1, HSP70, and HSP90 expressions were significantly upregulated (P < 0.05) in all CHMMs, while SOCS2 expression was downregulated (P < 0.05). Following infection with IHNV, feeding rainbow trout with varying amounts of CHMM resulted in noticeably increased (P < 0.05) T-SOD, ACP, and AKP activities and significantly decreased (P < 0.05) MDA content and AST and ALT activities. TNF-α, IFN-ß, IL-1ß, HSP70, and HSP90 expressions were significantly upregulated (P < 0.05) in all CHMMs, while the expressions of JAK1 and SOCS2 were downregulated. The expression level of the IHNV G protein gene at a dosage of 20 g/kg was notably lower than that of the other CHMM feeding groups. This study provides a solid scientific basis for promoting CHMM as an immunostimulant for boosting antiviral immunity in rainbow trout.

Low-cost and convenient fabrication of polymer micro/nanopores with the needle punching process and their applications in nanofluidic sensing.

Solid-state micro/nanopores play an important role in the sensing field because of their high stability and controllable size. Aiming at problems of complex processes and high costs in pore manufacturing, we propose a convenient and low-cost micro/nanopore fabrication technique based on the needle punching method. The thin film is pierced by controlling the feed of a microscale tungsten needle, and the size variations of the micropore are monitored by the current feedback system. Based on the positive correlation between the micropore size and the current threshold, the size-controllable preparation of micropores is achieved. The preparation of nanopores is realized by the combination of needle punching and chemical etching. First, a conical defect is prepared on the film with the tungsten needle. Then, nanopores are obtained by unilateral chemical etching of the film. Using the prepared conical micropores, resistive-pulse detection of nanoparticles is performed. Significant ionic current rectification is also obtained with our conical nanopores. It is proved that the properties of micro/nanopores prepared by our method are comparable to those prepared by the track-etching method. The simple and controllable fabrication process proposed here will advance the development of low-cost micro/nanopore sensors.

Perceptions and needs for a community nursing virtual simulation system for Chinese nursing students during the COVID-19 pandemic: A qualitative study.

Background: Virtual simulation systems are being increasingly used in the field of nursing education. However, these systems are mostly designed based on the perspective of developers, and the needs of the end users are often neglected. The purpose of this study was to explore the perceptions and needs of Chinese undergraduate nursing students for the development of a community nursing virtual simulation system. Methods: This was a descriptive qualitative study enrolling 12 undergraduate nursing students at a University in China. Data were collected through semi-structured interviews. The content analysis method was used for data analysis. Result: Three themes and 15 sub-themes were extracted from this study: (1) Positive perceptions regarding virtual systems: a) Provides space for trials and errors, b) Not limited by time and space, c) Provides auxiliary tools; (2) Design and use requirements: a) Performance needs, b) Contents design needs, c) Appearance design needs, d) Support Needs; (3) Competency enhancement needs: a) Community nursing practice ability, b) Critical thinking ability, c) Independent thinking ability, d) Ability to deal with emergencies, e)Teamwork skills, f) Self-efficacy, g) Resilience, h)Interpersonal communication skills. Conclusion: Designers and engineers should consider students' needs, aim to improve students' abilities, improve the diversity, the scientific and rigor of content, and enhance user immersion and interest. The system should be programmed to provide real-time feedback, timely technical and professional support, in order to optimize use experience of nursing students.

Controlling Nanoparticle Distance by On-Surface DNA-Origami Folding.

DNA origami is a flexible platform for the precise organization of nano-objects, enabling numerous applications from biomedicine to nano-photonics. Its huge potential stems from its high flexibility that allows customized structures to meet specific requirements. The ability to generate diverse final structures from a common base by folding significantly enhances design variety and is regularly occurring in liquid. This study describes a novel approach that combines top-down lithography with bottom-up DNA origami techniques to control folding of the DNA origami with the adsorption on pre-patterned surfaces. Using this approach, tunable plasmonic dimer nano-arrays are fabricated on a silicon surface. This involves employing electron beam lithography to create adsorption sites on the surface and utilizing self-organized adsorption of DNA origami functionalized with two gold nanoparticles (AuNPs). The desired folding of the DNA origami helices can be controlled by the size and shape of the adsorption sites. This approach can for example be used to tune the center-to-center distance of the AuNPs dimers on the origami template. To demonstrate this technique's efficiency, the Raman signal of dye molecules (carboxy tetramethylrhodamine, TAMRA) coated on the AuNPs surface are investigated. These findings highlight the potential of tunable DNA origami-based plasmonic nanostructures for many applications.

Advances in molecularly imprinted materials for selective adsorption of phenolic pollutants from the water environment: Synthesis, applications, and improvement.

The application of molecularly imprinted material (MIM) is widely employed as a material for removing phenolic pollutants from the water environment, owing to its exceptional capacity for selective adsorption and high sensitivity. In this paper, the preparation principle, bonding types, and preparation methods of MIM have been comprehensively introduced. Meanwhile, according to the binding type of MIM with phenolic pollutants, three categories of hydroxyl bonding, hydroxyl carboxyl bonding, and hydroxyl nitro bonding were carried out to explain its application to phenolic pollutants. Strategies for addressing the challenges of selective instability, high regeneration costs, and template leakage in MIM applications were summarized. These strategies encompassed the introduction of superior carriers, enhancements in preparation processes, and the utilization of molecular dynamics simulation-assisted technology. Finally, the prospects in the three aspects of material preparation, process coupling, and recycling. In summary, this paper has demonstrated the potential of utilizing MIM for the selective treatment of phenolic pollutants from the water environment.

A dual strategy of Na+/vacancy disorder and high Na to construct a P2-type cathode for high-stability sodium-ion batteries.

P2-type layered oxides are widely regarded as highly promising contenders for cathode materials in sodium-ion batteries. However, the occurrence of severe reactive phase transitions hinders satisfactory cycling stability and rate performance, thereby imposing limitations on their practical application. Here we prepared P2-type Na0.75Ni0.23Mg0.1Mn0.67O2 cathode materials using the agar gel approach. The use of agar reduces the synthesis time significantly, and the high Na content enhances the stability of the structure and contributes to its capacity. Meanwhile, the introduction of electrochemically inactive Mg ions into sodium layers not only disrupts the Na+/vacancy ordering, but also increases the spacing between sodium layers, thus reducing the diffusion barrier for sodium ions. The dual modification strategy led to excellent stability of Na0.75Ni0.23Mg0.1Mn0.67O2 with 94% capacity retention after 100 cycles at 1C. This work provides new insights into the design of sodium-ion cathode materials.

Populus euphratica PeNADP-ME interacts with PePLDδ to mediate sodium and ROS homeostasis under salinity stress.

Populus euphratica phospholipase Dδ (PePLDδ) is transcriptionally regulated and mediates reactive oxygen species (ROS) and ion homeostasis under saline conditions. The purpose of this study is to explore the post-transcriptional regulation of PePLDδ in response to salt environment. P. euphratica PePLDδ was shown to interact with the NADP-dependent malic enzyme (NADP-ME) by screening the yeast two-hybrid libraries. The transcription level of PeNADP-ME increased upon salt exposure to NaCl (200 mM) in leaves and roots of P. euphratica. PeNADP-ME had a similar subcellular location with PePLDδ in the cytoplasm, and the interaction between PeNADP-ME and PePLDδ was further verified by GST pull-down and yeast two-hybrid. To clarify whether PeNADP-ME interacts with PePLDδ to enhance salt tolerance, PePLDδ and PeNADP-ME were overexpressed singly or doubly in Arabidopsis thaliana. Dual overexpression of PeNADP-ME and PePLDδ resulted in an even more pronounced improvement in salt tolerance compared with single transformants overexpressing PeNADP-ME or PePLDδ alone. Greater Na+ limitation and Na+ efflux in roots were observed in doubly overexpressed plants compared with singly overexpressed plants with PeNADP-ME or PePLDδ. Furthermore, NaCl stimulation of SOD, APX, and POD activity and transcription were more remarkable in the doubly overexpressed plants. It is noteworthy that the enzymic activity of NADP-ME and PLD, and total phosphatidic acid (PA) concentrations were significantly higher in the double-overexpressed plants than in the single transformants. We conclude that PeNADP-ME interacts with PePLDδ in Arabidopsis to promote PLD-derived PA signaling, conferring Na+ extrusion and ROS scavenging under salt stress.

Optimizing carbon sources regulation in the biochemical treatment systems for coal chemical wastewater: Aromatic compounds biodegradation and microbial response strategies.

The complex composition of coal chemical wastewater (CCW), marked by numerous highly toxic aromatic compounds, induces the destabilization of the biochemical treatment system, leading to suboptimal treatment efficacy. In this study, a biochemical treatment system was established to efficiently degrade aromatic compounds by quantitatively regulating the dosage of co-metabolized substrates (specifically, the chemical oxygen demand (COD) Glucose: COD Sodium acetate = 3:1, 1:3, and 1:1). The findings demonstrated that the system achieved optimal performance under the condition that the ratio of COD Glucose to COD Sodium acetate was 3:1. When the co-metabolized substrate was added to the system at an optimal ratio, examination of pollutant removal and cumulative effects revealed that the removal efficiencies for COD and total organic carbon (TOC) reached 94.61 % and 86.40 %, respectively. The removal rates of benzene series, nitrogen heterocyclic compounds, polycyclic aromatic hydrocarbons, and phenols were 100 %, 100 %, 63.58 %, and 94.12 %, respectively. Research on the physiological response of microbial cells showed that, under optimal ratio regulation, co-metabolic substrates led to a substantial rise in microbial extracellular polymeric substances (EPS) secretion, particularly extracellular proteins. When the system reached the end of its operation, the contents of loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) for proteins in the optimal group were 7.12 mg/g-SS and 152.28 mg/g-SS, respectively. Meanwhile, the ratio of α-Helix / (ß-Sheet + Random coil) and the proportion of intermolecular interaction forces were also increased in the optimal group. At system completion, the ratio of α-Helix / (ß-Sheet + Random coil) reached 0.717 (LB-EPS) and 0.618 (TB-EPS), respectively. Additionally, the proportion of intermolecular interaction forces reached 74.83 % (LB-EPS) and 55.03 % (TB-EPS). An in-depth analysis of the metabolic regulation of microorganisms indicated that the introduction of optimal ratios of co-metabolic substrates contributed to a noteworthy upregulation in the expression of Catechol 2,3-dioxygenase (C23O) and Dehydrogenase (DHA). The expression levels of C23O and DHA were measured at 0.029 U/mg Pro·g MLSS and 75.25 mg TF·(g MLSS·h)-1 (peak value), respectively. Correspondingly, enrichment of aromatic compound-degrading bacteria, including Thauera, Saccharimonadales, and Candidatus_Competibacter, occurred, along with the upregulation of associated functional genes such as Catechol 1,2-dioxygenase, Catechol 2,3-dioxygenase, Protocatechuate 3,4-dioxygenase, and Protocatechuate 4,5-dioxygenase. Considering the intricate system of multiple coexisting aromatic compounds in real CCW, this study not only obtained an optimal ratio for carbon source addition but also enhanced the efficient utilization of carbon sources and improved the capability of the system to effectively degrade aromatic compounds. Additionally, this paper established a theoretical foundation for metabolic regulation and harmless treatment within the biochemical treatment of intricate systems, exemplified by real CCW.

Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.

DNA motifs are crucial patterns in gene regulation. DNA-binding proteins (DBPs), including transcription factors, can bind to specific DNA motifs to regulate gene expression and other cellular activities. Past studies suggest that DNA shape features could be subtly involved in DNA-DBP interactions. Therefore, the shape motif annotations based on intrinsic DNA topology can deepen the understanding of DNA-DBP binding. Nevertheless, high-throughput tools for DNA shape motif discovery that incorporate multiple features altogether remain insufficient. To address it, we propose a series of methods to discover non-redundant DNA shape motifs with the generalization to multiple motifs in multiple shape features. Specifically, an existing Gibbs sampling method is generalized to multiple DNA motif discovery with multiple shape features. Meanwhile, an expectation-maximization (EM) method and a hybrid method coupling EM with Gibbs sampling are proposed and developed with promising performance, convergence capability, and efficiency. The discovered DNA shape motif instances reveal insights into low-signal ChIP-seq peak summits, complementing the existing sequence motif discovery works. Additionally, our modelling captures the potential interplays across multiple DNA shape features. We provide a valuable platform of tools for DNA shape motif discovery. An R package is built for open accessibility and long-lasting impact: https://zenodo.org/doi/10.5281/zenodo.10558980.