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Abstract Background Blood cultures are essential for diagnosing bloodstream infections, but current phenotypic tests for antimicrobial resistance (AMR) provide limited information. Oxford Nanopore Technologies introduces nanopore sequencing with adaptive sampling, capable of real-time host genome depletion, yet its application directly from blood cultures remains unexplored. This study aimed to identify pathogens and predict AMR using nanopore sequencing. Methods In this cross-sectional genomic study, 458 positive blood cultures from bloodstream infection patients in central Taiwan were analyzed. Parallel experiments involved routine microbiologic tests and nanopore sequencing with a 15-h run. A bioinformatic pipeline was proposed to analyze the real-time sequencing reads. Subsequently, a comparative analysis was performed to evaluate the performance of species identification and AMR prediction. Results The pipeline identified 76 species, with 88 Escherichia coli, 74 Klebsiella pneumoniae, 43 Staphylococcus aureus, and 9 Candida samples. Novel species were also discovered. Notably, precise species identification was achieved not only for monomicrobial infections but also for polymicrobial infections, which was detected in 23 samples and further confirmed by full-length 16S rRNA amplicon sequencing. Using a modified ResFinder database, AMR predictions showed a categorical agreement rate exceeding 90% (3799/4195) for monomicrobial infections, with minimal very major errors observed for K. pneumoniae (2/186, 1.1%) and S. aureus (1/90, 1.1%). Conclusions Nanopore sequencing with adaptive sampling can directly analyze positive blood cultures, facilitating pathogen detection, AMR prediction, and outbreak investigation. Integrating nanopore sequencing into clinical practices signifies a revolutionary advancement in managing bloodstream infections, offering an effective antimicrobial stewardship strategy, and improving patient outcomes.

Abstract Cancer resistance to immune checkpoint inhibitors motivated investigations into leveraging the immunostimulatory properties of radiotherapy to overcome immune evasion and to improve treatment response. However, clinical benefits of radiotherapy-immunotherapy combinations have been modest. Routine concomitant tumor-draining lymph node irradiation (DLN IR) might be the culprit. As crucial sites for generating anti-tumor immunity, DLNs are indispensable for the in situ vaccination effect of radiotherapy. Simultaneously, DLN sparing is often not feasible due to metastatic spread. Using murine models of metastatic disease in female mice, here we demonstrate that delayed (adjuvant), but not neoadjuvant, DLN IR overcomes the detrimental effect of concomitant DLN IR on the efficacy of radio-immunotherapy. Moreover, we identify IR-induced disruption of the CCR7-CCL19/CCL21 homing axis as a key mechanism for the detrimental effect of DLN IR. Our study proposes delayed DLN IR as a strategy to maximize the efficacy of radio-immunotherapy across different tumor types and disease stages.

Abstract Photoimmunotherapy faces challenges due to insufficient intratumoral accumulation of photothermal agents and the reversion of the cancer‐immunity cycle during treatment. In this study, an anti‐PD‐L1‐immobilized magnetic gold nanohut, AuNH‐2‐Ab, with photoresponsive, thermosensitive, and immunomodulatory properties to effectively suppress the growth of primary tumors, elevate immunogenic cell death (ICD) levels, reverse the tumor immune microenvironment (TIME), and consequently inhibit metastases are developed. AuNH‐2‐Ab achieves high tumor accumulation (9.54% injected dose) following systemic administration, allowing the modulation of hyperthermia dose of over 50 °C in the tumor. By optimizing the hyperthermia dose, AuNH‐2‐Ab simultaneously target and eliminate cancer cells and tumor‐associated macrophages, thereby activating potent antitumor immunity without being compromised by immunosuppressive elements. Hyperthermia/pH induced morphological transformation of AuNH‐2‐Ab involving the detachment of the surface antibody for in situ PD‐L1 inhibition, and exposure of the inner fucoidan layer for natural killer (NK) cell activation. This precision photoimmunotherapy approach reprograms the TIME, significantly prolongs survival in a murine hepatocellular carcinoma model (Hep55.1c), and harnesses the synergistic effects of ICD production and checkpoint inhibitors by utilizing a single nanoplatform.

Abstract Gut microbiota rearrangement induced by cold temperature is crucial for browning in murine white adipose tissue. This study provides evidence that DUSP6, a host factor, plays a critical role in regulating cold-induced gut microbiota rearrangement. When exposed to cold, the downregulation of intestinal DUSP6 increased the capacity of gut microbiota to produce ursodeoxycholic acid (UDCA). The DUSP6-UDCA axis is essential for driving Lachnospiraceae expansion in the cold microbiota. In mice experiencing cold-room temperature (CR) transitions, prolonged DUSP6 inhibition via the DUSP6 inhibitor (E/Z)-BCI maintained increased cecal UDCA levels and cold-like microbiota networks. By analyzing DUSP6-regulated microbiota dynamics in cold-exposed mice, we identified Marvinbryantia as a genus whose abundance increased in response to cold exposure. When inoculated with human-origin Marvinbryantia formatexigens, germ-free recipient mice exhibited significantly enhanced browning phenotypes in white adipose tissue. Moreover, M. formatexigens secreted the methylated amino acid Nε-methyl-L-lysine, an enriched cecal metabolite in Dusp6 knockout mice that reduces adiposity and ameliorates nonalcoholic steatohepatitis in mice. Our work revealed that host-microbiota coadaptation to cold environments is essential for regulating the browning-promoting gut microbiome.

Abstract Background There is no consensus regarding the superiority of volatile or total intravenous anesthesia (TIVA) in reducing the incidence of postoperative pulmonary complications (PPCs) after lung resection surgery (LRS). Thus, the aim of this study was to investigate the different anesthetic regimens and the incidence of PPCs in patients who underwent LRS. We hypothesized that TIVA is associated with a lower incidence of PPCs than volatile anesthesia. Methods This was a retrospective cohort study of patients who underwent LRS at Taipei Veterans General Hospital between January 2016 and December 2020. The patients’ charts were reviewed and data on patient characteristics, perioperative features, and postoperative outcomes were extracted and analyzed. The patients were categorized into TIVA or volatile anesthesia groups and their clinical data were compared. Propensity score matching was performed to reduce potential selection bias. The primary outcome was the incidence of PPCs, whereas the secondary outcomes were the incidences of other postoperative events, such as length of hospital stay (LOS) and postoperative nausea and vomiting (PONV). Results A total of 392 patients each were included in the TIVA and volatile anesthesia groups. There was no statistically significant difference in the incidence of PPCs between the volatile anesthesia and TIVA groups. The TIVA group had a shorter LOS (p

Gadolinium-neutron capture therapy (Gd-NCT) in glioblastoma shows promise but is limited by toxicity and short-half life in the brain. Here, the authors present a magnetised stem cell-nanoparticle system to facilitate brain penetrance of Gd-NCT and demonstrate its utility in an orthotopic rat glioblastoma model.

Fibroblastic reticular cells (FRCs) support localisation of immune cells in secondary lymphoid tissues but less is known about the lamina propria. Here the authors use scRNA-seq and intestinal infection to characterise FRCs in the intestinal lamina propria and show specialised niches that foster innate lymphoid cells during homeostasis and infection.

Mathematics is an important foundation for the development of science education. In the past, when instructors taught mathematical concepts of geometry shapes, they usually used traditional textbooks and aids to conduct teaching activities, which resulted in students not being able to understand the principles completely. Nowadays, it has become a trend to integrate emerging technologies into mathematics courses and to use digital instructional aids. Emerging technologies can effectively enhance students’ sensory experience while strengthening their impressions and understandings of subject concepts. In this paper, we apply virtual reality immersive technologies to develop a “virtual reality immersive learning mathematics geometry system,” which is used to teach mathematical geometry concepts. Teachers use the system to develop three basic mathematical geometry learning materials: “Triangular pyramid volume = 1/3 prism volume,” “Cone volume calculation,” and “Triangle center of gravity derivation.” In the experimental activity, the teacher uses virtual reality teaching aids to guide students to learn mathematical geometry concepts in a fun way so that they can achieve the effectiveness of immersive learning. This study explores the impact of using the virtual reality immersive learning mathematics geometry system on students’ technology acceptance, learning motivations, and learning performance. The experimental result showed that using the virtual reality immersive learning mathematics geometry system can improve the learning motivation and learning performance of students. The findings indicated that the experimental group had better learning outcomes after completing the learning tasks of three geometric units. The experimental group used the virtual reality immersive learning mathematics geometry system which can lead to better learning outcomes. According to the ARCS questionnaire, students in the experimental group were confident to understand new subjects. At the same time, the mode of completing the game can effectively give students a sense of accomplishment. The use of emerging technologies in the classroom can be an attractive learning mode for students.

The white pulp of spleen is an important immune structure dynamically modulated during development and immune responses. Here the authors define, using multi-color lineage tracing and single-cell transcriptome analysis, the subset distribution and differentiation trajectory of fibroblastic reticular cells to serve structural insights for splenic white pulps.

Bacterial extracellular DNA (eDNA) and activated platelets have been found to contribute to biofilm formation by Streptococcus mutans on injured heart valves to induce infective endocarditis (IE), yet the bacterial component directly responsible for biofilm formation or platelet adhesion remains unclear. Using in vivo survival assays coupled with microarray analysis, the present study identified a LiaR-regulated PspC domain-containing protein (PCP) in S. mutans that mediates bacterial biofilm formation in vivo. Reverse transcriptase- and chromatin immunoprecipitation-polymerase chain reaction assays confirmed the regulation of pcp by LiaR, while PCP is well-preserved among streptococcal pathogens. Deficiency of pcp reduced in vitro and in vivo biofilm formation and released the eDNA inside bacteria floe along with reduced bacterial platelet adhesion capacity in a fibrinogen-dependent manner. Therefore, LiaR-regulated PCP alone could determine release of bacterial eDNA and binding to platelets, thus contributing to biofilm formation in S. mutans-induced IE.

Currently, the combination therapies based on immunotherapy have been rapidly developed, but the response rate has not always increased as expected. Nano-platform has become a potential strategy which can trigger multi-functions to increase immunotherapeutic efficacy via activating T-cells and photothermal effect. Herein, to avoid the self-degradation and provide pH-sensitive property, S-nitrosoglutathione (GSNO) was loaded in gold nanocubes (AuNCs) with polyacrylic acid (PAA) coating. Subsequently, the layer-by-layer (LbL) assembly of iron oxide nanoparticles (Fe3O4) and betanin can provide the conjugation of 1-methyl-D-tryptophan (1-M-DT) on the nanoparticle to form an NO gas-photothermal-immune nano-platform (GAPFBD) for achieving combinatory therapy of NO gas, photothermal therapy (PTT), and indoleamine 2,3-dioxygenase (IDO) immunotherapy. After irradiation by 808-nm laser, the GSNO was released under a lower pH environment due to the structural transformation of PAA and then transformed into NO production of 64.5 ± 1.6% under PTT. The combination of PTT and NO gas therapy can effectively eliminate cancer cells, resulting in a large amount of tumor-associated antigens (TAAs) compared to the individual treatment in vitro. Additionally, the released 1-M-DT inhibited IDO and combined with TAAs to enhance maturation of dendritic cells (DCs), indicating the excellent synergistic effect of PTT and NO with IDO inhibitors. These results revealed that this dual-sensitive nanoparticle presented a combination strategy of PTT/NO/IDO for the synergistic effect to promote DC maturation.

The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable de novo bacterial genome assembly. Although many algorithms and tools have been developed for base calling, read mapping, de novo assembly, and polishing, an automated pipeline is not available for one-stop analysis for circular bacterial genome reconstruction. In this paper, we present the pipeline CCBGpipe for completing circular bacterial genomes. Raw current signals are demultiplexed and base called to generate sequencing data. Sequencing reads are de novo assembled several times by using a sampling strategy to produce circular contigs that have a sequence in common between their start and end. The circular contigs are polished by using raw signals and sequencing reads; then, duplicated sequences are removed to form a linear representation of circular sequences. The circularized contigs are finally rearranged to start at the start position of dnaA/repA or a replication origin based on the GC skew. CCBGpipe implemented in Python is available at https://github.com/jade-nhri/CCBGpipe. Using sequencing data produced from a single MinION run, we obtained 48 circular sequences, comprising 12 chromosomes and 36 plasmids of 12 bacteria, including Acinetobacter nosocomialis, Acinetobacter pittii, and Staphylococcus aureus. With adequate quantities of sequencing reads (80×), CCBGpipe can provide a complete and automated assembly of circular bacterial genomes.

Fucoidan, a natural sulfated polysaccharide, which can activate the immune response and lessen adverse effects, is expected to be an adjuvant agent in combination with chemotherapy. Using natural hydrophilic anticancer polysaccharides to simultaneously encapsulate hydrophobic anticancer drugs is feasible, and a reduced side effect can be achieved to amplify the therapeutic efficacy. In this study, a novel type of fucoidan-PLGA nanocarrier (FPN-DTX) was developed for the encapsulation of the hydrophobic anticancer drug, docetaxel (DTX), as a drug delivery system. From the comparison between FPN-DTX and the PLGA particles without fucoidan (PLGA-DTX), FPNs–DTX with fucoidan were highly stable with smaller sizes and dispersed well without aggregations in an aqueous environment. The drug loading and release can be further modified by modulating relative ratios of Fucoidan (Fu) to PLGA. The (FPN 3-DTX) nanoparticles with a 10:3 ratio of Fu:PLGA displayed uniform particle size with higher encapsulation efficiency than PLGA NPs and sustained drug release ability. The biocompatible fucoidan-PLGA nanoparticles displayed low cytotoxicity without drug loading after incubation with MDA-MB-231 triple-negative breast cancer cells. Despite lower cellular uptake than that of PLGA-DTX due to a higher degree of negative zeta potential and hydrophilicity, FPN 3-DTX effectively exerted better anticancer ability, so FPN 3-DTX can serve as a competent drug delivery system.

Adaptive immune responses develop in secondary lymphoid organs such as lymph nodes (LNs) in a well-coordinated series of interactions between migrating immune cells and resident stromal cells. Although many processes that occur in LNs are well understood from an immunological point of view, our understanding of the fundamental organization and mechanisms that drive these processes is still incomplete. The aim of systems biology approaches is to unravel the complexity of biological systems and describe emergent properties that arise from interactions between individual constituents of the system. The immune system is greater than the sum of its parts, as is the case with any sufficiently complex system. Here, we review recent work and developments of computational LN models with focus on the structure and organization of the stromal cells. We explore various mathematical studies of intranodal T cell motility and migration, their interactions with the LN-resident stromal cells, and computational models of functional chemokine gradient fields and lymph flow dynamics. Lastly, we discuss briefly the importance of hybrid and multi-scale modeling approaches in immunology and the technical challenges involved.

The tumor microenvironment harbors cancer-associated fibroblasts that function as major modulators of cancer progression. Here, we assessed to which extent distinct cancer-associated fibroblast subsets impact mammary carcinoma growth and cancer cell stemness in an orthotopic murine model. We found that fibroblasts expressing the Cre recombinase under the control of the interleukin 7 promoter occupied mainly the tumor margin where they physically interacted with tumor cells. Intratumoral ablation of interleukin 7-expressing fibroblasts impaired breast tumor growth and reduced the clonogenic potential of cancer cells. Moreover, cDNA expression profiling revealed a distinct oncogenic signature of interleukin 7-producing fibroblasts. In particular, Cxcl12 expression was strongly enhanced in interleukin 7-producing fibroblasts and cell type-specific genetic ablation and systemic pharmacological inhibition revealed that the CXCL12/CXCR4 axis impacts breast tumor cell stemness. Elevated expression of CXCL12 and other stem cell factors in primary human breast cancer-associated fibroblasts indicates that certain fibroblast populations support tumor cell stemness and thereby promote breast cancer growth.

Hot embossing is a low-cost and flexible method for fabricating microstructures and nanostructures on polymers. However, the conventional hot embossing process poses two challenges: First, the plates that are used do not provide uniform pressure, and the size of the chamber limits the imprinting area. Second, heating with thick metal plates significantly lengthens cycle time. Finally, the uniformity of temperature also affects the embossing results. To achieve a high heating rate and uniform pressure over a large area, this study combined an induction heating system and roll-to-plate hot embossing. A movable plate was used to move the mold through the induction coil, increasing the heating area and overcoming limitations related to the embossing area posed by the coil length. The imprinting area reached 100 * 100 [mm.sup.2]. In addition, the temperature difference was less than 20[degrees] C at each molding temperature range from 150[degrees] C to 190[degrees] C. The mold and the substrate were placed on a vacuum absorber to prevent deformation and slippage of the mold and provide preloading and packing pressure. Cooling fans were employed to improve cooling efficiency. Experimental replication yielded replication rates higher than 97% at 190[degrees] C and 5 kgf/[cm.sup.2] with a cycle time of approximately 2 minutes. To verify the feasibility of the process, V-groove microstructures were successfully fabricated using a movable induction heating roller embossing facility. Highlights * The feasibility of the moving induction heating roller embossing process. * A vacuum movable platform prevents deformation and slippage of the substrate. * Improve the temperature uniformity of the movable platform. KEYWORDS hot embossing, induction heating, large area, microstructures, roll-to-plate, 1 | INTRODUCTION Advances in technology, such as the introduction of semiconductors and fiber optic communications, have accelerated the trend toward miniaturization, densification, and high precision in the development of [...]

The synergetic effects of metal(loid)s and soil characteristics on bacterial antibiotic resistance genes (ARGs) in green stormwater infrastructure (GSI) has been relatively understudied. Surface soil samples from six GSIs in Southern California over three time periods were assessed for selected ARGs, class 1 integron-integrase genes (intI1), 16S rRNA genes, and bioavailable and total concentrations of nine metal(loid)s, to investigate the relationships among ARGs, soil characteristics, and co-occurring metal(loid)s. Significant correlations existed among relative gene abundances (sul1, sul2, tetW, and intI1), total metal(loid)s (arsenic, copper, lead, vanadium, and zinc), and bioavailable metal(loid) (arsenic) (r = 0.29-0.61, padj

The dissemination of antibiotic resistance genes (ARGs) in the environment contributes to the global rise in antibiotic resistant infections. Therefore, it is of importance to further research the exposure pathways of these emerging contaminants to humans. This study explores commercially available garden products containing animal manure as a source of ARGs in a survey of 34 garden products, 3 recently landscaped soils, and 5 native soils. DNA was extracted from these soils and quantified for 5 ARGs, intI1, and 16S rRNA. This study found that both absolute and relative gene abundances in garden products ranged from approximately two to greater than four orders of magnitude higher than those observed in native soils. Garden products with Organic Materials Review Institute (OMRI) certification did not have significantly different ARG abundances. Results here indicate that garden products are important sources of ARGs to gardens, lawns, and parks.

In urban areas, untreated stormwater runoff can pollute downstream surface waters. To intercept and treat runoff, low-impact or "green infrastructure" approaches such as using biofilters are adopted. Yet, actual biofilter pollutant removal is poorly understood; removal is often studied in laboratory columns, with variable removal of viable and culturable microbial cell numbers including pathogens. Here, to assess bacterial pollutant removal in full-scale planted biofilters, stormwater was applied, unspiked or spiked with untreated sewage, in simulated storm events under transient flow conditions, during which biofilter influents versus effluents were compared. Based on microbial biomass, sequences of bacterial community genes encoding 16S rRNA, and gene copies of the human fecal marker HF183 and of the Enterococcus spp. marker Entero1A, removal of bacterial pollutants in biofilters was limited. Dominant bacterial taxa were similar for influent versus effluent aqueous samples within each inflow treatment of either spiked or unspiked stormwater. Bacterial pollutants in soil were gradually washed out, albeit incompletely, during simulated storm flushing events. In post-storm biofilter soil cores, retained influent bacteria were concentrated in the top layers (0-10 cm), indicating that the removal of bacterial pollutants was spatially limited to surface soils. To the extent that plant-associated processes are responsible for this spatial pattern, treatment performance might be enhanced by biofilter designs that maximize influent contact with the rhizosphere.