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Abstract Background Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples. Results Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 104 cells/g feces) and linearity (R 2 > 0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016 T, resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 103 cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016 T during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a much lower LOD and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing). Conclusions Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract

Abstract High-power terahertz (THz) quantum cascade laser, as an emerging THz solid-state radiation source, is attracting attention for numerous applications including medicine, sensing, and communication. However, due to the sub-wavelength confinement of the waveguide structure, direct beam brightness upscaling with device area remains elusive due to several mode competition and external optical lens is normally used to enhance the THz beam brightness. Here, we propose a metallic THz photonic crystal resonator with a phase-engineered design for single mode surface emission over a broad area. The quantum cascade surface-emitting laser is capable of delivering an output peak power over 185 mW with a narrow beam divergence of 4.4° × 4.4° at 3.88 THz. A high beam brightness of 1.6 × 107 W sr−1m−2 with near-diffraction-limited M2 factors of 1.4 in both vertical and lateral directions is achieved from a large device area of 1.6 × 1.6 mm2 without using any optical lenses. The adjustable phase shift between the lattices enables a stable and high-intensity surface emission over a broad device area, which makes it an ideal light extractor for large-scale THz emitters. Our research paves the way to high brightness solid-state THz lasers and facilitates new applications in standoff THz imaging, detection, and diagnosis.

Abstract We aimed to assess the cumulative incidences of cancer-specific mortality (CSM) in non-metastatic patients with non‑muscle invasive urothelial bladder cancer (NMIUBC) and establish competing risk nomograms to predict CSM. Patient data was sourced from the Surveillance, Epidemiology, and End Results database, as well as the electronic medical record system in our institution to form the external validation cohort. Sub-distribution proportional hazards model was utilized to determine independent risk factors influencing CSM in non-metastatic NMIUBC patients. Competitive risk nomograms were constructed to predict 3-year, 5-year, and 8-year cancer-specific survival (CSS) in all patients group, TURBT group and cystectomy group, respectively. The discrimination and accuracy of the model were validated through the concordance index (C-index), the area under the receiver operating characteristic curve (AUC), and calibration curves. Decision curve analysis (DCA) and a risk stratification system was employed to evaluate the clinical utility of the model. Race, age, marital status, surgery in other sites, tumor size, histological type, histological grade, T stage and N stage were identified as independent risk factors to predict CSS in all patients group. The C-index for 3-year CSS was 0.771, 0.770 and 0.846 in the training, testing and external validation sets, respectively. The ROC curves showed well discrimination and the calibration plots were well fitted and consistent. Moreover, DCA demonstrated well clinical effectiveness. Altogether, the competing risk nomogram displayed excellent discrimination and accuracy for predicting CSS in non-metastatic NMIUBC patients, which can be applied in clinical practice to help tailor treatment plans and make clinical decisions.

IntroductionCancer-associated fibroblasts (CAFs) are a diverse group of cells that significantly contribute to reshaping the tumor microenvironment (TME), and no research has systematically explored the molecular landscapes of senescence related CAFs (senes CAF) in NB.MethodsWe utilized pan-cancer single cell and spatial transcriptomics analysis to identify the subpopulation of senes CAFs via senescence related genes, exploring its spatial distribution characteristics. Harnessing the maker genes with prognostic significance, we delineated the molecular landscapes of senes CAFs in bulk-seq data. We established the senes CAFs related signature (SCRS) by amalgamating 12 and 10 distinct machine learning (ML) algorithms to precisely diagnose stage 4 NB and to predict prognosis in NB. Based on risk scores calculated by prognostic SCRS, patients were categorized into high and low risk groups according to median risk score. We conducted comprehensive analysis between two risk groups, in terms of clinical applications, immune microenvironment, somatic mutations, immunotherapy, chemotherapy and single cell level. Ultimately, we explore the biological function of the hub gene JAK1 in pan-cancer multi-omics landscape.ResultsThrough integrated analysis of pan-cancer spatial and single-cell transcriptomics data, we identified distinct functional subgroups of CAFs and characterized their spatial distribution patterns. With marker genes of senes CAF and leave-one-out cross-validation, we selected RF algorithm to establish diagnostic SCRS, and SuperPC algorithm to develop prognostic SCRS. SCRS demonstrated a stable predictive capability, outperforming the previously published NB signatures and clinic variables. We stratified NB patients into high and low risk group, which showed the low-risk group with a superior survival outcome, an abundant immune infiltration, a different mutation landscape, and an enhanced sensitivity to immunotherapy. Single cell analysis reveals biologically cellular variations underlying model genes of SCRS. Spatial transcriptomics delineated the molecular variant expressions of hub gene JAK1 in malignant cells across cancers, while immunohistochemistry validated the differential protein levels of JAK1 in NB.ConclusionBased on multi-omics analysis and ML algorithms, we successfully developed the SCRS to enable accurate diagnosis and prognostic stratification in NB, which shed light on molecular landscapes of senes CAF and clinical utilization of SCRS.

Air pollution, particularly fine particulate matter and gaseous pollutants including NO2 and NOx, presents significant public health challenges. While the harmful effects of these pollutants are well-documented, the molecular mechanisms underlying their impact on health remain incompletely understood. In this study, we utilized genome-wide association study (GWAS) data from the UK Biobank, expression quantitative trait loci (eQTL) data from the Genotype-Tissue Expression (GTEx) project, and protein quantitative trait loci (pQTL) data from the Atherosclerosis Risk in Communities (ARIC) study to conduct comprehensive analyses using the Unified Test for Molecular Signatures (UTMOST), Transcriptome-wide Association Studies (TWAS), and Proteome-wide Association Studies (PWAS). To integrate and synthesize these analyses, we developed the AirSigOmniTWP Hub, a specialized platform designed to consolidate and interpret the results from UTMOST, TWAS, and PWAS. TWAS analysis identified a significant association between PM10 exposure and the gene INO80E in females (P = 4.37×10⁻⁵, FDR = 0.0383), suggesting a potential role in chromatin remodeling. PWAS analysis revealed a significant association between NOx exposure and the gene PIP in females (P = 2.28×10⁻⁵, FDR = 0.0299), implicating its involvement in inflammatory pathways. Additionally, UTMOST analyses uncovered significant associations between various pollutants and genes including NCOA4P3 and SPATS2L with PM2.5 exposure, indicating potential mechanisms related to transcriptional regulation and gene-environment interactions.

Abstract Topological lasers (TLs) have attracted widespread attention due to their mode robustness against perturbations or defects. Among them, electrically pumped TLs have gained extensive research interest due to their advantages of compact size and easy integration. Nevertheless, limited studies on electrically pumped TLs have been reported in the terahertz (THz) and telecom wavelength ranges with relatively low output powers, causing a wide gap between practical applications. Here, we introduce a surface metallic Dirac-vortex cavity (SMDC) design to solve the difficulty of increasing power for electrically pumped TLs in the THz spectral range. Due to the strong coupling between the SMDC and the active region, robust 2D topological defect lasing modes are obtained. More importantly, enough gain and large radiative efficiency provided by the SMDC bring in the increase of the output power to a maximum peak power of 150 mW which demonstrates the practical application potential of electrically pumped TLs.

To analyse the effects of Moutan cortex radicis extract (ME) on lipid metabolism disorder via regulation of lipid accumulation and endoplasmic reticulum stress (ERS). C57BL/6 mice were fed an HFD for 11 weeks and then an HFD plus 200 mg/kg ME for 2 weeks. We found that ME reduced hepatic CHOL levels and lipid droplet deposition, and down-regulated PPARγ, SCD1, GRP78 and C/EBP compared to the HFD group (P

Micromagnets integrated into microelectromechanical systems devices are widely used in the fields of micro-energy harvesters, micro-actuators, and speakers. A novel method for fabricating NdFeB micromagnets based on vacuum negative pressure injection is presented. The influence of array element shape, size, and injection channel on the surface magnetic field was studied by Maxwell finite element analysis. A circle array of 600 µm diameter and 150 µm spacing could generate a stronger magnetic field at the edge of the magnet array. Micron-sized magnetic powders with a diameter of 5 µm mixed with the SU8 T2010 photoresist were filled into the microcavity on a PDMS (polydimethylsiloxane) elastomer, which was prepared by the SU8 positive membrane. The PDMS elastomer was bonded to the glass substrate and degassed by a vacuum pump to form negative pressure for rapid injection and uniform filling. By selecting a suitable binder and optimizing the mixing ratio of the magnetic powder, a 165 µm thick micromagnet with homogeneous dispersion of magnetic powder particles was achieved, and the weight percentage of magnetic powder in the SU8 photoresist was 41.8%. The remanent magnetization of micromagnets was 42 emu/g, the coercivity was 6895 Oe, and the maximum surface magnetic field strength was 1.3 mT after magnetization in a 2 T uniform magnetic field. Finally, the micromagnet array was utilized in a cantilever beam micro-actuator, which could drive the cantilever beam and exhibit an excellent linearity.

The photonic crystal surface-emitting laser (PCSEL) has attracted much attention due to the advantages of a small far-field divergence angle and high output power. Here, we report a high-power terahertz (THz) photonic crystal laser with high beam quality through the optimization of the absorption boundary condition and the introduction of the symmetrically distributed electrodes. Single-mode surface emission at 3.4 THz with the maximum peak output power of 50 mW is demonstrated. Meanwhile, a high symmetric far-field pattern with C6 symmetry and a small divergence angle is achieved. In this device, the integration of the stable single-mode operation, high beam quality and high output power is realized, which may have great significance for practical applications.

With the advent of the internet of things and artificial intelligence, flexible and portable pressure sensors have shown great application potential in human-computer interaction, personalized medicine and other fields. By comparison with traditional inorganic materials, flexible polymeric materials conformable to the human body are more suitable for the fabrication of wearable pressure sensors. Given the consumption of a huge amount of flexible wearable electronics in near future, it is necessary to turn their attention to biodegradable polymers for the fabrication of flexible pressure sensors toward the development requirement of green and sustainable electronics. In this paper, the structure and properties of silk fibroin (SF) are introduced, and the source and research progress of the piezoelectric properties of SF are systematically discussed. In addition, this paper summarizes the advance in the studies on SF-based capacitive, resistive, triboelectric, and piezoelectric sensors reported in recent years, and focuses on their fabrication methods and applications. Finally, this paper also puts forward the future development trend of high-efficiency fabrication and corresponding application of SF-based piezoelectric sensors. It offers new insights into the design and fabrication of green and biodegradable bioelectronics for in vitro and in vivo sensing applications.

Aldoxime dehydratases (Oxds) have received considerable attention recently due to their application in the asymmetric synthesis of nitriles without cyanide by catalyzing the dehydration of aldoxime. However, the low stability of Oxds remains a huge obstacle to achieving high conversions and productivities of hydrophobic substrates. OxdPsp was immobilized on a macroporous adsorption resin (IOP) via an ATPS coupled with in situ immobilization. IOP-catalyzed dehydration of 2-phenylpropanal oxime (1) to prepare (S)-2-phenylpropanenitrile ((S)-2) was successfully performed with 95.7% yield, 94.1% ee and 98.6% conversion. The enriched (S)-nitrile (ee 94.1%) was obtained by using (E)-enriched aldoximes (E/Z = 97/3) as the substrate, which is consistent with the Gröger enantiopreference rule. A kinetic model to predict the dehydration catalyzed by IOP was established with an average deviation of 7.6%. The IOP-catalyzed dehydration reaction follows a sequential mechanism including substrate and product inhibition. Developing a kinetic model is a key step in the application of artificial intelligence in chemical engineering. After three recycling steps of IOP, the yield of (S)-2 still reached 83.6%, indicating that the stability of IOP was greatly enhanced, which was attributed to employing an organic solvent with a higher lg P value as the working medium and the immobilization protocol. [ABSTRACT FROM AUTHOR]