Manipulation of magnetic beads for actively capturing Vibrio parahaemolyticus and nucleic acid based on microfluidic system.

Rapid biological detection of pathogen micro-organisms has attracted much attention for practical biomedical applications. Despite the development in this field, it is still challenging to achieve simple and rapid biological detection using the microfluidic method. Herein, we propose a novel strategy of biological detection that combines precise detection control of the capillary microfluidic chip and versatile manipulation of magnetic beads. The microfluidic chip was fabricated via laser cutting, which utilized capillary pressure to realize rapid passive injection of liquid samples. Under an external magnetic field, the aptamer-modified magnetic beads were actuated to mix with Vibrio parahaemolyticus (V. parahaemolyticus) and its nucleic acid in the capillary microfluidic chip for rapid selective capture and detection, which could be achieved within 40 min. The experimental results demonstrated that V. parahaemolyticus could be captured using on-chip immunomagnetic beads with a high efficiency and significantly enhanced detection value. Due to these superior performances, the capillary microfluidic system, based on the manipulation of magnetic beads, demonstrated great potential for automatic biological detection.

Allosteric strand displacement isothermal amplification for the visual detection of Toxoplasma gondii in 30 minutes.

Early detection of Toxoplasma gondii (T. gondii) is critical due to a lack of effective treatment for toxoplasmosis.This study established a simple, cost-effective, and rapid colorimetric detection method for T. gondii. The entire testing process, from sample collection to results, takes only 0.5 h. These characteristics fulfill the demands of researchers seeking rapid target detection with minimal equipment reliance. For genomic extraction, this study evaluated the ability of two filter papers to capture genomes. A rapid genomic extraction device combined with the two filter papers was designed to simplify the genomic extraction process, which was completed within 10 min and increased the detection sensitivity tenfold. The method utilized a simplified primer design for isothermal amplification, namely allosteric strand displacement (ASD), and employed an underutilized commercial color indicator, Bromothymol Blue (BTB), for signal output. Compared with other reported indicators, BTB exhibited a more pronounced color change, shifting from blue to yellow in positive samples, facilitating easier visual differentiation. The reaction was completed in 20 min with a limit of detection (LOD) as low as 0.014 T. gondii per microliter.

Exploring the therapeutic potential of Sirt6-enriched adipose stem cell-derived exosomes in myocardial ischemia-reperfusion injury: unfolding new epigenetic frontiers.

BACKGROUND: The management of myocardial ischemia-reperfusion injury (MIRI) presents continuous therapeutic challenges. NAD-dependent deacetylase Sirtuin 6 (Sirt6) plays distinct roles in various disease contexts and is hence investigated for potential therapeutic applications for MIRI. This study aimed to examine the impact of Sirt6-overexpressing exosomes derived from adipose stem cells (S-ASC-Exo) on MIRI, focusing on their influence on AIM2-pyroptosis and mitophagy processes. The sirtuin family of proteins, particularly Sirtuin 6 (Sirt6), play a pivotal role in these processes. This study aimed to explore the potential therapeutic effects of Sirt6-enriched exosomes derived from adipose stem cells (S-ASC-Exo) on regulating MIRI. RESULTS: Bioinformatic analysis revealed a significant downregulation of Sirt6 in MIRI subjected to control group, causing a consequential increase in mitophagy and pyroptosis regulator expressions. Therefore, our study revealed that Sirt6-enriched exosomes influenced the progression of MIRI through the regulation of target proteins AIM2 and GSDMD, associated with pyroptosis, and p62 and Beclin-1, related to mitophagy. The introduction of S-ASC-Exo inhibited AIM2-pyroptosis while enhancing mitophagy. Consequently, this led to a significant reduction of GSDMD cleavage and pyroptosis in endothelial cells, catalyzing a deceleration in the progression of atherosclerosis. Extensive in vivo and in vitro assays were performed to validate the expressions of these specific genes and proteins, which affirmed the dynamic modulation by Sirt6-enriched exosomes. Furthermore, treatment with S-ASC-Exo drastically ameliorated cardiac functions and limited infarct size, underlining their cardioprotective attributes. CONCLUSIONS: Our study underscores the potential therapeutic role of Sirt6-enriched exosomes in managing MIRI. We demonstrated their profound cardioprotective effect, evident in the enhanced cardiac function and attenuated tissue damage, through the strategic modulation of AIM2-pyroptosis and mitophagy. Given the intricate interplay between Sirt6 and the aforementioned processes, a comprehensive understanding of these pathways is essential to fully exploit the therapeutic potential of Sirt6. Altogether, our findings indicate the promise of Sirt6-enriched exosomes as a novel therapeutic strategy in treating ischemia-reperfusion injuries and cardiovascular diseases at large. Future research needs to underscore optimizing the balance of mitophagy during myocardial ischemia to avoid potential loss of normal myocytes.

Biotemplated precise assembly approach toward ultra-scaled high-performance electronics.

Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 µA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.

A nodal EBV-positive T cell lymphoma with a T follicular helper cell phenotype.

AIMS: Nodal T follicular helper (TFH) cell lymphoma (nTFHL) is a rare type of clinically aggressive T cell lymphoma. With this lymphoma type, Epstein-Barr virus (EBV) infection is frequently detected in non-neoplastic B lymphocytes, but not yet identified in neoplastic T cells. We report two cases of nTFHL showing a classic morphology and immunoprofile, with EBV-encoded small RNAs (EBER) in-situ hybridisation positivity in neoplastic TFH cells. METHODS AND RESULTS: Clonal T cell receptor (TR) gene rearrangement was detected in both cases. Whole exome sequencing identified TET2, RHOA p. G17V, as well as gene mutations unique to each case. Microdissection analysis showed EBER positivity in tumour cells and in background non-neoplastic T lymphocytes. CONCLUSION: These two immunocompetent cases of nTFHL with EBV-positive tumour cells exhibit the featured gene mutation profile and poor prognosis of this disease. This novel finding of EBV positivity in our cases expands the currently recognised spectrum of EBV-positive nodal T cell lymphomas to include rare cases of nTFHL.

Point Cloud Scene Completion With Joint Color and Semantic Estimation From Single RGB-D Image.

We present a deep reinforcement learning method of progressive view inpainting for colored semantic point cloud scene completion under volume guidance, achieving high-quality scene reconstruction from only a single RGB-D image with severe occlusion. Our approach is end-to-end, consisting of three modules: 3D scene volume reconstruction, 2D RGB-D and segmentation image inpainting, and multi-view selection for completion. Given a single RGB-D image, our method first predicts its semantic segmentation map and goes through the 3D volume branch to obtain a volumetric scene reconstruction as a guide to the next view inpainting step, which attempts to make up the missing information; the third step involves projecting the volume under the same view of the input, concatenating them to complete the current view RGB-D and segmentation map, and integrating all RGB-D and segmentation maps into the point cloud. Since the occluded areas are unavailable, we resort to a A3C network to glance around and pick the next best view for large hole completion progressively until a scene is adequately reconstructed while guaranteeing validity. All steps are learned jointly to achieve robust and consistent results. We perform qualitative and quantitative evaluations with extensive experiments on the 3D-FUTURE data, obtaining better results than state-of-the-arts.

Explore Contextual Information for 3D Scene Graph Generation.

3D scene graph generation (SGG) has been of high interest in computer vision. Although the accuracy of 3D SGG on coarse classification and single relation label has been gradually improved, the performance of existing works is still far from being perfect for fine-grained and multi-label situations. In this article, we propose a framework fully exploring contextual information for the 3D SGG task, which attempts to satisfy the requirements of fine-grained entity class, multiple relation labels, and high accuracy simultaneously. Our proposed approach is composed of a Graph Feature Extraction module and a Graph Contextual Reasoning module, achieving appropriate information-redundancy feature extraction, structured organization, and hierarchical inferring. Our approach achieves superior or competitive performance over previous methods on the 3DSSG dataset, especially on the relationship prediction sub-task.

The relationships of OSBPL3 expression with KI-67 expression and KRAS mutations in CRC: implications for diagnosis and prognosis.

BACKGROUND: OSBPL3 is overexpressed in a variety of malignancies and is closely associated with tumor growth and metastasis. However, its expression and function in colorectal cancer (CRC) are unclear. We aimed to investigate its prognostic and therapeutic value in this disease by detecting its expression in CRC and its correlation with the clinicopathological characteristics and prognosis of patients. METHODS: A total of 92 CRC samples were included in this study. According to the 2020 WHO diagnostic criteria, the criteria of the American Joint Committee on Cancer (AJCC) 8th edition staging system were used. OSBPL3 and Ki-67 expression in these samples was detected by immunohistochemistry. OSBPL3 mRNA expression was detected by qRT-PCR. KRAS/NRAS mutations were detected by an amplification refractory mutation system (ARMS). Data analysis was performed using the statistical analysis software Prism 8. RESULTS: OSBPL3 was found to be significantly overexpressed in CRC tumor tissues and was associated with worse progression-free survival and overall survival in patients. Additionally, OSBPL3 expression was negatively correlated with the degree of tumor differentiation. KRAS mutations were detected in approximately 32.6% of patients and were significantly associated with high OSBPL3 expression. In addition, OSBPL3 and Ki-67 expression was significantly correlated. CONCLUSIONS: OSBPL3 is highly expressed in CRC samples and predicts a worse prognosis. OSBPL3 may become a new potential therapeutic target for CRC.

The value of CT radiomics features to predict visceral pleural invasion in ≤3 cm peripheral type early non-small cell lung cancer.

OBJECTIVE: To investigate predictive value of CT-based radiomics features on visceral pleural invasion (VPI) in ≤3.0 cm peripheral type early non-small cell lung cancer (NSCLC). METHODS: A total of 221 NSCLC cases were collected. Among them, 115 are VPI-positive and 106 are VPI-negative. Using a stratified random sampling method, 70% cases were assigned to training dataset (n = 155) and 30% cases (n = 66) were assigned to validation dataset. First, CT findings, imaging features, clinical data and pathological findings were retrospectively analyzed, the size, location and density characteristics of nodules and lymph node status, the relationship between lesions and pleura (RAP) were assessed, and their mean CT value and the shortest distance between lesions and pleura (DLP) were measured. Next, the minimum redundancy-maximum relevance (mRMR) and least absolute shrinkage and selection operator (LASSO) features were extracted from the imaging features. Then, CT imaging prediction model, texture feature prediction model and joint prediction model were built using multifactorial logistic regression analysis method, and the area under the ROC curve (AUC) was applied to evaluate model performance in predicting VPI. RESULTS: Mean diameter, density, fractal relationship with pleura, and presence of lymph node metastasis were all independent predictors of VPI. When applying to the validation dataset, the CT imaging model, texture feature model, and joint prediction model yielded AUC = 0.882, 0.824 and 0.894, respectively, indicating that AUC of the joint prediction model was the highest (p < 0.05). CONCLUSION: The study demonstrates that the joint prediction model containing CT morphological features and texture features enables to predict the presence of VPI in early NSCLC preoperatively at the highest level.

Comprehensive metabolite quantitative assay based on alternate metabolomics and lipidomics analyses.

Metabolomics-based precision medicine is facing several obstacles including cross-platform data comparison issue and the lack of metabolome benchmark values of healthy population, one of main reasons is the shortage of comprehensive metabolome quantitation methods. Here, we developed an alternate reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) method to quantitatively determine metabolites and lipids. Assisted by a wide set of reference standards and real samples, up to 397 multiple reaction monitoring (MRM) transitions (239 for positive and 158 for negative ion modes) and 1080 MRM transitions (607 for positive and 473 for negative ion modes) were defined respectively in the metabolomic and lipidomic analyses with more than 1000 metabolites and lipids being quantified. Among them, 144 analytes including amines, amino acids, benzenoids, peptides, nucleobases and related, bile acids, carboxylic acids, fatty acids, hormones, indoles and others were absolutely quantified, while carnitines, lyso-phosphatidylcholines, lyso-phosphatidylethanolamines, free fatty acids, sphingomyelins, phosphatidylcholines (PCs), alkyl and alkenyl substituted PCs, phosphatidylethanolamines (PEs), alkyl and alkenyl substituted PEs and triacylglycerols were semiquantified. The developed method was validated to have good analytical characteristics. Analytical results of standard reference material 1950 human plasma had a good agreement with literature data. As a proof of application, this method was used to study serum metabolic pattern changes of patients with hyperuricemia and nonalcoholic fatty liver. This alternate RPLC-MS method for quantitative metabolites and lipids analysis can further be used to provide technology and large-scale data support for precision medicine and life sciences.

A novel transcriptional activation mechanism of inulinase gene in Kluyveromyces marxianus involving a glycolysis regulator KmGcr1p with unique and functional Q-rich repeats.

Kluyveromyces marxianus is the most suitable fungus for inulinase industrial production. However, the underlying transcriptional activation mechanism of the inulinase gene (INU1) is hitherto unclear. Here, we undertook genetic and biochemical analyses to elucidate that a glycolysis regulator KmGcr1p with unique Q-rich repeats is the key transcriptional activator of INU1. We determined that INU1 and glycolytic genes share similar transcriptional activation patterns and that inulinase activity is induced by fermentable carbon sources including the hydrolysis products of inulin (fructose and glucose), which suggests a novel model of product feedback activation. Furthermore, all four CT-boxes in the INU1 promoter are important for KmGcr1p DNA-binding in vitro, but the most downstream CT-box 1 primarily confers upstream activating sequence activity in vivo. More intriguingly, the use of artificial and natural GCR1 mutants suggests that the Q-rich repeats act as a functional module to maintain KmGcr1p transcriptional activity by contributing to its solubility and DNA-binding affinity. Altogether, this study uncovers a novel transcriptional activation mechanism for the inulinase gene, that is different from the previous understanding for filamentous fungi, but might have universal significance among inulinase-producing yeasts, thereby leading to a better understanding of the regulation mechanism of yeast inulinase genes.

Anti-virus effects of interferon regulatory factors (IRFs) identified in ascidian Ciona savignyi.

Interferon regulatory factors (IRFs) are key transcription factors that function in the immune system via the interferon (IFN) pathway. In the current study, we identified and characterized three IRFs (CsIRFL1, CsIRFL2, and CsIRFL3) from ascidian Ciona savignyi. Phylogenetic analysis showed that CsIRFL1 was clustered with two IRFs from Ciona robusta and shrimp IRF apart from the vertebrate IRFs, whereas CsIRFL2 and CsIRFL3 were grouped with an unnamed protein from Oikopleura dioica into a sub-branch highly identifying with the vertebrate IRF4, IRF8, and IRF9. Gene expression analysis revealed that CsIRFL1 and CsIRFL2 expressed in all the examined adult tissues (stomach, intestines, eggs, hemocytes, gonad, heart, and pharynx) and predominantly in hemocytes. However, the expression of CsIRFL3 was undetectable in the tested adult tissues. Furthermore, in situ hybridization showed that CsIRFL1 and CsIRFL2 mainly expressed in immunocytes within hemolymph, including phagocytes, macrophage-like cells, morula cells, and amoebocytes, suggesting CsIRFL1 and CsIRFL2 were involved in ascidian immune responses. We then performed LPS and poly(I:C) challenge assay and found that CsIRFL1 highly expressed in the cultured hemocytes following LPS infection for 24 h. After viral analogue poly(I:C) stimulation, the expression of CsIRFL2 was dramatically upregulated from 12 to 24 h. Meanwhile, two critical components of the IFN signaling pathways, STAT and TBK1, showed the increased expression as well after poly(I:C) induction, indicating that CsIRFL2 and IFN pathways genes were activated under the infection of viral analogue. Thus, our findings suggested that CsIRFL2 was a potential transcriptional regulatory factor that participated in regulating the ascidian anti-virus immune response.

DNA-directed nanofabrication of high-performance carbon nanotube field-effect transistors.

Biofabricated semiconductor arrays exhibit smaller channel pitches than those created using existing lithographic methods. However, the metal ions within biolattices and the submicrometer dimensions of typical biotemplates result in both poor transport performance and a lack of large-area array uniformity. Using DNA-templated parallel carbon nanotube (CNT) arrays as model systems, we developed a rinsing-after-fixing approach to improve the key transport performance metrics by more than a factor of 10 compared with those of previous biotemplated field-effect transistors. We also used spatially confined placement of assembled CNT arrays within polymethyl methacrylate cavities to demonstrate centimeter-scale alignment. At the interface of high-performance electronics and biomolecular self-assembly, such approaches may enable the production of scalable biotemplated electronics that are sensitive to local biological environments.

Radial Extracorporeal Shock Wave Therapy as a Novel Agent for Benign Prostatic Hyperplasia Refractory to Current Medical Therapy.

This study aimed to assess efficacy and safety data from pilot trials of the radial extracorporeal shock wave therapy (rESWT) to treat benign prostatic hyperplasia (BPH) refractory to current medical therapy. A total of 29 men with lower urinary tract symptoms (LUTS) suggestive of BPH who had responded poorly to medical therapy for at least 6 months and were poor surgical candidates were enrolled. Each participant was treated with rESWT once a week for 8 weeks, each by 2000 impulses at 2.0 bar and 10 hertz of frequency. International Prostate Symptom Score (IPSS), quality of life (QoL), and International Index of Erectile Function-5 (IIEF-5) were evaluated before treatment, after the fourth and eighth rESWT, and 3 months after the end of treatment. Peak urinary flow ( Qmax) and postvoid residual (PVR) were assessed. Safety was also documented. Statistically significant clinical improvements were reported for IPSS, QoL, and IIEF-5 after treatment, and those were sustained until 3 months follow-up. Qmax and PVR improved evidently at 8 weeks with a 63% and 70% improvement, respectively. The only adverse event was the occasional perineum pain or discomfort, which usually disappeared within 3 days. The rESWT may be an effective, safe, and noninvasive treatment for symptomatic BPH in selected patients whose medical treatment has faced failure and are poor surgical candidates.

Efficacy of Radial Extracorporeal Shock Wave Therapy for Chronic Pelvic Pain Syndrome: A Nonrandomized Controlled Trial.

This study aims to determine the effect of radial extracorporeal shock wave therapy (rESWT) versus drug when treating chronic pelvic pain syndrome (CPPS; type III B chronic prostatitis). The study included 45 participants with CPPS, divided into two groups: Group I comprised 25 participants, who were treated with rESWT (3,000 pulses each; pressure: 1.8-2.0 bar; frequency: 10 Hz) once a week; Group II consisted of 20 participants who received a combination of an α-blocker and an anti-inflammatory agent. Participants were treated for 8 weeks. The assessments were done before treatment, after the fourth and eighth rESWT, and 3 months after the end of treatment by Visual Analogue Scale (VAS) for pain, National Institutes of Health-developed Chronic Prostatitis Symptom Index (NIH-CPSI), International Prostate Symptom Score (IPSS), quality of life (QoL), and International Index of Erectile Function-5 (IIEF-5). Both groups of participants showed statistically significant improvement in all the assessments ( p < .001) after the treatment, with significantly better results in Group I in NIH-CPSI ( p < .001). The recurrence rate of symptoms in Group I at 3 months after end of treatment was much lower than that in Group II (4% vs. 50%, p < .001). This prospectively nonrandomized, control study revealed perineal rESWT as a new therapy option for CPPS with statistically significant effects in comparison to drugs at least for 3 months after cessation of treatment.

High expression of SLC34A2 is a favorable prognostic marker in lung adenocarcinoma patients.

Dysregulation of SLC34A2 (NaPi2b) in tumors has attracted wide attention, but its expression and function in non-small cell lung cancer remains unclear. By examining its expression in lung adenocarcinoma and correlation to patient outcome, we aimed to explore its prognostic and therapeutic values in this deadly disease. Overall, 175 cases of lung adenocarcinoma sample were included in this study. Histological subtyping of them was diagnosed according to standards of the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society in 2011. Protein expression of SLC34A2 and anaplastic lymphoma kinase in these samples was determined by immunohistochemistry. Epidermal growth factor receptor mutations were examined using amplification refractory mutation system. Statistical analysis was performed using software of Pearson's correlation coefficient. High expression of SLC34A2 was identified in about 2/3 patients and correlated with significantly better patient's overall survival. Epidermal growth factor receptor mutations were detected in about 53% of patients with no statistically significant difference to patient's overall survival. Anaplastic lymphoma kinase rearrangement was found in 8 out of 175 patients, harboring this abnormality leads to shorter overall survival. No correlation has been found between SLC34A2 expression and epidermal growth factor receptor mutation or anaplastic lymphoma kinase rearrangements in lung adenocarcinoma. High expression of SLC34A2 is present in about 3/4 lung adenocarcinoma samples and predicts better outcome. Since it is a membrane protein, antibody-based drugs targeting this marker might bring new resolution to this deadly disease.