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Abstract Background Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. Results Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. Conclusions LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.

Abstract Background Postoperative pulmonary complications (PPCs) extend the length of stay of patients and increase the perioperative mortality rate after video-assisted thoracoscopic (VATS) pulmonary surgery. Thoracic paravertebral block (TPVB) provides effective analgesia after VATS surgery; however, little is known about the effect of TPVB on the incidence of PPCs. The aim of this study is to determine whether TPVB combined with GA causes fewer PPCs and provides better perioperative lung protection in patients undergoing VATS pulmonary surgery than simple general anaesthesia. Methods A total of 302 patients undergoing VATS pulmonary surgery will be randomly divided into two groups: the paravertebral block group (PV group) and the control group (C group). Patients in the PV group will receive TPVB: 15 ml of 0.5% ropivacaine will be administered to the T4 and T7 thoracic paravertebral spaces before general anaesthesia induction. Patients in the C group will not undergo the intervention. Both groups of patients will be subjected to a protective ventilation strategy during the operation. Perioperative protective mechanical ventilation and standard fluid management will be applied in both groups. Patient-controlled intravenous analgesia is used for postoperative analgesia. The primary endpoint is a composite outcome of PPCs within 7 days after surgery. Secondary endpoints include blood gas analysis, postoperative lung ultrasound score, NRS score, QoR-15 score, hospitalization-related indicators and long-term prognosis indicators. Discussion This study will better evaluate the impact of TPVB on the incidence of PPCs and the long-term prognosis in patients undergoing VATS lobectomy/segmentectomy. The results may provide clinical evidence for optimizing perioperative lung protection strategies. Trial registration ClinicalTrials.gov NCT05922449 . Registered on June 25, 2023.

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

ABSTRACTObjectives POEMS syndrome is a rare disorder which has been increasingly recognized. The clonal origin is controversial. Some people argue that POEMS syndrome originates from abnormal plasma cell clones. So, treatment frequently targets the plasma cell clone. Nevertheless, others believe that both plasma cells and B cells can be the potential culprit in POEMS syndrome.Methods A 65-year-old male came to the emergency department of our hospital with the complaints of bilateral soles numbness and weight loss for half a year, abdominal distension for half a month, and chest tightness and shortness of breath for one day. He was then diagnosed as POEMS syndrome complicated with monoclonal B-cell lymphocytosis (non-CLL type). A standard bendamustine plus rituximab (BR) regimen combined with low dose of lenalidomide was administered.Results After four cycles of treatment, the ascites of the patient was absent and the neurological symptom disappeared. The renal function, the IgA level, and the VEGF level all returned to normal.Discussion POEMS syndrome, a multi-system disorder, is easily misdiagnosed. The clonal origin of POEMS syndrome is controversial and needs further study. For now, there are no approved treatment regimens. Treatments mainly target the plasma cell clone. This case suggested that other therapy besides anti-plasma cell treatment may also be effective in POEMS syndrome.Conclusion We report a patient with POEMS syndrome who achieved complete response after treatment with the combination of a standard BR regimen and low dose of lenalidomide. POEMS syndrome's pathological mechanisms and therapies warrant further studies.

The heterogeneous catalytic activation of peroxymonosulfate (PMS) for wastewater treatment is attracting increased research interest. Therefore, it is essential to find a sustainable, economical, and effective activated material for wastewater treatment. In this study, metal–organic framework (MOF)-5 was used as the precursor, and a stable and recyclable material ZnO@Ni3ZnC0.7 that exhibited good adsorption and catalytic properties, was obtained by the addition of nickel and subsequent calcination. To investigate and optimize the practical application conditions, the elimination of rhodamine B (RhB) in water was selected as the model process. This study demonstrated that the degradation of organic matter in the system involved a coupling of the adsorption and degradation processes. Based on this, the mechanism of the entire process was proposed. The results of scanning electron microscopy, infrared spectrum analysis, and theoretical analysis confirmed that the van der Waals forces, electrostatic attraction, and hydrogen bonding influenced the adsorption process. Electron paramagnetic resonance analysis, masking experiments, and electrochemical tests conducted during the oxidative degradation process confirmed that the degradation mechanism of RhB included both radical and non-free radical pathways, and that the surface hydroxyl group was the key active site. The degradation of the adsorbed substrates enabled the regeneration of the active sites. The material regenerated using a simple method exhibited good efficiency for the removal of organic compounds in four-cycle tests. Moreover, this material can effectively remove a variety of organic pollutants, and can be easily recovered owing to its magnetic properties. The results demonstrated that the use of heterogeneous catalytic materials with good adsorption capacity could be an economical and beneficial strategy.

Graphitic carbon nitride (CN) was a promising candidate for efficient environmental remediation in the advanced oxidation processes (AOPs). However, whether CN itself had some potential environmental risks, such as affecting the production of disinfection byproducts (DBPs) was still unknown. This study investigated the formation potential of DBPs in the presence of CN. The experimental data revealed that CN had a high potential to form DBPs, and dichloroacetonitrile (DCAN) was the most produced species during the chlorination and chloramination processes. Moreover, the effects of chlorine time, chlorine dosage, pH, and CN dosage during the chlorination process were evaluated to understand the formation pattern of DBPs. The possible mechanism of DBPs formation was deduced by analyzing the results of FTIR, Raman, and XPS before and after chlorination. Finally, the DBPs formation potential and cytotoxicity of the CN leaching solution were investigated, indicating CN could leach the precursors of DBPs and that the potential toxicity of the leaching solution increased with the extension of CN immersion time. In general, this research adds an understanding of the DBP formation of CN in water treatment systems and sheds light on CN's environmental potential risks. HIGHLIGHTS g-C3N4(CN) has a high potential to form DBPs and dichloroacetonitrile (DCAN) was the dominant species.; Chorine dosage, pH, and CN dosage could significantly affect DBPs formation.; Chlorine attacked the N-containing aromatic ring and the surface amino group of CN to produce DBPs.; CN could leach the precursors of DBPs and DCAN was the major contributor to the formed DBPs cytotoxicity.;

Areca nut (Areca catechu L.) seeds are rich in polyphenols, while few studies focused on it. This study was designed to obtain the maximum extraction yield of areca nut seed polyphenol (ACP). An ultrasonic-assisted extraction method optimized by response surface methodology (RSM) was established to extract ACP. Under the optimal conditions (ultrasonic power of 87 W, ethanol concentration of 65%, extraction temperature of 62℃, and extraction time of 153 min), the actual extraction yield of ACP was 139.62 mg/g. Then we investigated the effects of ACP on the proliferation, differentiation and mineralization of MC3T3-E1 pre-osteoblasts. Results suggested that ACP notably promoted the proliferation of MC3T3-E1 cells without cytotoxicity, and the contents of collagen type Ⅰ (COL-Ⅰ) and osteocalcin (OCN) were rising. Meanwhile, the alkaline phosphatase (ALP) activity and mineralized nodules were enhanced. These findings demonstrated that ACP could induce the proliferation, differentiation and mineralization of osteoblasts in vitro. This work provided a certain experimental basis for the developing and utilization of polyphenols from Areca nut seeds.

BackgroundOsteoarthritis (OA) is a degenerative joint disease frequently diagnosed in the elderly and middle-aged population. However, its specific pathogenesis has not been clarified. This study aimed to identify biomarkers for OA diagnosis and elucidate their potential mechanisms for restoring OA-dysregulated autophagy and inhibiting chondrocyte apoptosis in vitro.Material and methodsTwo publicly available transcriptomic mRNA OA-related datasets (GSE10575 and GSE51588) were explored for biomarker identification by least absolute shrinkage and selection operator (LASSO) regression, weighted gene co-expression network analysis (WGCNA), and support vector machine recursive feature elimination (SVM-RFE). We applied the GSE32317 and GSE55457 cohorts to validate the markers’ efficacy for diagnosis. The connections of markers to chondrocyte autophagy and apoptosis in OA were also comprehensively explored in vitro using molecular biology approaches, including qRT-PCR and Western blot.ResultsWe identified 286 differentially expressed genes (DEGs). These DEGs were enriched in the ECM-receptor interaction and PI3K/AKT signaling pathway. After external cohort validation and protein-protein interaction (PPI) network construction, PDK1 was finally identified as a diagnostic marker for OA. The pharmacological properties of BX795-downregulated PDK1 expression inhibited LPS-induced chondrocyte inflammation and apoptosis and rescued OA-dysregulated autophagy. Additionally, the phosphorylation of the mediators associated with the MAPK and PI3K/AKT pathways was significantly downregulated, indicating the regulatory function of PDK1 in apoptosis and autophagy via MAPK and PI3K/AKT-associated signaling pathways in chondrocytes. A significantly positive association between the PDK1 expression and Neutrophils, Eosinophils, Plasma cells, and activated CD4 memory T cells, as well as an evident negative correlation between T cells follicular helper and CD4 naive T cells, were detected in the immune cell infiltration analysis.ConclusionsPDK1 can be used as a diagnostic marker for OA. Inhibition of its expression can rescue OA-dysregulated autophagy and inhibit apoptosis by reducing the phosphorylation of PI3K/AKT and MAPK signaling pathways.

In recent years, the development of safe and effective anti-osteoporosis factors has attracted extensive attention. In this study, an estrogen-deficient osteoporosis rat model was employed to study the improving mechanism of sialoglycoprotein isolated from Gadus morhua eggs (Gds) against osteoporosis. The results showed that compared with OVX, Gds ameliorated the trabecular microstructure, especially the increased trabecular thickness, decreased trabecular separation, and enhanced the trabecular number. The analysis of qRT-PCR and western blotting found that Gds reduced bone resorption by inhibiting RANKL-induced osteoclastogenesis. The LC-MS/MS was used to investigate serum metabolism, and the enrichment metabolites were analyzed by the KEGG pathway. The results revealed that the Gds significantly altered the fat anabolism pathway, which includes ovarian steroidogenesis pathway and arachidonic acid metabolism pathway. Altogether, Gds could improve osteoporosis by suppressing high bone turnover via controlling OPG/RANKL/TRAF6 pathway, which is implicated with ovarian steroidogenesis pathway and arachidonic acid metabolism pathway. These findings indicated that Gds could be a candidate factor for anti-osteoporosis.

ABSTRACTThe RNA interference (RNAi) pathway directs an important antiviral immunity mechanism in plants and invertebrates. Recently, we and others have demonstrated that the antiviral RNAi response is also conserved in mammals, at least to five distinct RNA viruses, including Zika virus (ZIKV). ZIKV may preferentially infect neuronal progenitor cells (NPCs) in the developing foetal brain. Ex vivo ZIKV infection induces RNAi-mediated antiviral response in human NPCs, but not in the more differentiated NPCs or somatic cells. However, litter is known about the in vivo property or function of the virus-derived small-interfering RNAs (vsiRNAs) targeting ZIKV. Here we report a surprising observation: different from ex vivo observations, viral small RNAs (vsRNAs) targeting ZIKV were produced in vivo upon infection in both central neuron system (CNS) and muscle tissues. In addition, our findings demonstrate the production of canonical vsiRNAs in murine CNS upon antiviral RNAi activation by Sindbis virus (SINV), suggesting the possibility of antiviral immune strategy applied by mammals in the CNS.

The interferon-regulated antiviral responses are essential for the induction of both innate and adaptive immunity in mammals. Production of virus-derived small-interfering RNAs (vsiRNAs) to restrict virus infection by RNA interference (RNAi) is a recently identified mammalian immune response to several RNA viruses, which cause important human diseases such as influenza and Zika virus. However, little is known about Dicer processing of viral double-stranded RNA replicative intermediates (dsRNA-vRIs) in mammalian somatic cells. Here we show that infected somatic cells produced more influenza vsiRNAs than cellular microRNAs when both were produced by human Dicer expressed de novo, indicating that dsRNA-vRIs are not poor Dicer substrates as previously proposed according to in vitro Dicer processing of synthetic long dsRNA. We report the first evidence both for canonical vsiRNA production during wild-type Nodamura virus infection and direct vsiRNA sequestration by its RNAi suppressor protein B2 in two strains of suckling mice. Moreover, Sindbis virus (SINV) accumulation in vivo was decreased by prior production of SINV-targeting vsiRNAs triggered by infection and increased by heterologous expression of B2 in cis from SINV genome, indicating an antiviral function for the induced RNAi response. These findings reveal that unlike artificial long dsRNA, dsRNA-vRIs made during authentic infection of mature somatic cells are efficiently processed by Dicer into vsiRNAs to direct antiviral RNAi. Interestingly, Dicer processing of dsRNA-vRIs into vsiRNAs was inhibited by LGP2 (laboratory of genetics and physiology 2), which was encoded by an interferon-stimulated gene (ISG) shown recently to inhibit Dicer processing of artificial long dsRNA in cell culture. Our work thus further suggests negative modulation of antiviral RNAi by a known ISG from the interferon response.

In this study, a total of 24 male Sprague Dawley rats were randomly divided into 3 group (Collagen peptide of Salmon salar skin group, Ss-SCP; Collagen peptide of Tilapia nilotica skin group, Tn-SCP and Model control group, MC) to investigate the impact of a high-collagen peptide diet on the gut microbiota and host health. After 16 days intervention, the body weights of the Ss-SCP and Tn-SCP intervention groups were significantly increased and the liver index was also remarkably higher than that of the MC group. The acetic acid and propionic acid levels in feces were both significantly increased in the diet high-collagen peptide groups and valerate acid level was lower than that in the MC group. With the intervention of a high-dose collagen peptide diet, the gut microbiota of the groups was shifted with increased abundance of Lactobacillus, Unidentified-Prevotellaceae, Allobaculum, and Parasutterella, whereas the Tn-SCP administration have caused low abundance of Anaerostipes, Blautia, and Fusicatenibacter. The relative abundance of Allobaculum as well as Parasutterella was positively correlated with propionic acid and acetic acid levels, respectively. In addition, Allobaculum abundance was negatively correlated with valerate acid level. The serum valerate acid content was potentially harmful to rat health and significantly increased in the groups intervened with collagen peptide. All together, these results showed that administration of diet high-collagen peptide shifts the gut microbiota in rats and induced a disturbance in short-chain fatty acid metabolism which is potentially harmful to health.

Metal oxide nanocrystals have garnered significant attention owing to their unique properties, including luminescence, ferroelectricity, and catalytic activity. Among the various synthetic methods, hydrothermal synthesis is a promising method for synthesizing metal oxide nanocrystals and nanoclusters. Because the shape and surface structure of the nanocrystals largely affect their properties, their analytical methods should be developed. Further, the arrangement of nanocrystals should be studied because the properties of nanoclusters largely depend on the arrangement of the primary nanocrystals. However, the analysis of nanocrystals and nanoclusters remains difficult because of their sizes. Conventionally, transmission electron microscopy (TEM) is widely used to study materials in nanoscale. However, TEM images are obtained as the projection of three-dimensional structures, and it is difficult to observe the surface structures and the arrangement of nanocrystals using TEM. On the other hand, scanning electron microscopy (SEM) relies on the signals from the surface of the samples. Therefore, SEM can visualize the surface structures of samples. Previously, the spatial resolution of SEM was not enough to observe nanoparticles and nanomaterials with sizes of between 10 and 50 nm. However, recent developments, including the low-landing electron-energy method, improved the spatial resolution of SEM, which allows us to observe fine details of the nanocluster surface directory. Additionally, improved detectors allow us to visualize the elemental mapping of materials even at low voltage with high solid angle. Further, the use of a liquid sample holder even enabled the observation of nanocrystals in water. In this paper, we discuss the development of SEM and related observation technologies through the observation of hydrothermally prepared nanocrystals and nanoclusters.

ABSTRACT Dicer enzymes process virus-specific double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) to initiate specific antiviral defense by related RNA interference (RNAi) pathways in plants, insects, nematodes, and mammals. Antiviral RNAi in Caenorhabditis elegans requires Dicer-related helicase 1 (DRH-1), not found in plants and insects but highly homologous to mammalian retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), intracellular viral RNA sensors that trigger innate immunity against RNA virus infection. However, it remains unclear if DRH-1 acts analogously to initiate antiviral RNAi in C. elegans. Here, we performed a forward genetic screen to characterize antiviral RNAi in C. elegans. Using a mapping-by-sequencing strategy, we uncovered four loss-of-function alleles of drh-1, three of which caused mutations in the helicase and C-terminal domains conserved in RLRs. Deep sequencing of small RNAs revealed an abundant population of Dicer-dependent virus-derived small interfering RNAs (vsiRNAs) in drh-1 single and double mutant animals after infection with Orsay virus, a positive-strand RNA virus. These findings provide further genetic evidence for the antiviral function of DRH-1 and illustrate that DRH-1 is not essential for the sensing and Dicer-mediated processing of the viral dsRNA replicative intermediates. Interestingly, vsiRNAs produced by drh-1 mutants were mapped overwhelmingly to the terminal regions of the viral genomic RNAs, in contrast to random distribution of vsiRNA hot spots when DRH-1 is functional. As RIG-I translocates on long dsRNA and DRH-1 exists in a complex with Dicer, we propose that DRH-1 facilitates the biogenesis of vsiRNAs in nematodes by catalyzing translocation of the Dicer complex on the viral long dsRNA precursors. IMPORTANCE The helicase and C-terminal domains of mammalian RLRs sense intracellular viral RNAs to initiate the interferon-regulated innate immunity against RNA virus infection. Both of the domains from human RIG-I can substitute for the corresponding domains of DRH-1 to mediate antiviral RNAi in C. elegans, suggesting an analogous role for DRH-1 as an intracellular dsRNA sensor to initiate antiviral RNAi. Here, we developed a forward genetic screen for the identification of host factors required for antiviral RNAi in C. elegans. Characterization of four distinct drh-1 mutants obtained from the screen revealed that DRH-1 did not function to initiate antiviral RNAi. We show that DRH-1 acted in a downstream step to enhance Dicer-dependent biogenesis of viral siRNAs in C. elegans. As mammals produce Dicer-dependent viral siRNAs to target RNA viruses, our findings suggest a possible role for mammalian RLRs and interferon signaling in the biogenesis of viral siRNAs.

Abstract Objectives Allergic rhinitis (AR) is a complex disorder with variable pathogenesis. Increasing evidence suggests that the LRRC8A is involved in maintaining cellular stability, regulating immune cell activation and function, and playing significant roles in inflammation. However, the involvement of LRRC8A in AR inflammation and its underlying mechanisms remain unclear. Methods LRRC8A expression in AR patients, confirmed by qRT-PCR and Western blotting, was analyzed to investigate its relationship with the clinical characteristics of AR patients. In vitro, IL-13 stimulated HNEpCs to establish a Th2 inflammation model, with subsequent LRRC8A knockout or overexpression. NOX1/NOX4 inhibitor (GKT137831) and chloride channel inhibitor (DCPIB) were utilized to investigate AR development mechanisms during LRRC8A overexpression. An OVA-induced AR model with nasal mucosa LRRC8A knockdown confirmed LRRC8A's regulatory role in AR inflammation. Results LRRC8A mRNA and protein levels were significantly elevated in AR patients, positively correlating with NADPH oxidase subunits and Th2 inflammatory markers. In vitro, IL-13 stimulation of HNEpCs resulted in upregulation of LRRC8A and increased expression of NOX1, NOX4, and p22phox, along with mitochondrial dysfunction and NF-κB pathway activation. The knockout of LRRC8A reversed these effects. In nasal mucosal epithelial cells, DCPIB and GKT137831 completely blocked mitochondrial dysfunction caused by the overexpression of LRRC8A, which led to up-regulation of NOX1, NOX4, and p22phox. In vivo, knocking down LRRC8A reduced eosinophil infiltration, downregulated the expression of NOX1, NOX4, p22phox IL-4, IL-5, and IL-13, and decreased NF-κB pathway activation. Conclusion LRRC8A drives the upregulation of NOX1, NOX4, and p22phox, leading to ROS overproduction and mitochondrial dysfunction. It also activates NF-κB, ultimately leading to nasal mucosal epithelial inflammation. LRRC8A may be a potential target for the treatment of AR.

The planting and afforestation of mulberry and its application as animal feed conform to the spirit that comprehensive utilization of biomass such as agriculture and forestry is the direction of sustainable development in the National Program for Medium-to-Long-Term Scientific and Technological Development. The application of mulberry as animal feed has attracted international attention, but the cultivar identification of forage mulberry is still controversial in the industry. The paper summarizes the current situation of forage mulberry in animal husbandry, and expounds how to define and classify forage mulberry. [ABSTRACT FROM AUTHOR]