Tinnitus classification based on resting-state functional connectivity using a convolutional neural network architecture.

OBJECTIVES: Many studies have investigated aberrant functional connectivity (FC) using resting-state functional MRI (rs-fMRI) in subjective tinnitus patients. However, no studies have verified the efficacy of resting-state FC as a diagnostic imaging marker. We established a convolutional neural network (CNN) model based on rs-fMRI FC to distinguish tinnitus patients from healthy controls, providing guidance and fast diagnostic tools for the clinical diagnosis of subjective tinnitus. METHODS: A CNN architecture was trained on rs-fMRI data from 100 tinnitus patients and 100 healthy controls using an asymmetric convolutional layer. Additionally, a traditional machine learning model and a transfer learning model were included for comparison with the CNN, and each of the three models was tested on three different brain atlases. RESULTS: Of the three models, the CNN model outperformed the other two models with the highest area under the curve, especially on the Dos_160 atlas (AUC = 0.944). Meanwhile, the model with the best classification performance highlights the crucial role of the default mode network, salience network, and sensorimotor network in distinguishing between normal controls and patients with subjective tinnitus. CONCLUSION: Our CNN model could appropriately tackle the diagnosis of tinnitus patients using rs-fMRI and confirmed the diagnostic value of FC as measured by rs-fMRI.

Inhibitor Development for α-Synuclein Fibril's Disordered Region to Alleviate Parkinson's Disease Pathology.

The amyloid fibrils of α-synuclein (α-syn) are crucial in the pathology of Parkinson's disease (PD), with the intrinsically disordered region (IDR) of its C-terminal playing a key role in interacting with receptors like LAG3 and RAGE, facilitating pathological neuronal spread and inflammation. In this study, we identified Givinostat (GS) as an effective inhibitor that disrupts the interaction of α-syn fibrils with receptors such as LAG3 and RAGE through high-throughput screening. By exploring the structure-activity relationship and optimizing GS, we developed several lead compounds, including GSD-16-24. Utilizing solution-state and solid-state NMR, along with cryo-EM techniques, we demonstrated that GSD-16-24 binds directly to the C-terminal IDR of α-syn monomer and fibril, preventing the fibril from binding to the receptors. Furthermore, GSD-16-24 significantly inhibits the association of α-syn fibrils with membrane receptors, thereby reducing neuronal propagation and pro-inflammatory effects of α-syn fibrils. Our findings introduce a novel approach to mitigate the pathological effects of α-syn fibrils by targeting their IDR with small molecules, offering potential leads for the development of clinical drugs to treat PD.

Investigation of Persistent Photoconductivity of Gallium Nitride Semiconductor and Differentiation of Primary Neural Stem Cells.

A gallium nitride (GaN) semiconductor is one of the most promising materials integrated into biomedical devices to play the roles of connecting, monitoring, and manipulating the activity of biological components, due to its excellent photoelectric properties, chemical stability, and biocompatibility. In this work, it was found that the photogenerated free charge carriers of the GaN substrate, as an exogenous stimulus, served to promote neural stem cells (NSCs) to differentiate into neurons. This was observed through the systematic investigation of the effect of the persistent photoconductivity (PPC) of GaN on the differentiation of primary NSCs from the embryonic rat cerebral cortex. NSCs were directly cultured on the GaN surface with and without ultraviolet (UV) irradiation, with a control sample consisting of tissue culture polystyrene (TCPS) in the presence of fetal bovine serum (FBS) medium. Through optical microscopy, the morphology showed a greater number of neurons with the branching structures of axons and dendrites on GaN with UV irradiation. The immunocytochemical results demonstrated that GaN with UV irradiation could promote the NSCs to differentiate into neurons. Western blot analysis showed that GaN with UV irradiation significantly upregulated the expression of two neuron-related markers, ßIII-tubulin (Tuj-1) and microtubule-associated protein 2 (MAP-2), suggesting that neurite formation and the proliferation of NSCs during differentiation were enhanced by GaN with UV irradiation. Finally, the results of the Kelvin probe force microscope (KPFM) experiments showed that the NSCs cultured on GaN with UV irradiation displayed about 50 mV higher potential than those cultured on GaN without irradiation. The increase in cell membrane potential may have been due to the larger number of photogenerated free charges on the GaN surface with UV irradiation. These results could benefit topical research and the application of GaN as a biomedical material integrated into neural interface systems or other bioelectronic devices.

Retention of titanium copings to implant-supported fixed dental prostheses.

PURPOSE: The aim of this in vitro study was to assess the effects of using different cements and titanium copings designs on the retention of implant-supported fixed dental prostheses (IFDPs) using a pull-out test. MATERIALS AND METHODS: Fifty zirconia (ZirCAD; Ivoclar Vivadent) and 20 prepolymerized denture acrylic resin (AvaDent) rectangular (36 mm × 12 mm × 8 mm) specimens were milled to mimic the lower left segmental portion of the All-on-Four IFDPs. Cylindrical titanium copings (Variobase; Straumann) (V) were used in 2 prepolymerized denture acrylic resin groups (n = 10) while conical titanium copings (Straumann) (C) were used as a control group for zirconia with 4 groups using cylindrical titanium copings. Before cementation, the outer surfaces of all titanium copings and the intaglio bonding surface of prosthetic specimens were airborne-particle abraded. All specimens were cemented following the manufacturer's recommendations and instructions according to the experimental design. After artificial aging (5000 cycles of 5°C 55°C, dwelling time 20 s; 150 N, 1.5 Hz in a 37°C water bath), all specimens were subjected to retention force testing using a pull-out test using a universal testing machine and a custom fixture with a crosshead speed 5 mm/min. Modes of failure were classified as Type 1, 2, or 3. Retention force values were analyzed by the t-test for the prepolymerized denture acrylic resin specimen groups, and 1-way ANOVA and the Tukey test for the zirconia groups at α = 0.05. RESULTS: Mean and standard deviation retention force values varied from 101.1 ± 67.1 to 509.0 ± 65.2 N for the prepolymerized denture acrylic resin specimen groups. The zirconia groups ranged from 572.8 ± 274.7 to 1416.1 ± 258.0 N. There is no statistically significant difference in retention force values between V and C specimens cementing to zirconia with Panavia SA cement (Kuraray Noritake) (p = 0.587). The retention forces and failure modes were influenced by the cement used (p < 0.05). Modes of failure were predominantly Type 2 (mixed failure) and Type 1 (adhesive fracture from prosthetic materials) except for the quick-set resin group (Type 3, adhesive failure from coping). CONCLUSIONS: When bonding IFDPs onto titanium copings, quick-set resin provided significantly higher retention force for prepolymerized denture acrylic resin prostheses. Conical and cylindrical titanium copings performed similarly when cemented to zirconia with Panavia SA cement under the same protocol. The stability of the bonded interface and retention forces between zirconia prostheses and titanium copings varied from the cement used.

Conformational Dynamics of an α-Synuclein Fibril upon Receptor Binding Revealed by Insensitive Nuclei Enhanced by Polarization Transfer-Based Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy.

Many amyloid fibrils associated with neurodegenerative diseases consist of an ordered fibril core (FC) and disordered terminal regions (TRs). The former represents a stable scaffold, while the latter is rather active in binding with various partners. Current structural studies mainly focus on the ordered FC since the high flexibility of TRs hinders structural characterization. Here, by combining insensitive nuclei enhanced by polarization transfer-based 1H-detected solid-state NMR and cryo-EM, we explored the intact structure of an α-syn fibril including both FC and TRs and further studied the conformational dynamics of the fibril upon binding to lymphocyte activation gene 3 (LAG3)─a cell surface receptor that is involved in α-syn fibril transmission in brains. We found that both the N- and C-TRs of α-syn are disordered in free fibrils featuring similar conformation ensembles as those in soluble monomers. While in the presence of the D1 domain of LAG3 (L3D1), the C-TR directly binds to L3D1, meanwhile the N-TR folds into a ß-strand and further integrates with the FC, which leads to alteration of the overall fibril structure and surface property. Our work reveals synergistic conformational transition of the intrinsically disordered TRs of α-syn, which sheds light on mechanistic understanding of the essential role of TRs in regulating the structure and pathology of amyloid fibrils.

Early autoimmunity and outcome in virus encephalitis: a retrospective study based on tissue-based assay.

To explore the autoimmune response and outcome in the central nervous system (CNS) at the onset of viral infection and correlation between autoantibodies and viruses. METHODS: A retrospective observational study was conducted in 121 patients (2016-2021) with a CNS viral infection confirmed via cerebrospinal fluid (CSF) next-generation sequencing (cohort A). Their clinical information was analysed and CSF samples were screened for autoantibodies against monkey cerebellum by tissue-based assay. In situ hybridisation was used to detect Epstein-Barr virus (EBV) in brain tissue of 8 patients with glial fibrillar acidic protein (GFAP)-IgG and nasopharyngeal carcinoma tissue of 2 patients with GFAP-IgG as control (cohort B). RESULTS: Among cohort A (male:female=79:42; median age: 42 (14-78) years old), 61 (50.4%) participants had detectable autoantibodies in CSF. Compared with other viruses, EBV increased the odds of having GFAP-IgG (OR 18.22, 95% CI 6.54 to 50.77, p<0.001). In cohort B, EBV was found in the brain tissue from two of eight (25.0%) patients with GFAP-IgG. Autoantibody-positive patients had a higher CSF protein level (median: 1126.00 (281.00-5352.00) vs 700.00 (76.70-2899.00), p<0.001), lower CSF chloride level (mean: 119.80±6.24 vs 122.84±5.26, p=0.005), lower ratios of CSF-glucose/serum-glucose (median: 0.50[0.13-0.94] vs 0.60[0.26-1.23], p=0.003), more meningitis (26/61 (42.6%) vs 12/60 (20.0%), p=0.007) and higher follow-up modified Rankin Scale scores (1 (0-6) vs 0 (0-3), p=0.037) compared with antibody-negative patients. A Kaplan-Meier analysis revealed that autoantibody-positive patients experienced significantly worse outcomes (p=0.031). CONCLUSIONS: Autoimmune responses are found at the onset of viral encephalitis. EBV in the CNS increases the risk for autoimmunity to GFAP.

Detection of co-infection with Orientia tsutsugamushand and hemorrhagic fever with renal syndrome by next-generation sequencing.

Purpose: The co-infection with Orientia tsutsugamushand and hemorrhagic fever with renal syndrome is rare. There are many similarities in early clinical practice between the two diseases, and sometimes it is easy to misdiagnose, especially when co-infection occurs.Methods: We describe a patient who presented with fever and headache after bitten by an insect and whose physical examination showed conjunctival hyperemia, eschar and petechiae in tongue and the soft palate. To lead to a diagnosis, the serum antibody of Hantaan virus, Weil-Felix test and  next-generation sequencing of cerebrospinal fluid was performed.Results: The Weil-Felix test was negative on the 15th day after the onset of the disease and a repeated Weil-Felix test on the 21st day showed a titer of 1:160 and the IgM against Hantaan virus was positive. The number of sequence reads identified corresponding to O. tsutsugamushi was 239 with a genomic coverage of 0.9178%. This patient was diagnosed with intracranial infection with Orientia tsutsugamushi and co-infection with epidemic hemorrhagic fever. The symptoms in our patient quickly decreased after the administration of tetracycline.Conclusion: Next-generation sequencing is helpful for the early diagnosis of scrub typhus, especially when the Weil-Felix test is negative. Clinicians need to be reminded to screen for common pathogens that may be co-infected, such as epidemic hemorrhagic fever.

Effect of airborne-particle abrasion with a novel spherical abrasive on the zirconia surface.

STATEMENT OF PROBLEM: A novel zirconia-alumina composite (ZAC) particle has yet to be studied for airborne-particle abrasion in a bonding protocol for the zirconia surface. PURPOSE: The purpose of this in vitro study was to evaluate the shear bond force of resin cement to yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) when using spherical ZAC particles to conduct airborne-particle abrasion and modify the topography of Y-TZP. MATERIAL AND METHODS: Spherical 30- to 70-µm ZAC particles were fabricated by using a hybrid gel technique. A total of 160 Ø6.6×4.0-mm zirconia disks were fabricated from 4 commercially available zirconia blanks, e.max ZirCAD zirconia (EM), NexxZr T zirconia (NE), Lava Plus High Translucency zirconia (LP), and Imagine High Translucency Zirconia (IM), by using computer-aided manufacturing technology. As-sintered specimens without further surface treatment were used as controls (ZR0). Surface treatment groups included sharp-edged alumina airborne-particle abrasion (ABC), 50 µm, 0.2 MPa; airborne-particle abrasion with ZAC particle at 0.2 MPa (2ZA); and airborne-particle abrasion with spherical ZAC particle at 0.4 MPa (4ZA). All surface treatment groups were airborne-particle abraded at the specified pressures for 10 seconds at a standardized distance of 10 mm. The surface roughness (Ra) and area roughness (Sa) of specimens from each group were measured. Following the application of an adhesive (Scotchbond Universal), Ø6.6×4.0-mm resin cement (RelyX Ultimate) buttons were fabricated for shear bond testing by using a universal testing machine at a 5-mm/min crosshead speed (n=10). The data were analyzed by using a 2-way ANOVA, Tukey HSD test, and regression analysis (α=0.05). Scanning electron microscopy (SEM) was performed to observe changes of the zirconia surface and the failure modes of each group before and after shear bond testing. RESULTS: The mean ±standard deviation shear bond force values ranged from 272.6 ±41.4 N to 686.7 ±152.8 N. Statistically significant higher force values than those of the controls (P<.05) were obtained by using airborne-particle abrasion. No significant differences were found among any of the airborne-particle abrasion treatment groups (P>.05). The mean of Ra values ranged from 0.27 µm to 0.74 µm, and the mean of Sa values, from 0.48 µm to 1.48 µm. SEM observation revealed that the zirconia surface was made jagged by abrasion with sharp-edged alumina particles. The spherical ZAC particles create microcraters on the zirconia surface. Fractographic observation disclosed that failures were adhesive-cohesive failure modes with residual resin cement attached on the zirconia surface. CONCLUSIONS: The surface treatment of zirconia with sharp-edged alumina or the spherical ZAC abrasives improved the bonding force between the zirconia and resin cement. No statistically significant differences in shear bond force values were found between airborne-particle abrasion surface treatment groups.

Clinical and functional characterisation of the SMAD4 germline variant c.1035C > A in a family with juvenile polyposis syndrome by whole-exome sequencing.

Juvenile polyposis syndrome (JPS) is a rare autosomal dominant inherited disease characterised by multiple juvenile polyps. Genes with JPS-associated mutations and their correlation with the phenotype are currently unknown. Gastrointestinal endoscopy results of a 31-year-old female patient showed multiple polyps in the digestive tract, and the presence of juvenile polyps was confirmed by pathological examination. During follow-up, the patient underwent total gastrectomy and polypectomy several times. Five members of this family were diagnosed with JPS, of which two died and three survived. Full exon gene sequencing of eight members of this family revealed a SMAD4 (NM-005359.3) c.1035C > A (p.Cys345*) mutation. This mutation leads to premature codon termination, causing protein truncation. SMAD4 is a pathogenic gene associated with JPS. This is the first report of an association between the c.1035C > A mutation and JPS pathogenesis. Detection of JPS-related mutations in family members with a genetic predisposition for JPS is very important for genetic counselling, surgical intervention, long-term monitoring and follow-up, and drug treatment.

Effect of Fiber Reinforcement on the Flexural Strength of the Transitional Implant-Supported Fixed Dental Prosthesis.

PURPOSE: The aim of this in vitro study was to assess the efficacy of fiber reinforcement to enhance flexural strength of the transitional implant-supported fixed dental prosthesis (TISFDP). MATERIALS AND METHODS: One hundred and forty denture acrylic resin plates (64 mm × 12 mm × 5 mm) with two 7 mm diameter holes were fabricated using heat-polymerized type (Lucitone 199) and CAD-CAM prepolymerized type (AvaDent) materials to simulate a chair-side reconstruction of the TISFDP. Specimens were divided into 7 groups (n = 10) according to the airborne-particle abrasion of titanium cylinder (Straumann) surface and locations of fiber reinforcement ribbons (Ribbond-ULTRA). No cylinder surface abrasion and no fiber added acrylate specimens were used as the controls. The prosthetic screws were hand-tightened on a custom fixture with analogs. Specimen hole and cylinder were joined using a 50:50 mixture of chemically polymerized resin (QYK-SET; Holmes Dental) and repair resin (Dentsply Sirona). Ten acrylate specimens with no holes were fabricated from each tested material and assigned as positive controls. A modified four-point bending test (ASTM standard-D6272) was conducted using a universal testing machine and a custom fixture with a crosshead speed 1 mm/min. The maximum failure loads were recorded. Data were statistically analyzed using 2-way ANOVA and the Tukey tests at α = 0.05. RESULTS: The flexural strength values ranged from 55.4 ±8.3 to 140.9 ±15.4 MPa. The flexural strength decreased significantly when fiber was attached on the titanium cylinder surface (p < 0.05). There were no statistically significant differences in flexural strength values between specimens with and without titanium cylinder surface abrasion (p > 0.05). Statistically significant improvement in flexural strength was observed in specimens with fibers attached around the specimen holes (p < 0.05) buccally and lingually. The obtained values were not statistically significantly different from the positive controls (p > 0.05). Some fixation screw fractures were observed before catastrophic failure of specimens during testing. CONCLUSIONS: Fiber reinforcement significantly improved the flexural strength of denture acrylic resins only if placed around the specimen holes on the tension side at the site of initiation of crack propagation. Even when the specimens underwent catastrophic failure, the segments remained attached to each other with the attached fibers.

N6-methyladenosine methylation modification patterns reveal immune profiling in pancreatic adenocarcinoma.

BACKGROUND: Several studies have revealed that N6-methyladenosine (m6A) regulation is involved in various biological processes and cancer progression. Nevertheless, the potential effects of m6A modifications in the tumor immune microenvironment (TIME) and on immune regulation in pancreatic adenocarcinoma (PAAD) remains unclear. METHODS: A consensus clustering algorithm was used to identify different m6A modification patterns and construct an m6A-associated gene signature based on 23 m6A regulators in PAAD. The CIBERSORT and ssGSEA algorithms were used to estimate the components of the immune cells in each sample. The PCA algorithm was used to develop the m6Ascore system for the evaluation of m6A modification patterns in each sample. RESULTS: Two m6A modification patterns with different biological properties and prognoses were identified in 176 PAAD patient samples. The features of TIME between the two patterns were similar, with two definite immune phenotypes: immune-inflamed and immune-excluded. Based on the m6A phenotype-associated signature genes, we constructed an m6Ascore system to investigate the m6A modification pattern of each sample, profile the dissection of physiological processes, immune infiltration, clinical prognosis, immunotherapy, and genetic variation. Patients with low m6Ascore scores had better clinical outcomes, enhanced immune infiltration, and lower expression of immunotherapeutic drug targets, such as CD274 and PDCD1LG2. Further research indicated that the m6Ascore and tumor mutation burden were significantly correlated, and patients with low m6Ascore had higher mutation rates in SMAD4 and TTN. Moreover, TNFRSF21 was significantly upregulated in PAAD tumor tissues and cell lines. Lower expression of TNFRSF21 had a prominent advantage in survival and was correlated with a low level of immune infiltration. PAAD samples with different TNFRSF21 expression levels showed significantly distinct sensitivities to chemotherapeutic agents. CONCLUSIONS: This study revealed that m6A modification patterns could play an important role in the diversity and complexity of TIME, and the m6Ascore system could serve as an independent and powerful prognostic biomarker and is latently related to PAAD immunotherapies. Quantitative determination of m6A modification patterns in individual patients will be instrumental in mapping the TIME landscape and further optimizing precision immunotherapy.

Abnormal fractional amplitude of low-frequency fluctuations in MOG-lgG optic neuritis patients: a resting-state functional MRI study.

Optic neuritis (ON) is a general term for inflammation of any part of the optic nerve resulting from demyelination or infection. The number of patients with MOG-lgG antibody-related optic neuritis is increasing recently. Our study uses the fractional amplitude of low-frequency fluctuation (fALFF) method to compare the activity of specific brain regions in MOG-lgG ON patients and healthy controls (HCs). We selected a total of 21 MOG-lgG ON patients and 21 HCs were included in the study. All subjects underwent resting-state functional magnetic resonance imaging (rs-fMRI). The independent-samples t-test was used to compare demographic data and average fALFF values between groups. The specificity and sensitivity of fALFF values for distinguishing between MOG-lgG ON patients and HCs were evaluated by receiver operating characteristic (ROC) curve analysis. Pearson's correlation analysis was used to analyze the relationship between fALFF values and clinical characteristics in MOG-lgG ON patients. Our results showed that fALFF values of the right cerebellum and left middle cingulum were lower whereas those of bilateral inferior temporal lobes, right gyrus rectus, and the left superior and right middle frontal lobes of MOG-lgG ON patients were higher than those of HCs (P < 0.05). The average fALFF value of the left superior frontal lobe in MOG-lgG ON patients was positively correlated with Hospital Anxiety and Depression Scale score (HADS) (r = 0.6004; P < 0.05) and duration of MOG-lgG ON (r = 6487; P < 0.05). Thus, patients with MOG-lgG ON have abnormal activity in the brain regions related to vision. Changes in fALFF value can reflect functional sequelae of MOG-lgG ON, including abnormal anxiety or depressive emotional changes.

Clinical M2 macrophages-related genes to aid therapy in pancreatic ductal adenocarcinoma.

BACKGROUND: Increasing evidence supports that infiltration M2 Macrophages act as pivotal player in tumor progression of pancreatic ductal adenocarcinoma (PDAC). Nonetheless, comprehensive analysis of M2 Macrophage infiltration and biological roles of hub genes (FAM53B) in clinical outcome and immunotherapy was lack. METHOD: The multiomic data of PDAC samples were downloaded from distinct datasets. CIBERSORT algorithm was performed to uncover the landscape of TIME. Weighted gene co-expression network analysis (WGCNA) was performed to identify candidate module and significant genes associated with M2 Macrophages. Kaplan-Meier curve and receiver operating characteristic (ROC) curves were applied for prognosis value validation. Mutation data was analyzed by using "maftools" R package. Gene set variation analysis (GSVA) was employed to assign pathway activity estimates to individual sample. Immunophenoscore (IPS) was implemented to estimate immunotherapeutic significance of risk score. The half-maximal inhibitory concentration (IC50) of chemotherapeutic drugs was predicted by using the pRRophetic algorithm. Finally, quantitative real-time polymerase chain reaction was used to determine FAM53B mRNA expression and TIMER database was utilized to uncover its possible role in immune infiltration of PDAC. RESULTS: Herein, 17,932 genes in 234 samples (214 tumor and 20 normal) were extracted from three platforms. Taking advantage of WGCNA, significant module (royalblue) and 135 candidate genes were considered as M2 Macrophages-related genes. Subsequently, risk signature including 5 hub genes was developed by multiple analysis, which exhibited excellent prognostic performance. Besides, comprehensive prognostic nomogram was constructed to quantitatively estimate risk. Then, intrinsic link between risk score with tumor mutation burden (TMB) was explored. Additionally, risk score significantly correlated with diversity of tumor immune microenvironment (TIME). PDAC samples within different risk presented diverse signaling pathways activity and experienced significantly distinct sensitivity to administering chemotherapeutic or immunotherapeutic agents. Finally, the biological roles of FAM53B were revealed in PDAC. CONCLUSIONS: Taken together, comprehensive analyses of M2 Macrophages profiling will facilitate prognostic prediction, delineating complexity of TIME, and contribute insight into precision therapy for PDAC.

Prognostic value of tumor immune cell infiltration patterns in colon adenocarcinoma based on systematic bioinformatics analysis.

BACKGROUND: Although immunotherapy for colon cancer has made promising progress, only a few patients currently benefit from it. A recent study revealed that infiltrating immune cells are highly relevant to tumor prognosis and influence the expression of immune-related genes. However, the characterization of immune cell infiltration (ICI) has not yet been comprehensively analyzed and quantified in colon adenocarcinoma (COAD). METHODS: The multiomic data of COAD samples were downloaded from TCGA. ESTIMATE algorithm, ssGSEA method and CIBERSORT analysis were conducted to estimate the subpopulations of infiltrating immune cells. COAD subtypes based on ICI pattern were identified by consensus clustering then principal-component analysis was performed to obtain ICI scores to quantify the ICI patterns in individual tumors. Kaplan-Meier analysis was employed to validate prognostic value. Gene set enrichment analysis (GSEA) was applied for functional annotation. Finally, the mutation data was analyzed by employing "maftools" package. RESULTS: Three bioinformatics algorithms were used to evaluate the ICI patterns from 538 patients with COAD. Two ICI subtypes were determined using consensus clustering, and the ICI score was constructed by performing principal component analysis. Our findings showed that a higher ICI score often indicated a more advanced tumor and worse prognosis. The high-ICI score subgroup had a higher stromal score and more M0 macrophages but fewer plasma cells and decreased CD8 T cell infiltration. In addition, patients with high ICI scores had significantly higher expression levels of HAVCR2 and PCDC1LG2. Real-time polymerase chain reaction (PCR) was conducted to determine the prognostic significances of ICI-related genes. CONCLUSIONS: In conclusion, ICI score may be considered as an original and useful indicator for independent prognostic prediction and individual immune-related therapy.

Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) was the sixth common malignancies characteristic with highly aggressive in the world. It was well established that tumor mutation burden (TMB) act as indicator of immunotherapeutic responsiveness in various tumors. However, the role of TMB in tumor immune microenvironment (TIME) is still obscure. METHOD: The mutation data was analyzed by employing "maftools" package. Weighted gene co-expression network analysis (WGCNA) was implemented to determine candidate module and significant genes correlated with TMB value. Differential analysis was performed between different level of TMB subgroups employing R package "limma". Gene ontology (GO) enrichment analysis was implemented with "clusterProfiler", "enrichplot" and "ggplot2" packages. Then risk score signature was developed by systematical bioinformatics analyses. K-M survival curves and receiver operating characteristic (ROC) plot were further analyzed for prognostic validity. To depict comprehensive context of TIME, XCELL, TIMER, QUANTISEQ, MCPcounter, EPIC, CIBERSORT, and CIBERSORT-ABS algorithm were employed. Additionally, the potential role of risk score on immune checkpoint blockade (ICB) immunotherapy was further explored. The quantitative real-time polymerase chain reaction was performed to detect expression of HTRA3. RESULTS: TMB value was positively correlated with older age, male gender and early T status. A total of 75 intersection genes between TMB-related genes and differentially expressed genes (DEGs) were screened and enriched in extracellular matrix-relevant pathways. Risk score based on three hub genes significantly affected overall survival (OS) time, infiltration of immune cells, and ICB-related hub targets. The prognostic performance of risks score was validated in the external testing group. Risk-clinical nomogram was constructed for clinical application. HTRA3 was demonstrated to be a prognostic factor in HCC in further exploration. Finally, mutation of TP53 was correlated with risk score and do not interfere with risk score-based prognostic prediction. CONCLUSION: Collectively, a comprehensive analysis of TMB might provide novel insights into mutation-driven mechanism of tumorigenesis further contribute to tailored immunotherapy and prognosis prediction of HCC.

Immunological significance of prognostic alternative splicing signature in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) ranks the sixth prevalent tumors with high mortality globally. Alternative splicing (AS) drives protein diversity, the imbalance of which might act an important factor in tumorigenesis. This study aimed to construct of AS-based prognostic signature and elucidate the role in tumor immune microenvironment (TIME) and immunotherapy in HCC. METHODS: Univariate Cox regression analysis was performed to determine the prognosis-related AS events and gene set enrichment analysis (GSEA) was employed for functional annotation, followed by the development of prognostic signatures using univariate Cox, LASSO and multivariate Cox regression. K-M survival analysis, proportional hazards model, and ROC curves were conducted to validate prognostic value. ESTIMATE R package, ssGSEA algorithm and CIBERSORT method and TIMER database exploration were performed to uncover the context of TIME in HCC. Quantitative real-time polymerase chain reaction was implemented to detect ZDHHC16 mRNA expression. Cytoscape software 3.8.0 were employed to visualize AS-splicing factors (SFs) regulatory networks. RESULTS: A total of 3294 AS events associated with survival of HCC patients were screened. Based on splicing subtypes, eight AS prognostic signature with robust prognostic predictive accuracy were constructed. Furthermore, quantitative prognostic nomogram was developed and exhibited robust validity in prognostic prediction. Besides, the consolidated signature was significantly correlated with TIME diversity and ICB-related genes. ZDHHC16 presented promising prospect as prognostic factor in HCC. Finally, the splicing regulatory network uncovered the potential functions of splicing factors (SFs). CONCLUSION: Herein, exploration of AS patterns may provide novel and robust indicators (i.e., risk signature, prognostic nomogram, etc.,) for prognostic prediction of HCC. The AS-SF networks could open up new approach for investigation of potential regulatory mechanisms. And pivotal players of AS events in context of TIME and immunotherapy efficiency were revealed, contributing to clinical decision-making and personalized prognosis monitoring of HCC.

Altered Brain Network Centrality in Patients with Diabetic Optic Neuropathy: A Resting-State FMRI Study.

OBJECTIVE: Recent studies have suggested that diabetic optic neuropathy (DON) independently increases the incidence of brain diseases like cerebral infarction and hemorrhage. In this study, voxel-level degree centrality (DC) was used to study potential changes in functional network brain activity in DON patients. METHODS: The study included 14 DON patients and 14 healthy controls (HCs) matched by age, sex, and weight. All subjects underwent resting functional magnetic resonance imaging. Receiver operating characteristic curves and Pearson correlation analysis were performed. RESULTS: The DC values of the left frontal mid-orb and right middle frontal gyrus/right frontal sup were significantly lower in DON patients compared to HCs. The DC value of the left temporal lobe was also significantly higher than in HCs. CONCLUSION: Three different brain regions show DC changes in DON patients, suggesting common optic neuropathy in the context of diabetes and providing new ideas for treating optic nerve disease in patients with long-term diabetes. ABBREVIATIONS: AUC = area under the curve; BCVA = best corrected visual acuity; DC = degree centrality; DON = diabetic optic neuropathy; fMRI = functional magnetic resonance imaging; HC = healthy control; LFMO = left frontal mid orb; LTL = left temporal lobe; RFS = right frontal sup; RMFG = right middle frontal gyrus; ROC = receiver operating characteristic.

miR-129-2-3p directly targets SYK gene and associates with the risk of ischaemic stroke in a Chinese population.

Spleen tyrosine kinase (SYK) gene has been identified as novel susceptibility locus for ischaemic stroke (IS) previously. However, regulation of SYK gene remains unknown in IS. In this study, we aimed to identify miRNAs that might be involved in the development of IS by targeting SYK gene. miRNAs were firstly screened by bioinformatics predicting tool. The expression levels of SYK gene were detected by qRT-PCR and western blotting, respectively, after miRNA transfection. Luciferase reporter assay was applied to investigate the direct binding between miRNAs and target gene. miRNA levels were detected by miRNA TaqMan assays in the blood cells of 270 IS patients and 270 control volunteers. Results suggest that SYK gene might be a direct target of miR-129-2-3p. The blood level of miR-129-2-3p was significantly lower in IS patients (P < 0.05), and negatively associated with the risk of IS (adjusted OR: 0.88; 95% CI: 0.80-0.98; P = 0.021) by multivariable logistic regression analysis. The blood levels of SYK gene were significantly higher in IS patients, and miR-129-2-3p expression was negatively correlated with mean platelet volume. In summary, our study suggests that miR-129-2-3p might be involved in the pathogenesis of IS through interrupting SYK expression and the platelet function, and further investigation is needed to explore the underlying mechanism.

Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa.

miRNAs (microRNAs) are ~ 21-nt non-coding small RNAs (sRNAs) that play crucial regulatory roles in plant biotic and abiotic stress responses. Phosphorus (Pi) deficiency constrains plant growth and reduces yields worldwide. To identify tree miRNAs and evaluate their functions in the response to low Pi, we identified 261 known and 31 candidate novel miRNA families from three sRNA libraries constructed from Populus tomentosa subjected to sufficient or Pi deficiency condition or to restoration of a sufficient Pi level after Pi deficiency. Pi deficiency resulted in significant changes in the abundance of TPM (transcript per million) of 65 known and 3 novel miRNAs. Interestingly, four miRNAs responsive to low N-miR167, miR394, miR171, and miR857-were found to be involved in the response to low Pi. Thirty-five known and one novel miRNAs responded dynamically to Pi fluctuations, suggesting their involvement in the response to Pi deficiency. miRNA clusters comprising 36 miRNAs were identified in 10 chromosomes. Intriguingly, nine pairs of sense and antisense miRNAs transcribed from the same loci were detected in P. tomentosa, which is the first such report in woody plants. Moreover, target genes of the known miRNAs and novel miRNA candidates with significantly changed abundance were predicted, and their functions were annotated. Degradome sequencing supported the identified targets of miRNAs in P. tomentosa. These findings will enhance our understanding of universal and specific molecular regulatory mechanisms of trees under nutrition stress and may facilitate improvement of the Pi utilization efficiency of woody plants.

Altered Spontaneous Brain Activity in Patients with Classical Trigeminal Neuralgia Using Regional Homogeneity: A Resting-State Functional MRI Study.

OBJECTIVE: Neuroimaging studies have shown that patients with pain-related conditions have altered neuronal activity and structural functions. The purpose of this study was to investigate whether patients with classical trigeminal neuralgia (CTN) exhibit changes in corresponding neuronal activity via analysis of neuronal activity regional homogeneity (ReHo). METHODS: A total of 28 patients presenting with sore eyes (12 men and 16 women) were matched with 28 healthy controls (12 men and 16 women). All participants underwent functional magnetic resonance imaging (fMRI). This ReHo method was used to assess the consistency of changes in neural activity in various brain regions. The receiver operating characteristic (ROC) curve was applied to differentiate ReHo values of patients with CTN from ReHo values of healthy controls. Pearson's correlation analysis was applied to evaluate the correlation between ReHo values of different brain regions of patients with CTN and clinical manifestations. RESULTS: Compared with healthy controls, patients with CTN were found to have increased ReHo values in the inferior cerebellum bilaterally, right inferior temporal gyrus, right middle occipital gyrus, right fusiform gyrus, right superior frontal gyrus, and right precentral gyrus. ROC curve analysis of each brain region revealed near-perfect accuracy regarding the area under the curve. However, no correlation between ReHo values and clinical manifestations in patients with CTN was found. CONCLUSIONS: CTN is associated with altered neuronal networks in different areas of the brain. ReHo values all possess different degrees of change, implying that CTN has a certain impact on cerebral function.