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Abstract ATG9A is the only integral membrane protein among core autophagy-related (ATG) proteins. We previously found that ATG9A does not co-assemble into synaptophysin-positive vesicles, but rather, localizes to a distinct pool of vesicles within synapsin condensates in both fibroblasts and nerve terminals. The endocytic origin of these vesicles further suggests the existence of different intracellular sorting or segregation mechanisms for ATG9A and synaptophysin in cells. However, the precise underlying mechanism remains largely unknown. In this follow-up study, we investigated the endosomal localization of these two proteins by exploiting the advantages of a Rab5 mutant that induces the formation of enlarged endosomes. Notably, ATG9A and synaptophysin intermix perfectly and do not segregate on giant endosomes, indicating that the separation of these two proteins is not solely caused by the inherent properties of the proteins, but possibly by other unknown factors.

Abstract Background Recent studies have provided evidence supporting the functional role and mechanism of lactate in suppressing anticancer immunity. However, there is no systematic analysis of lactate metabolism-related genes (LMRGs) and ovarian cancer (OV) prognosis. Results Six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) were selected as prognostic genes and a prognostic model was utilized. Kaplan-Meier (K-M) and Receiver Operating Characteristic (ROC) analyses were further performed and indicated that the prognostic model was effective. Subsequently, the neoplasm_cancer_status and RiskScore were determined as independent prognostic factors, and a nomogram was established with relatively accurate forecasting ability. Additionally, 2 types of immune cells (Central memory CD8 T cell and Immature B cell), 4 types of immune functions (APC co inhibition, DCs, Tfh and Th1 cells), 9 immune checkpoints (BTLA, CTLA4, IDO1, LAG3, VTCN1, CXCL10, CXCL9, IFNG, CD27) and tumor immune dysfunction and exclusion (TIDE) scores were significantly different between risk groups. The expression of 6 genes were verified by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and the expression of 6 genes were higher in the high-grade serous carcinoma (HGSC) samples. Conclusion A prognostic model related to lactate metabolism was established for OV based on six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) that could provide new insights into therapy.

ObjectiveDisulfidptosis is a newly recognized form of regulated cell death that has been linked to cancer progression and prognosis. Despite this association, the prognostic significance, immunological characteristics and treatment response of disulfidptosis-related lncRNAs (DRLs) in ovarian cancer have not yet been elucidated.MethodsThe lncRNA data and clinical information for ovarian cancer and normal samples were obtained from the UCSC XENA. Differential expression analysis and Pearson analysis were utilized to identify core DRLs, followed by LASSO algorithm. Random Survival Forest was used to construct a prognostic model. The relationships between risk scores, RNA methylation, immune cell infiltration, mutation, responses to immunotherapy and drug sensitivity analysis were further examined. Additionally, qRT-PCR experiments were conducted to validate the expression of the core DRLs in human ovarian cancer cells and normal ovarian cells and the scRNA-seq data of the core DRLs were obtained from the GEO dataset, available in the TISCH database.ResultsA total of 8 core DRLs were obtained to construct a prognostic model for ovarian cancer, categorizing all patients into low-risk and high-risk groups using an optimal cutoff value. The AUC values for 1-year, 3-year and 5-year OS in the TCGA cohort were 0.785, 0.810 and 0.863 respectively, proving a strong predictive capability of the model. The model revealed the high-risk group patients exhibited lower overall survival rates, higher TIDE scores and lower TMB levels compared to the low-risk group. Variations in immune cell infiltration and responses to therapeutic drugs were observed between the high-risk and low-risk groups. Besides, our study verified the correlations between the DRLs and RNA methylation. Additionally, qRT-PCR experiments and single-cell RNA sequencing data analysis were conducted to confirm the significance of the core DRLs at both cellular and scRNA-seq levels.ConclusionWe constructed a reliable and novel prognostic model with a DRLs cluster for ovarian cancer, providing a foundation for further researches in the management of this disease.

[INLINE:1] β-Sitosterol is a type of phytosterol that occurs naturally in plants. Previous studies have shown that it has anti-oxidant, anti-hyperlipidemic, anti-inflammatory, immunomodulatory, and anti-tumor effects, but it is unknown whether β-sitosterol treatment reduces the effects of ischemic stroke. Here we found that, in a mouse model of ischemic stroke induced by middle cerebral artery occlusion, β-sitosterol reduced the volume of cerebral infarction and brain edema, reduced neuronal apoptosis in brain tissue, and alleviated neurological dysfunction; moreover, β-sitosterol increased the activity of oxygen- and glucose-deprived cerebral cortex neurons and reduced apoptosis. Further investigation showed that the neuroprotective effects of β-sitosterol may be related to inhibition of endoplasmic reticulum stress caused by intracellular cholesterol accumulation after ischemic stroke. In addition, β-sitosterol showed high affinity for NPC1L1, a key transporter of cholesterol, and antagonized its activity. In conclusion, β-sitosterol may help treat ischemic stroke by inhibiting neuronal intracellular cholesterol overload/endoplasmic reticulum stress/apoptosis signaling pathways.

To investigate the spatial and temporal patterns of environmental factors influencing the activity of purse seine tuna fishing vessels, data on fishing efforts of purse seine tuna fleets and environmental factors in the Western and Central Pacific Ocean (WCPO) from 2015 to 2020 were utilized to develop a geographically weighted regression (GWR) model. The results showed that fishing activity was primarily concentrated in the area between 140°E and 175°W, and between 10°S and 5°N. The GWR model showed excellent fitting performance and was suitable for correlation analysis. The environmental factors had a significant spatially heterogeneous effect on the fishing activity of purse seine tuna fishing vessels. The sea surface temperature, primary productivity at 200 m depth, and dissolved oxygen below the surface had the greatest spatially heterogeneous effect and are important environmental variables influencing the activity of purse seine tuna vessels in the WCPO. This study provides new methods for exploring the spatial distribution of fishing vessel activity to support science-based conservation and management.

BackgroundIn 2023, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant caused a large-scale outbreak of coronavirus disease 2019 (COVID-19) in China. It is not clear the risk factors that lead to the exacerbation of symptoms in patients with inflammatory bowel disease (IBD) after COVID-19 infection. Our study aims to find out the risk factors for the exacerbation of IBD-related symptoms in IBD patients with COVID-19 infection and to provide guidance for the clinical management of IBD.MethodsThis is a retrospective, observational study. The online questionnaire was distributed to conduct a survey to collect demographic, clinical, and IBD related characteristics in IBD patients. Univariate and multivariate regression analyses were conducted to assess the independent effects.ResultsIn total, 534 cases of IBD patients were analyzed in our study. Among them, 466 (87.3%) cases diagnosed with COVID-19, 160 (34.3%) cases experienced exacerbation of IBD symptoms, and 84 (18.0%) patients opted for medication discontinuation. Male sex (OR 2.04, 95% CI 1.34–3.49, p = 0.001), and the decrease in body mass index (BMI) (OR 0.93, 95% CI 0.87–1.00, p = 0.035) were positively correlated with the exacerbation of IBD symptoms. Furthermore, the medication discontinuation (OR 2.60, 95% CI 1.58–4.30, p < 0.001) was strongly positively correlated with the exacerbation of IBD symptoms. No significant association was seen between age, comorbidities, smoking, disease activity, vaccination, therapy for COVID-19 and the worsening of IBD symptoms.ConclusionThis study confirms that the infection rate of COVID-19 in China IBD patients was comparable to the general population. Male sex, the decrease in BMI and medication discontinuation are significant risk factors for the exacerbation of IBD-related symptoms in IBD patients with COVID-19 infection.

In the digital economy era, the pathways of digital transformation and intelligent development have emerged as crucial avenues for enterprises’ high-quality development. Focusing on listed private enterprises from 2011 to 2020, this study uses text mining to extract keywords related to digital transformation, as disclosed in annual reports. We construct a digital transformation index and empirically examine its impact on enterprise innovation and innovation incentive policies’ synergistic effects. The results demonstrate that digital transformation significantly promotes innovation in private enterprises, with a more pronounced catalytic effect in economically developed regions characterised by higher levels of the digital economy and larger enterprises. Simultaneously, innovation incentive policies play a crucial role in enhancing digital transformation's impact on innovation in private enterprises. Further investigation reveals that digital transformation's impact mechanism on private enterprise innovation is driven primarily by four paths—specifically improving information transparency, reducing operational risks, alleviating financing constraints, and enhancing total factor productivity. This study provides empirical evidence regarding innovation breakthroughs and driving paths for private enterprises to achieve high-quality development as well as valuable references and insights for policy formulation.

Chub mackerel (Scomber japonicus) is a commercially important fish species which are widely distributed in the North Pacific. Based on the fishery data from China’s high-sea light-purse seine fishing from 2014 to 2020 and the marine environment factors, a mixed linear model considering the actual spatiotemporal stratification of the catch per unit effort (CPUE) was established to analyze the fixed and random effects of marine environmental factors on the CPUE of chub mackerel and to investigate the relationship between the abundance of chub mackerel resources in the Northwest Pacific and two marine environmental factors: sea surface temperature (SST) and chlorophyll-a concentration (CHL). The results showed that SST had a significant fixed effect on the CPUE. In contrast, the natural logarithm of chlorophyll (logCHL) had no fixed effect on the CPUE. Based on the monthly analysis, random fluctuations were observed in the impact of logCHL on the CPUE. LogCHL and CPUE show a positive correlation during spawning and wintering periods and a negative correlation during the feeding period. The study showed that when fishery sampling data exhibit spatiotemporal stratification, linear mixed models can effectively incorporate both the fixed and random effects of environmental factors on the CPUE of chub mackerel. Linear mixed models can play an important role in analyzing the fluctuations in resource abundance and the mechanisms governing the formation of fishing grounds for chub mackerel in the Northwest Pacific.

Abstract Motivation Ovarian cancer (OC) is a highly lethal gynecological malignancy. Extensive research has shown that OC cells undergo significant metabolic alterations during tumorigenesis. In this study, we aim to leverage these metabolic changes as potential biomarkers for assessing ovarian cancer. Methods A functional module-based approach was utilized to identify key gene expression pathways that distinguish different stages of ovarian cancer (OC) within a tissue biopsy cohort. This cohort consisted of control samples (n = 79), stage I/II samples (n = 280), and stage III/IV samples (n = 1016). To further explore these altered molecular pathways, minimal spanning tree (MST) analysis was applied, leading to the formulation of metabolic biomarker hypotheses for OC liquid biopsy. To validate, a multiple reaction monitoring (MRM) based quantitative LCMS/MS method was developed. This method allowed for the precise quantification of targeted metabolite biomarkers using an OC blood cohort comprising control samples (n = 464), benign samples (n = 3), and OC samples (n = 13). Results Eleven functional modules were identified as significant differentiators (false discovery rate, FDR

Abstract Background Townes-Brocks syndrome is a rare autosomal dominant genetic syndrome caused by mutations in SALL1. The clinical features of Townes-Brocks syndrome are highly heterogonous. Identification of new SALL1 mutations and study of the relation between SALL1 mutations and clinical features can facilitate diagnosis of Townes-Brocks syndrome. Methods We collected clinical data and blood samples of the two patients and their family members for whole-exome sequencing and Sanger sequencing. Prediction analysis of the SALL1variation protein structure was achieved using Alphafold. The clinical materials and gene sequencing results were analyzed. The clinical materials and gene sequencing results were analyzed. The related literature of Townes-Brocks syndrome were searched and the genotype-renal phenotype analysis was performed combined with this two cases. Results Based on the clinical features and gene sequencing results, the two patients were diagnosed as Townes-Brocks syndrome. Two novel SALL1 mutations (c.878-887del and c.1240G > T) were identified, both of which were pathogenic mutations. The correlation between genotypes and renal phenotypes in Townes-Brocks syndrome patients caused by SALL1 mutation were summarized. Conclusion This study identified two novel mutations and provided new insights into the correlation of genotypes and renal phenotypes of Townes-Brocks syndrome.

In recent years, there have been frequent jellyfish outbreaks in Chinese coastal waters, significantly impacting the structure, functionality, safety, and economy of nuclear power plant cooling water intake and nearby ecosystems. Therefore, this study focuses on jellyfish outbreaks in Chinese coastal waters, particularly near the Shandong Peninsula. By analyzing jellyfish abundance data, a Generalized Additive Model integrating environmental factors reveals that temperature and salinity greatly influence jellyfish density. The results show variations in jellyfish density among years, with higher densities in coastal areas. The model explains 42.2% of the variance, highlighting the positive correlation between temperature (20–26 °C) and jellyfish density, as well as the impact of salinity (27.5–29‰). Additionally, ocean currents play a significant role in nearshore jellyfish aggregation, with a correlation between ocean currents and site coordinates. This study aims to investigate the relationship between jellyfish blooms and environmental factors. The results obtained from the study provide data support for the prevention and control of blockages in nuclear power plant cooling systems, and provide a data basis for the implementation of monitoring measures in nuclear power plants.

Abstract The mortality rate of epithelial ovarian cancer (EOC) remains the first in malignant tumors of the female reproductive system. The characteristics of rapid proliferation, extensive implanted metastasis, and treatment resistance of cancer cells require an extensive metabolism rewiring during the progression of cancer development. EOC cells satisfy their rapid proliferation through the rewiring of perception, uptake, utilization, and regulation of glucose, lipids, and amino acids. Further, complete implanted metastasis by acquiring a superior advantage in microenvironment nutrients competing. Lastly, success evolves under the treatment stress of chemotherapy and targets therapy. Understanding the above metabolic characteristics of EOCs helps to find new methods of its treatment.

Abstract Background According to research, the fatty liver index (FLI) is associated with diabetes. However, few studies have been conducted to investigate the relationship between FLI and diabetes risk from various perspectives. This study comprehensively investigated the relationship between FLI and incident diabetes in a large Japanese population. Methods This retrospective cohort study included 14,280 participants from Murakami Memorial Hospital in Japan from 2004 to 2015. The independent and dependent variables are FLI and risk of type 2 diabetes mellitus (T2DM), respectively. To examine the link between FLI and incident T2DM, Cox proportional-hazards regression was employed. In addition, we performed a number of sensitivity studies to guarantee the validity of the results. Moreover, we conducted subgroup analyses. Results After adjusting covariates, the results showed that FLI was positively associated with the risk of T2DM (HR = 1.019, 95%CI: 1.012, 1.025). Additionally, the sensitivity analysis showed how reliable the outcomes were. And a stronger association between FLI and incident T2DM was observed in the regular exercisers (HR = 1.036, 95%CI: 1.019–1.053, P

Standardized catch per unit effort (CPUE) data not only yield precise and biologically meaningful abundance indices but also provide crucial insights into the spatio-temporal distribution of fisheries resources, critical for their sustainable utilization and management. In this study, we integrated chub mackerel fishery statistics from the Northwest Pacific Ocean (NPO) and marine remote sensing environmental data, and constructed CPUE standardization models for chub mackerel based on the generalized linear mixed model (GLMM) and spatio-temporal GLMM (Vector Autoregressive Spatio-Temporal, VAST) and evaluated their performance. GLMM is a statistical technique extending GLM with random effects for complex datasets with non-independent observations and correlations or hierarchies. The VAST model is a statistical model for multivariate time series data with observations at different spatial locations, displaying both temporal autocorrelation and spatial dependence. Additionally, influence analysis and simulation testing were employed to quantify the effects of explanatory variables on the differences between nominal CPUE and standardized CPUE, and to assess the estimation accuracy of different models in CPUE standardization, respectively. Finally, the distribution pattern of chub mackerel in the NPO was analyzed by estimating centers of gravity (COGs). The results indicated that: 1) The GLMM model containing all explanatory variables was considered the best model with the smallest conditional Akaike Information Criterion (CAIC), while the VAST model, with only the covariate SST, performed the best. 2) Interactions of year and spatial effects in GLMM and the spatio-temporal variable in VAST, exerted a notable influence on annual standardized CPUE and should be accounted for in the model. 3) Based on simulation testing results, the VAST model exhibited lower model error (root mean square error, RMSE) and model bias, outperforming the GLMM model in CPUE standardization. 4) From 2014 to 2018, chub mackerel exhibited high biomass density widely distributed throughout almost the entire NPO, which shifted to the central-north region from 2019 to 2021. There was no significant northing and easting shift in COGs for the population (P > 0.05). The findings of this research enhance our understanding of the variations in resource abundance indices and spatio-temporal distribution patterns of chub mackerel in the NPO.

Endometrial cancer (EC) is one of the three most prevalent gynecological tumors affecting women and is the most prevalent gynecological malignancy in the developed world. Its incidence is rapidly increasing worldwide, mostly affecting postmenopausal women, whereas recently its prevalence has increased in younger people. EC is an immune gene disease and many studies have shown that the tumor-immunosuppressive microenvironment plays an important role in cancer progression. In recent years, findings regarding the immunosuppressive tumor microenvironment (ITME) of EC have included immune evasion mechanisms and immunotherapy, which are mostly immune checkpoint inhibitors (ICI) for EC. Recently studies on the ITME of different molecular types of EC have found that different molecular types may have different ITME. With the research on the immune microenvironment of EC, a new immunophenotype classification based on the immune microenvironment has been carried out in recent years. However, the impact of the ITME on EC remains unclear, and the immunophenotype of EC remains limited to the research stage. Our review describes recent findings regarding the ITME features of different EC molecular types. The advent of immunotherapy has brought hope for improved efficacy and prognosis in patients with advanced or recurrent EC. The efficacy and safety of ICIs combination therapy remains the focus of future research.

Abstract Parkinson’s disease (PD) is a neurodegenerative disorder characterized by defective dopaminergic (DAergic) input to the striatum. Mutations in two genes encoding synaptically enriched clathrin-uncoating factors, synaptojanin 1 (SJ1) and auxilin, have been implicated in atypical Parkinsonism. SJ1 knock-in (SJ1-KIRQ) mice carrying a disease-linked mutation display neurological manifestations reminiscent of Parkinsonism. Here we report that auxilin knockout (Aux-KO) mice display dystrophic changes of a subset of nigrostriatal DAergic terminals similar to those of SJ1-KIRQ mice. Furthermore, Aux-KO/SJ1-KIRQ double mutant mice have shorter lifespan and more severe synaptic defects than single mutant mice. These include increase in dystrophic striatal nerve terminals positive for DAergic markers and for the PD risk protein SV2C, as well as adaptive changes in striatal interneurons. The synergistic effect of the two mutations demonstrates a special lability of DAergic neurons to defects in clathrin uncoating, with implications for PD pathogenesis in at least some forms of this condition.

ATG9 is the only transmembrane protein of the core autophagy machinery known to be present at presynapses. Here, the authors show that both synaptophysin and ATG9A vesicles assemble into condensates with synapsin but remain segregated from each other.

Abstract Pinocembrin (Pin) has been confirmed to exert anti-inflammatory and antiatherosclerotic effects. Here we have explored whether and how Pin would protect vascular endothelial cells against pyroptosis elicited by the exposure to oxidized low density lipoprotein (oxLDL). Our results showed that Pin preconditioning dose-dependently suppressed oxLDL-stimulated HUVEC injury and pyroptosis, which were manifested by improved cell viability, lower lactate dehydrogenase (LDH) levels and DNA damage as well as decreased expression of pyroptosis-related markers, such as NOD-like receptor pyrin domain-containing 3 (NLRP3), apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (ASC), pro-Caspase-1, cleaved Caspase-1, N-terminus of Gasdermin D-N (GSDMD-N), pro-interleukins-1β (pro-IL-1β), IL-1β and inflammatory cytokines (IL-18 and IL-1β). All of the effects were similar to those of MCC950 (an NLRP3 inhibitor). As expected, Pin distinctly activated the Nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidative signaling pathway assessed through increased expressions of Nrf2, heme oxygenase-1 (HO-1) and NAD(P)H quinone oxidoreductase 1 (NQO1). Furthermore, after transfection with small interfering RNA of Nrf2, the inhibitory effects of Pin on oxLDL-triggered NLRP3 inflammasome/GSDMD-mediated pyroptosis and oxidative stress in HUVECs were weakened. Additionally, Pin up-regulated Nrf2/HO-1 axis and down-regulated NLRP3 inflammasome/GSDMD-mediated pyroptosis signals in Apoe−/− mice fed with high fat diet. These results contribute to the understanding of the anti-pyroptosis mechanisms of Pin and provide a reference for future research on the anti-atherosclerotic effect of Pin.

In recent years, with the development of pelagic fishing, the working environment and monitoring of crew (squid jigger) members have become increasingly important. However, traditional methods of pelagic human observers suffer from high costs, low coverage, poor timeliness, and susceptibility to subjective factors. In contrast, the Electronic Monitoring System (EMS) has advantages such as continuous operation under various weather conditions; more objective, transparent, and efficient data; and less interference with fishing operations. This paper shows how the 3DCNN model, LSTM+ResNet model, and TimeSformer model are applied to video-classification tasks, and for the first time, they are applied to an EMS. In addition, this paper tests and compares the application effects of the three models on video classification, and discusses the advantages and challenges of using them for video recognition. Through experiments, we obtained the accuracy and relevant indicators of video recognition using different models. The research results show that when NUM_FRAMES is set to 8, the LSTM+ResNet-50 model has the best performance, with an accuracy of 88.47%, an F1 score of 0.8881, and an map score of 0.8133. Analyzing the EMS for pelagic fishing can improve China’s performance level and management efficiency in pelagic fishing, and promote the development of the fishery knowledge service system and smart fishery engineering.

Helicobacter pylori infection is a prevalent infectious disease, associated with many gastric diseases, including gastritis, gastric ulcer, and gastric cancer. To reveal the characteristics of the gastric microbiome in patients infected with H. pylori, we performed metagenomic shotgun sequencing of stomach swab samples from 96 patients and then conducted metagenomic association analyses between alterations in the gastric microbiome and H. pylori infection status. The overall composition of the gastric microbiota in H. pylori‐infected individuals was distinctly different from the negative controls; H. pylori became the dominant species after colonizing the human stomach and significantly decreased the α‐diversity of the gastric community (P 0.05, Wilcoxon rank‐sum test). This study revealed alterations in gastric microbial taxa and function associated with HPI in the Chinese population, which provides an insight into gastric microbial interactions and their potential role in the pathological process of gastric diseases.

Objectives: Ovarian cancer is the most lethal gynecologic malignancy, and targeted therapy for different pathological types and molecular phenotypes is urgent to be studied. Studies have shown that MicroRNA-592 (miR-592) plays an important negative regulatory role in the occurrence of gastrointestinal malignancies, breast cancer, non-small cell lung cancer, and glioma, but the expression of miR-592 in ovarian cancer and the mechanism of action are still unclear. Methods: The expressions of miR-592 were examined by RT-PCR and Western Blot. Cell viability and migratory capacity were detected by CCK-8 and transwell assay. TargetScan ( http://www.targetscan.org ) was analyzed to predict potential targets of miR-592. Then Dual-luciferase reporter gene assay was performed to verify the targeting relationship between miR-592 and ERBB3. A mouse xenograft model was applied to confirm the effect of miR-592. Results: In our study, we found that the expression of miR-592 is reduced in epithelial ovarian cancer tissues. The exogenous expression of miR-592 inhibits the proliferation, migration, and invasion in epithelial ovarian cancer tumor cells. Furthermore, the exogenous expression of miR-592 inhibits tumor growth in the nude mouse xenograft model. Therefore, miR-592 may play a role of tumor suppressor miRNA in the occurrence and development of ovarian cancer. Further experiments demonstrated that tumor-related ERBB3 is a target gene mediated by miRNA-592. The dual-luciferase reporter system was used to identify miRNA-592 target genes; qPCR and Western Blot were used to detect the expression of ERBB3. Mechanical experiments confirmed that miRNA-592 negatively regulated ERBB3. Conclusion: Together, these findings identify a heretofore unrecognized link between miR-592 and ERBB3 and suggest that targeting on miR-592 warrants attention as a novel and potential therapeutic strategy for ovarian cancer.

Heterogeneous defect prediction (HDP) is a significant research topic in cross-project defect prediction (CPDP), due to the inconsistency of metrics used between source and target projects. While most HDP methods aim to improve the performance of models trained on data from one source project, few studies have investigated how the number of source projects affects predictive performance. In this paper, we propose a new multi-source heterogeneous kernel mapping (MSHKM) algorithm to analyze the effects of different numbers of source projects on prediction results. First, we introduce two strategies based on MSHKM for multi-source HDP. To determine the impact of the number of source projects on the predictive performance of the model, we regularly vary the number of source projects in each strategy. Then, we compare the proposed MSHKM with state-of-the-art HDP methods and within-project defect prediction (WPDP) methods, in terms of three common performance measures, using 28 data sets from five widely used projects. Our results demonstrate that, (1) in the multi-source HDP scenario, strategy 2 outperforms strategy 1; (2) for MSHKM, a lower number of source projects leads to better results and performance under strategy 1, while n = 4 is the optimal number under strategy 2; (3) MSHKM performs better than related state-of-the-art HDP methods; and (4) MSHKM outperforms WPDP. In summary, our proposed MSHKM algorithm provides a promising solution for heterogeneous cross-project defect prediction, and our findings suggest that the number of source projects should be carefully selected to achieve optimal predictive performance.

Objective: To compare the degree of agreement and consistency of urodynamic studies (UDS) with low urinary tract symptoms (LUTS) questionnaires for evaluating LUTS in cervical cancer patients following radical hysterectomy (RH) and pelvic lymphadenectomy. Methods: From January 2012 to March 2015, 204 cervical cancer patients who underwent RH in 13 hospitals were evaluated using the Incontinence Questionnaire-Female Lower Urinary Tract Symptoms (ICIQ-FLUTS) and the Overactive Bladder Symptom Score (OABSS). Urodynamic tests were also performed on these patients during the same period. Results: Study participants’ age ranged from 23 to 75 years, with a mean (standard deviation) of 48.0 ​± ​9.3 years. Using questionnaires, the prevalence of patients with LUTS symptoms, including storage symptoms, voiding symptoms, stress urinary incontinence (SUI) and overactive bladder (OAB) was 86.3%, 77.0%, 62.7%, 52.9% and 14.7%, respectively. For UDS, the corresponding prevalence was 89.7%, 70.1%, 66.7%, 46.6% and 13.2%, respectively. The diagnostic concordance of questionnaires and UDS for storage symptoms, voiding symptoms, SUI and OAB was 79.9%, 66.7%, 66.7%, 57.4% and 79.9%, respectively. For voiding symptoms, the correlation coefficient was 0.272, which was higher than that of storage symptoms, SUI and OAB. Conclusions: In cervical cancer patients who have undergone RH, there was a moderate degree of agreement between UDS and symptom questionnaires in evaluating LUTS, but the consistency was poor. Medical personnel should be adequately trained in UDS to ensure LUTS are adequately diagnosed in patients.

Synaptic vesicle clusters were proposed to represent phase separated condensates. Here, the authors show that only two proteins, synapsin and synaptophysin, are sufficient to make vesicle clusters in fibroblasts which are similar to those found at synapses in morphology and liquid-like properties.

Abstract Background As we all know, patients with epithelial ovarian carcinoma have poor prognosis and high recurrence rate. It is critical and challenging to screen out the patients with high risk of recurrence. At present, there are some models predicting the overall survival of epithelial ovarian carcinoma, however, there is no widely accepted tool or applicable model predicting the recurrence risk of epithelial ovarian carcinoma patients. The objective of this study was to establish and verify a nomogram to predict the recurrence risk of EOC. Methods We reviewed the clinicopathological and prognostic data of 193 patients with EOC who achieved clinical complete remission after cytoreductive surgery and chemotherapy between January 2003 and December 2013 in Peking University First Hospital. The nomogram was established with the risk factors selected by LASSO regression. The medical data of 187 EOC patients with 5-year standard follow-up in Peking University Third Hospital and Beijing Obstetrics and Gynecology Hospital were used for external validation of the nomogram. AUC curve and Hosmer-Lemeshow test were used to evaluate the discrimination and calibration. Results The nomogram for 3-year recurrence risk was established with FIGO stage, histological grade, histological type, lymph node metastasis status and serum CA125 level at diagnosis. The total score can be obtained by adding the grading values of these factors together. The C statistics was 0.828 [95% CI, 0.764–0.884] and the Chi-square value is 3.6 (P = 0.731 > 0.05) with the training group. When the threshold value was set at 198, the sensitivity, specificity, positive predictive value, negative predictive value and concordance index were 88.8, 67.0, 71.8, 86.3% and 0.558 respectively. In the external validation, the C statistics was 0.803 [95%CI, 0.738–0.867] and the Chi-square value is 11.04 (P = 0.135 > 0.05). With the threshold value of 198, the sensitivity, specificity, positive predictive value, negative predictive value and concordance index of the nomogram were 75.7, 77.0, 83.2, 67.9%, and 0.52 respectively. Conclusions We established and validated a nomogram to predict 3-year recurrence risk of patients with EOC who achieved clinical complete remission after cytoreductive surgery and chemotherapy. This nomogram with good discrimination and calibration might be useful for screening out the patients with high risk of recurrence.

Aiming at the problems of basic genetic algorithm in the field of path planning to system resilience recovery such as excessive randomness of initial population, slow convergence, low efficiency of evolution operator, and poor population diversity, this paper uses quotient model to measure resilience, uses overall task importance to measure system performance, and proposes an improved genetic algorithm on initial population and evolutionary operation. Improved genetic algorithm (IHGA) proposes a new greedy model that considers system node tasks importance, travel time, and maintenance time, which uses greedy ideas to generate partial high-quality initial population. And a new operator is also designed as intra-group head-to-head mutation operator (IHMO) to control the evolution to be more determinate and less ineffectively random. The simulation results in three cases show that the IHGA overcomes the defects and can better effectively recover system resilience with comparison to basic genetic algorithm (BGA) and multi-chromosome genetic algorithm (MCGA). Specially, it has obviously better optimal solution, convergence, and stability, especially in the harsh conditions as shorter repair time, more and unbalanced demands for spare parts, which shows the IHGA has great value to deal with measurement and control of system resilience recovery in practice.

The cellular slime mold Dictyostelium discoideum is a powerful model organism that can be utilized to investigate human health and disease. One particular strength of Dictyostelium is that it can be utilized for high throughput genetic screens. For many phenotypes, one limitation of utilizing Dictyostelium is that screening can be an arduous and time-consuming process, limiting the genomic depth one can cover. Previously, we utilized a restriction enzyme-mediated integration screen to identify suppressors of polyglutamine aggregation in Dictyostelium. However, due to the time required to perform the screen, we only obtained ∼4% genome coverage. Here we have developed an efficient screening pipeline that couples chemical mutagenesis with the 5-fluoroorotic acid counterselection system to enrich for mutations in genes of interest. Here we describe this new screening methodology and highlight how it can be utilized for other biological systems.

Ischemic stroke is a leading cause of death and disability worldwide. Currently, only a limited number of drugs are available for treating ischemic stroke. Hence, studies aiming to explore and develop other potential strategies and agents for preventing and treating ischemic stroke are urgently needed. Ginseng Rb1 (GRb1), a saponin from natural active ingredients derived from traditional Chinese medicine (TCM), exerts neuroprotective effects on the central nervous system (CNS). We conducted this review to explore and summarize the protective effects and mechanisms of GRb1 on cerebral ischemic injury, providing a valuable reference and insights for developing new agents to treat ischemic stroke. Our summarized results indicate that GRb1 exerts significant neuroprotective effects on cerebral ischemic injury both in vivo and in vitro, and these network actions and underlying mechanisms are mediated by antioxidant, anti-inflammatory, and antiapoptotic activities and involve the inhibition of excitotoxicity and Ca2+ influx, preservation of blood–brain barrier (BBB) integrity, and maintenance of energy metabolism. These findings indicate the potential of GRb1 as a candidate drug for treating ischemic stroke. Further studies, in particular clinical trials, will be important to confirm its therapeutic value in a clinical setting.

Labrasol, as a non-ionic surfactant, can enhance the permeation and absorption of drugs, and is extensively used in topical, transdermal, and oral pharmaceutical preparations as an emulsifier and absorption enhancer. Recent studies in our laboratory have indicated that labrasol has a strong absorption enhancing effect on different types of drugs in vitro and in vivo. This study was performed to further elucidate the action mechanism of labrasol on the corneal penetration. In this research, the fluorescein sodium, a marker of passive paracellular transport of tight junction, was selected as the model drug to assess the effect of labrasol on in vitro corneal permeability. To investigate the continuous and real-time influence of labrasol on the membrane permeability and integrity, the Ussing chamber system was applied to monitor the electrophysiological parameters. And, furthermore, we elucidated the effect of labrasol on excised cornea at the molecular level by application of RT-PCR, Western blot, and immunohistochemical staining. The results indicated that labrasol obviously enhance the transcorneal permeability of fluorescein sodium, and the enhancement was realized by interacting with and down-regulating the associated proteins, such as F-actin, claudin-1 and β-catenin, which were contributed to cell-cell connections, respectively. Keywords: Enhanced corneal permeation, Tight junctions associated proteins, Labrasol, Ussing chamber, Western blot, Immunohistochemistry

Blindness and vision impairment are the most devastating global health problems resulting in a substantial economic and social burden. Delivery of drug to particular parts of the anterior or posterior segment has been a major challenge due to various protective barriers and elimination mechanisms associated with the unique anatomical and physiological nature of the ocular system. Drug administration to the eye by conventional delivery systems results in poor ocular bioavailability (

Modern software systems need to autonomously adapt their behavior at runtime in order to maintain their utility in response to continuous environmental changes. Most studies on models at runtime focus on providing suitable techniques to manage the complexity of software at runtime but neglect reliability caused by adaptation activities. Therefore, adaptive behaviors may lead to a decrease in reliability, which may result in severe financial loss or life damage. Runtime software architecture (RSA) is an abstract of a running system, which describes the elements of the current system, the states of these elements and the relation between the elements and their states at runtime. The main difference between RSA and software architecture at design time (DSA) is that RSA has a causal connection with the running system, whereas DSA does not. However, RSA and DSA have both symmetry and asymmetry in software architecture. To ensure that architecture-centric software can provide reliable services after adaptation adjustment, a method is proposed to analyze the impact of changes caused by adaptation strategy on the overall software reliability, which will be predicted at the runtime architecture model layer. Based on a Java platform, through non-intrusive monitoring, an RSA behavioral model is obtained followed by runtime reliability analysis model. Following this, reliability prediction results are obtained through a discrete-time Markov chain (DTMC). Finally, an experiment is conducted to verify the feasibility of the proposed method.

Abstract Neuronal inclusions composed of α-synuclein (α-syn) characterize Parkinson’s Disease (PD) and Dementia with Lewy bodies (DLB). Cognitive dysfunction defines DLB, and up to 80% of PD patients develop dementia. α-Syn inclusions are abundant in the hippocampus, yet functional consequences are unclear. To determine if pathologic α-syn causes neuronal defects, we induced endogenous α-syn to form inclusions resembling those found in diseased brains by treating hippocampal neurons with α-syn fibrils. At seven days after adding fibrils, α-syn inclusions are abundant in axons, but there is no cell death at this time point, allowing us to assess for potential alterations in neuronal function that are not caused by neuron death. We found that exposure of neurons to fibrils caused a significant reduction in mushroom spine densities, adding to the growing body of literature showing that altered spine morphology is a major pathologic phenotype in synucleinopathies. The reduction in spine densities occurred only in wild type neurons and not in neurons from α-syn knockout mice, suggesting that the changes in spine morphology result from fibril-induced corruption of endogenously expressed α-syn. Paradoxically, reduced postsynaptic spine density was accompanied by increased frequency of miniature excitatory postsynaptic currents (EPSCs) and presynaptic docked vesicles, suggesting enhanced presynaptic function. Action-potential dependent activity was unchanged, suggesting compensatory mechanisms responding to synaptic defects. Although activity at the level of the synapse was unchanged, neurons exposed to α-syn fibrils, showed reduced frequency and amplitudes of spontaneous Ca2+ transients. These findings open areas of research to determine the mechanisms that alter neuronal function in brain regions critical for cognition at time points before neuron death.

Tumor-targeted delivery is considered a crucial component of current anticancer drug development and is the best approach to increase the efficacy and reduce the toxicity. Nanomedicine, particularly ligand-based nanoparticles have shown a great potential for active targeting of tumor. Cell penetrating peptide is one of the promising ligands in a targeted cancer therapy. In this study, the gambogic acid-loaded nanostructured lipid carrier (GA-NLC) was modified with two kinds of cell penetrating peptides (cRGD and RGERPPR). The GA-NLC was prepared by emulsification and solvent evaporation method and coupled with cRGD, RGERPPR, and combination cRGD and RGERPPR to form GA-NLC-cRGD, GA-NLC-RGE, and GA-NLC-cRGD/RGE, respectively. The formulations were characterized by their particle size and morphology, zeta potential, encapsulation efficiency, and differential scanning calorimetry. In vitro cytotoxicity and cellular uptake study of the formulations were performed against breast cancer cell (MDA-MB-231). Furthermore, in vivo biodistribution and antitumor activity of the formulations were determined by in vivo imaging and in tumor-bearing nude mice, respectively. The result of in vitro cytotoxicity study showed that GA-NLC-RGE exhibited a significantly higher cytotoxicity on MDA-MB-231 as compared with GA-NLC and GA-Sol. Similarly, RGE-Cou-6-NLC showed remarkably higher uptake by the cells than other NLCs over the incubation period. The in vivo imaging study has demonstrated that among the formulations, the RGE-decorated DiR-NLC were more accumulated in the tumor site. The in vivo antitumor activity revealed that RGE-GA-NLC inhibits the tumor growth more efficiently than other formulations. In conclusion, RGERPPR has a potential as an effective carrier in targeting drug delivery of anticancer agents.

[This corrects the article DOI: 10.1371/journal.pone.0149379.].

Software defect prediction (SDP) is an effective technique to lower software module testing costs. However, the imbalanced distribution almost exists in all SDP datasets and restricts the accuracy of defect prediction. In order to balance the data distribution reasonably, we propose a novel resampling method LIMCR on the basis of Naïve Bayes to optimize and improve the SDP performance. The main idea of LIMCR is to remove less-informative majorities for rebalancing the data distribution after evaluating the degree of being informative for every sample from the majority class. We employ 29 SDP datasets from the PROMISE and NASA dataset and divide them into two parts, the small sample size (the amount of data is smaller than 1100) and the large sample size (larger than 1100). Then we conduct experiments by comparing the matching of classifiers and imbalance learning methods on small datasets and large datasets, respectively. The results show the effectiveness of LIMCR, and LIMCR+GNB performs better than other methods on small datasets while not brilliant on large datasets.

A UHPLC-QQQ-MS/MS method was developed to quantify the significant constituents in Wen-Dan Decoction (WDD), a traditional Chinese medicine. Analysis of 19 compounds was conducted on an ACQUITY UPLC® BEH C18 Column (2.1 × 50 mm, 1.7 μm) using elution with a gradient elution of acetonitrile and 0.05% (v/v) formic acid in water. A triple quadrupole mass spectrometer was operated in negative ionization mode and positive ionization mode by multiple reaction monitoring (MRM), respectively. All calibration curves showed acceptable linearity (r ≥ 0.9950). The RSDs of intra- and inter-day precisions of low, mid and high concentrations were ≤ 8.88%. The repeatabilities (RSDs ≤ 7.17%) and stabilities (RSD ≤ 4.79%) of the samples were qualified. The recoveries were found in the range of 93.07 ± 3.86 to 103.98 ± 2.98% with the RSD varying between 1.30 and 7.86%. The final rapid, sensitive, precise, accurate and reliable UHPLC-QQQ-MS/MS method was used for the simultaneous quantification of 19 constituents in WDD and its commercial preparations. The strategy of combining the contents of the 19 chemicals in a daily dose of the WDD preparations with the hierarchical cluster analysis and the 3D principal component analysis was employed to effectively distinguish the WDD preparations provided by the different suppliers, which represents a contribution to the evaluation and control of the quality of WDD (or other decoctions consisting of the same herbs) and the preparations of WDD in other dosage forms such as tablets and granules.

The rat is a preferred model system over the mouse for neurological studies, and cell type-specific Cre expression in the rat enables precise ablation of gene function in neurons of interest, which is especially valuable for neurodegenerative disease modeling and optogenetics. Yet, few such Cre rats are available. Here we report the characterization of two Cre rats, tyrosine hydroxylase (TH)-Cre and dopamine active transporter (DAT or Slc6a3)-Cre, by using a combination of immunohistochemistry (IHC) and mRNA fluorescence in situ hybridization (FISH) as well as a fluorescent reporter for Cre activity. We detected Cre expression in expected neurons in both Cre lines. Interestingly, we also found that in Th-Cre rats, but not DAT-Cre rats, Cre is expressed in female germ cells, allowing germline excision of the floxed allele and hence the generation of whole-body knockout rats. In summary, our data demonstrate that targeted integration of Cre cassette lead to faithful recapitulation of expression pattern of the endogenous promoter, and mRNA FISH, in addition to IHC, is an effective method for the analysis of the spatiotemporal gene expression patterns in the rat brain, alleviating the dependence on high quality antibodies that are often not available against rat proteins. The Th-Cre and the DAT-Cre rat lines express Cre in selective subsets of dopaminergic neurons and should be particularly useful for researches on Parkinson's disease.

Epsin is an evolutionarily conserved endocytic clathrin adaptor whose most critical function(s) in clathrin coat dynamics remain(s) elusive. To elucidate such function(s), we generated embryonic fibroblasts from conditional epsin triple KO mice. Triple KO cells displayed a dramatic cell division defect. Additionally, a robust impairment in clathrin-mediated endocytosis was observed, with an accumulation of early and U-shaped pits. This defect correlated with a perturbation of the coupling between the clathrin coat and the actin cytoskeleton, which we confirmed in a cell-free assay of endocytosis. Our results indicate that a key evolutionary conserved function of epsin, in addition to other roles that include, as we show here, a low affinity interaction with SNAREs, is to help generate the force that leads to invagination and then fission of clathrin-coated pits.

The exocytosis of synaptic vesicles (SVs) elicited by potent stimulation is rapidly compensated by bulk endocytosis of SV membranes leading to large endocytic vacuoles (‘bulk’ endosomes). Subsequently, these vacuoles disappear in parallel with the reappearance of new SVs. We have used synapses of dynamin 1 and 3 double knock-out neurons, where clathrin-mediated endocytosis (CME) is dramatically impaired, to gain insight into the poorly understood mechanisms underlying this process. Massive formation of bulk endosomes was not defective, but rather enhanced, in the absence of dynamin 1 and 3. The subsequent conversion of bulk endosomes into SVs was not accompanied by the accumulation of clathrin coated buds on their surface and this process proceeded even after further clathrin knock-down, suggesting its independence of clathrin. These findings support the existence of a pathway for SV reformation that bypasses the requirement for clathrin and dynamin 1/3 and that operates during intense synaptic activity.

Vertebrate limbs originate from the lateral plate mesoderm (LPM) and the overlying ectoderm. While normal limb formation in defined regions has been well studied, the question of whether other positions retain limb-forming potential has not been fully investigated in mice. By ectopically activating β-catenin in the ectoderm with Msx2-cre, we observed that local tissue outgrowths were induced, which either progressed into limb-like structure within the inter-limb flank or formed extra tissues in other parts of the mouse embryo. In the presumptive abdominal region of severely affected embryos, ectopic limb formation was coupled with impaired abdominal ventral body wall (AVBW) closure, which indicates the existence of a potential counterbalance of limb formation and AVBW closure. At the molecular level, constitutive β-catenin activation was sufficient to trigger, but insufficient to maintain the ectopic expression of a putative limb-inducing factor, Fgf8, in the ectoderm. These findings provide new insight into the mechanism of limb formation and AVBW closure, and the crosstalk between the Wnt/β-catenin pathway and Fgf signal.

Diminished adult neurogenesis is considered a potential mechanism in the pathogenesis of HIV-1-associated dementia (HAD). In HAD, HIV-1-infected and immune-activated brain mononuclear phagocytes (MP; perivascular macrophages and microglia) drive central nervous system (CNS) inflammation and may alter normal neurogenesis. We previously demonstrated HIV-1-infected and lipopolysaccharide (LPS) activated monocyte-derived macrophages (MDM) inhibit human neural progenitor cell (NPC) neurogenesis, while enhancing astrogliogenesis through the secretion of the inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), in vitro and in vivo. Here we further test the hypothesis that HIV-1-infected/activated MDM promote NPC astrogliogenesis via activation of the transcription factor signal transducer and activator of transcription 3 (STAT3), a critical factor for astrogliogenesis. Our results show that LPS-activated MDM-conditioned medium (LPS-MCM) and HIV-infected/LPS-activated MDM-conditioned medium (LPS+HIV-MCM) induced Janus kinase 1 (Jak1) and STAT3 activation. Induction of the Jak-STAT3 activation correlated with increased glia fibrillary acidic protein (GFAP) expression, demonstrating an induction of astrogliogenesis. Moreover, STAT3-targeting siRNA (siSTAT3) decreased MCM-induced STAT3 activation and NPC astrogliogenesis. Furthermore, inflammatory cytokines (including IL-6, IL-1β and TNF-α) produced by LPS-activated and/or HIV-1-infected MDM may contribute to MCM-induced STAT3 activation and astrocytic differentiation. These observations were confirmed in severe combined immunodeficient (SCID) mice with HIV-1 encephalitis (HIVE). In HIVE mice, siRNA control (without target sequence, sicon) pre-transfected NPCs injected with HIV-1-infected MDM showed more astrocytic differentiation and less neuronal differentiation of NPCs as compared to NPC injection alone. siSTAT3 abrogated HIV-1-infected MDM-induced astrogliogenesis of injected NPCs. Collectively, these observations demonstrate that HIV-1-infected/activated MDM induces NPC astrogliogenesis through the STAT3 pathway. This study generates important data elucidating the role of brain inflammation in neurogenesis and may provide insight into new therapeutic strategies for HAD.

Members of the synaptophysin and synaptogyrin family are vesicle proteins with four transmembrane domains. In spite of their abundance in synaptic vesicle (SV) membranes, their role remains elusive and only mild defects at the cellular and organismal level are observed in mice lacking one or more family members. Here, we show that coexpression with synapsin in fibroblasts of each of the four brain-enriched members of this family--synaptophysin, synaptoporin, synaptogyrin 1, and synaptogyrin 3--is sufficient to generate clusters of small vesicles in the same size range of SVs. Moreover, mice lacking all these four proteins have larger SVs. We conclude that synaptophysin and synaptogyrin family proteins play an overlapping function in the biogenesis of SVs and in determining their small size. [ABSTRACT FROM AUTHOR]