[Clinical and genetic analyses of Joubert syndrome in children]. / 儿童Joubertç»¼åˆå¾ä¸´åºŠåŠé—ä¼ å­¦åˆ†æž.

OBJECTIVES: To study the clinical and genetic features of Joubert syndrome (JS) in children. METHODS: A retrospective analysis was performed on the clinical data, genetic data, and follow-up data of 20 children who were diagnosed with JS in the Department of Children's Rehabilitation, the Third Affiliated Hospital of Zhengzhou University, from January 2017 to July 2022. RESULTS: Among the 20 children with JS, there were 11 boys and 9 girls. The common clinical manifestations were developmental delay (20 children, 100%), abnormal eye movement (19 children, 95%), and hypotonia (16 children, 80%), followed by abnormal respiratory rhythm in 5 children (25%) and unusual facies (including prominent forehead, low-set ears, and triangular mouth) in 3 children (15%), and no limb deformity was observed. All 20 children (100%) had the typical "molar tooth sign" and "midline cleft syndrome" on head images, and 6 children (30%) had abnormal eye examination results. Genetic testing was performed on 7 children and revealed 6 pathogenic genes, i.e., the CPLANE1, RPGRIP1L, MKS1, CC2D2A, CEP120, and AHI1 genes. CONCLUSIONS: For children with developmental delay, especially those with abnormal eye movement and hypotonia, it is recommended to perform a head imaging examination to determine the presence or absence of "molar tooth sign" and "midline cleft syndrome", so as to screen for JS to avoid missed diagnosis and misdiagnosis. There are many pathogenic genes for JS, and whole-exome sequencing can assist in the diagnosis of JS.

Old drug new tricks: Chlorhexidine acts as a potential allosteric inhibitor toward PAK1.

This paper describes the identification of chlorhexidine, an agent commonly used in clinical as a novel potential allosteric inhibitor of PAK1. In cellular assays, chlorhexidine showed a good inhibitory profile, and its inhibitory profile was even better than IPA-3, a well-known allosteric inhibitor. In pharmacology experiments, chlorhexidine successfully inhibited the relief of PAK1 dimer and inhibited the activation of PAK1. Our findings offer an insight for the new drug development of PAK1 inhibitor. We also provide a possible explanation for the phenomenon that the application of the chlorhexidine in peritoneal lavage inhibited the development of tumor.

A travel guide to Cytoscape plugins.

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5-2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.

[Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

Cytoscape 2.8: new features for data integration and network visualization.

UNLABELLED: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features--Custom Node Graphics and Attribute Equations--which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. AVAILABILITY AND IMPLEMENTATION: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org.

Risk of station 12a lymph node metastasis in patients with lower-third gastric cancer.

BACKGROUND: Controversy over the issue that No. 12a lymph node involvement is distant or regional metastasis remains, and the possible inclusion of 12a lymph nodes in D2 lymphadenectomy is unclear. As reported, gastric cancer (GC) located in the lower third is highly related to the metastasis of station 12a lymph nodes. AIM: To investigate whether the clinicopathological factors and metastasis status of other perigastric nodes can predict station 12a lymph node metastasis and evaluate the prognostic significance of station 12a lymph node dissection in patients with lower-third GC. METHODS: A total of 147 patients with lower-third GC who underwent D2 or D2+ lymphadenectomy, including station 12a lymph node dissection, were included in this retrospective study from June 2003 to March 2011. Survival prognoses were compared between patients with or without station 12a lymph node metastasis. Logistic regression analyses were used to clarify the association between station 12a lymph node metastasis and clinicopathological factors or metastasis status of other perigastric nodes. The metastasis status of each regional lymph node was evaluated to identify the possible predictors of station 12a lymph node metastasis. RESULTS: Metastasis to station 12a lymph nodes was observed in 18 patients with lower-third GC, but not in 129 patients. The incidence of station 12a lymph node involvement was reported as 12.2% in patients with lower-third GC. The overall survival of patients without station 12a lymph node metastasis was significantly better than that of patients with station 12a metastasis (P < 0.001), which could also be seen in patients with or without extranodal soft tissue invasion. Station 12a lymph node metastasis and extranodal soft tissue invasion were identified as independent predictors of poor prognosis in patients with lower-third GC. Advanced pN stage was defined as independent risk factor significantly correlated with station 12a lymph node positivity. Station 3 lymph node staus was also proven to be significantly correlated with station 12a lymph node involvement. CONCLUSION: Metastasis of station 12a lymph nodes could be considered an independent prognosis factor for patients with lower-third GC. The dissection of station 12a lymph nodes may not be ignored in D2 or D2+ lymphadenectomy due to difficulties in predicting station 12a lymph node metastasis.

Thirty-year trends in clinicopathologic characteristics and prognosis after gastrectomy for gastric cancer: A single institution in Northern China.

Background: We integrated changes in the trends in clinicopathologic characteristics and postoperative prognosis in patients with gastric cancer Northern China over a 30-year period. Methods: A retrospective analysis of patients undergoing gastric cancer resection and complete follow-up information from January 1981 to December 2010 in the first affiliated Hospital of China Medical University was carried out. We divided the patients into three consecutive periods. Results: A total of 3,520 patients were included in this study. The proportion of lower tumors increased (from 58.8 to 66.9%), while that of upper tumors decreased (from 21.3 to 13.4%). The proportion of tumors > 5cm decreased (from 58.6 to 41.1 %), but the increasing trend of poorly differentiated gastric cancer was obvious (from 60.1 to 75.7%). The percentage of early gastric cancer increased from 10.0 to 15.5 during the study periods, and that of TNM stage Ⅳ cancer decreased from 38.6 to 28.1. In surgery treatment, the rate of radical resection increased to 92.1% in recent period, and the average number of retrieved lymph nodes increased. The 5-year survival rate gradually increased from 36.5% to 48.5% (p<0.001). The Multivariate analysis showed that age, tumor size, T stage, N stage, number of retrieved lymph nodes and resection type were independent prognostic factors for gastric cancer. Conclusion: The patterns of clinicopathologic features for gastric cancer changed during the 30-year period in North China. Overall survival (OS) could be increased by early detection of tumors and standard surgical treatment.

Should All Stage N3b Patients with Advanced Gastric Cancer Be Considered Equivalent? A 30-Year Single Center Study.

PURPOSE: To investigate the survival of stage N3b patients with advanced gastric cancer (AGC) after radical surgery and to evaluate the TNM staging of subgroups of stage N3b patients. METHODS: We reviewed the data of 222 stage N3b patients with AGC who underwent D2/D3 radical surgery. Depending on the number of metastatic lymph nodes (MLNs), we divided N3b patients into several groups and compared the survival differences among them. We found that survival of patients with 16-20 MLNs was better than that of patients with ≥ 21 MLNs. Therefore, we divided the N3b patients into two subgroups and defined patients with 16-21 MLNs as N3b1 and patients with ≥ 21 MLNs as N3b2. Then, we compared survival differences between the two groups and their subgroups. Patients who underwent palliative surgery served as the reference group. In addition, we selected stage IIIB, IIIC, and IV patients from the same database to properly re-classify the N3b subgroups in the TNM staging system. RESULTS: Survival differed significantly between the new N3b1and N3b2 groups and between the new N3b1 group and the palliative group. However, the survival of the new N3b2 group was similar to that of the palliative group. Comparisons of survival according to T staging revealed similarities between the following groups: (1) stages T2-3N3b1 and IIIB, (2) stages T4N3b1 and IIIC, and (3) stages T2-4N3b2 and IV. CONCLUSIONS: All stage N3b patients with AGC should not be considered equivalent. A significant difference in survival was observed between stage N3b1 and N3b2 patients after radical surgery, while the survival of stage N3b2 patients was similar to that of patients who undergo palliative surgery. We recommend re-classifying stage T2-3N3b1 as TNM stage IIIB, stage T4N3b1 as stage IIIC, and T2-4N3b2 as stage IV.

A Proposal of a Personalized Surveillance Strategy for Gastric Cancer: A Retrospective Analysis of 9191 Patients.

BACKGROUND: In gastric cancer, various surveillance strategies are suggested in international guidelines. The current study is intended to evaluate the current strategies and provide more personalized proposals for personalized cancer medicine. MATERIALS AND METHODS: In the aggregate, 9191 patients with gastric cancer after gastrectomy from 1998 to 2009 were selected from the Surveillance, Epidemiology, and End Results database. Disease-specific survival was analyzed by Kaplan-Meier method and the log-rank test. Cox proportional hazards regression analyses were used to confirm the independent prognostic factors. As well, hazard ratio (HR) curves were used to compare the risk of death over time. Conditional survival (CS) was applied to dynamically assess the prognosis after each follow-up. RESULTS: Comparisons from HR curves on different stages showed that earlier stages had distinctly lower HR than advanced stages. The curve of stage IIA was flat and more likely the same as that of stage I while that of stage IIB is like that of stage III with an obvious peak. After estimating CS at intervals of three months, six months, and 12 months in different periods, stages I and IIA had high levels of CS all along, while there were visible differences among CS levels of stages IIB and III. CONCLUSIONS: The frequency of follow-up for early stages, like stages I and IIA, could be every six months or longer in the first three years and annually thereafter. And those with unfavorable conditions, such as stages IIB and III, could be followed up much more frequently and sufficiently than usual.

Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.

Author Correction: Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

In the original version of this Data Descriptor the word "Gulf" was incorrectly spelled in the affiliation "Ocean College, Beibu Gulf University, Qinzhou, 535011, Guangxi, China". This has now been corrected in both the HTML and PDF versions.

Structure activity relationships of chrysoeriol and analogs as dual c­Met and VEGFR2 tyrosine kinase inhibitors.

Vascular endothelial growth factor receptor 2 (VEGFR2) and c­Met are tyrosine kinases, which are involved in the tumorigenesis of various types of cancer. Previous studies have demonstrated that the elevated activation of c­Met is associated with the drug resistance of VEGFR2 inhibitors. Therefore, dual c­Met and VEGFR2 kinase inhibitors are expected to overcome VEGFR2 inhibitor resistance and subsequently lead to a superior therapeutic outcome to regular VEGFR2 inhibitors. In the present study, it was found that chrysoeriol, which can be extracted from several natural plants, was a potential dual c­Met and VEGFR2 kinase inhibitor. The results of docking experiments revealed that chrysoeriol was able to efficiently bind in the active site cavity of c­Met and VEGFR2. The results of enzymatic assays showed relatively high binding affinities of chrysoeriol to c­Met (Kd=12 µM) and VEGFR2 (Kd=11 µM). The structure activity relationships (SARs) of chrysoeriol and its analogs were investigated using pharmacological and molecular docking experiments. To the best of our best knowledge, the present study is the first to report a natural product with both c­Met and VEGFR2 inhibitory profiles, and provides insights into future dual c­Met and VEGFR2 kinase inhibitor development.

Development of a risk-scoring system to evaluate the serosal invasion for macroscopic serosal invasion positive gastric cancer patients.

BACKGROUND: The status of serosal invasion is often discordance between pathological and intraoperative evaluation. Our study sought to develop a risk-scoring system (RSS) to predict the probability of pT4a for macroscopic serosal invasion (MSI) positive patients and reevaluate the serosal invasion status. PATIENTS AND METHODS: A total of 1301 pT3/pT4a gastric cancer patients with curative surgery were reviewed. We constructed the RSS to predict the probability of pT4a and assigned MSI-positive patients into different risk groups based on the risk scores. The prognostic significance of these risk groups was also evaluated. RESULTS: Univariate and multivariate analyses identified that tumor location, Lauren type, Borrmann type, tumor size, lymphovascular invasion and pN stage were risk factors related to pT4a. Survival analyses showed that pT3 MSI-positive patients in high-risk group had similar survival with pT4a patients. We incorporated these two groups into one stage and proposed a novel revised-T stage. Two-step multivariate analyses indicated that the revised-T stage showed better prediction ability for prognosis and peritoneal recurrence assessment than original pT stage and MSI status. CONCLUSIONS: In our present study, we developed a RSS to predict the probability of pT4a for MSI-positive patients. Based on our RSS, we proposed a treatment algorithm to reevaluate the tumor invasion for MSI-positive patients in clinical practice. Future studies should include other preoperative predictors to improve the clinical utility of our model.

Alcohol drinking and gastric cancer risk: a meta-analysis of observational studies.

BACKGROUND: Many studies investigated the association between alcohol drinking and gastric cancer risk, but the results were controversial. We performed a meta-analysis of observational studies to explore the association. MATERIALS AND METHODS: We searched PubMed to identify the relevant studies that reported the association between alcohol drinking and gastric cancer risk up to December 31, 2016. We pooled relative risks (RRs) in random effects model and performed dose-response analysis to quantify the association. Cochran Q test and I2 analyses were used to evaluate the heterogeneity. Meta-regression, subgroup, sensitivity and publication bias analyses were also performed. RESULTS: 75 studies were included in our study. The pooled RR of high vs low total alcohol drinking was 1.25 (95% CI, 1.15-1.37, P < 0.001), and a nonlinear association was further observed. Subgroup analysis showed that alcohol drinking significantly associated with the risk of gastric noncardia cancer (RR, 1.19; 95% CI, 1.01-1.40, P = 0.033), but not with the risk of gastric cardia cancer (RR, 1.16; 95% CI, 0.98-1.39, P = 0.087). Notably, the pooled RRs of high vs low analyses were 1.13 (95% CI, 1.03-1.24, P = 0.012) for beer drinking, 1.22 (95% CI, 1.06-1.40, P = 0.005) for liquor drinking, and 0.99 (95% CI, 0.84-1.16, P = 0.857) for wine drinking. CONCLUSIONS: Our meta-analysis found a nonlinear association between alcohol drinking and gastric cancer risk, and heavy drinking level was strongly related to gastric cancer risk. Beer and liquor had significant positive associations with gastric cancer risk, while wine drinking would not increase gastric cancer risk. These results need to be verified in future research.

A Nomogram for Predicting Overall Survival of Gastric Cancer Patients with Insufficient Lymph Nodes Examined.

Insufficient number of examined lymph nodes (eLNs) was considered to increase significantly the risk of stage migration in gastric cancer patients. The aim of our study is to establish a nomogram predicting the overall survival (OS) for patients with an insufficient number of eLNs. A total of 872 gastric cancer patients with extended lymphadenectomies were assigned randomly (2:1) to the development cohort and the validation cohort. The nomogram was established based on the Cox regression model using the development cohort. The concordance index (C-index) was used to evaluate the discriminative ability. We also compared our model with two other staging systems. Using multivariate analysis, age, sex, tumor location, depth of invasion, macroscopic type, lymphovascular invasion, the number of eLNs, and metastatic lymph nodes were selected and incorporated into the nomogram. The C-index of the nomogram was 0.742 and 0.743 in development and validation cohorts, respectively, which were significantly superior to the C-indices (range 0.705-0.712, all P < 0.001) of American Joint Committee on Cancer (AJCC) seventh edition and lymph node ratio staging systems in both cohorts. We established a nomogram which could predict accurately OS for gastric cancer patients with insufficient number of eLNs.

Rare upper gastrointestinal hemorrhage of cetuximab: A case report.

RATIONALE: cetuximab, an epidermal growth factor receptor inhibitor, is a targeted therapeutic regimen of colorectal cancers. Several common adverse effects have been found, such as cutaneous or gastrointestinal toxicity. However, according to the articles had been published, upper gastrointestinal bleeding (UGIB) is considered to be rare and its mechanism remains unclear. PATIENT CONCERNS: In this report, we presented a 42-year-old male patient with advanced recto-sigmoid cancer. After palliative operation, the patient suffered from complete upper gastrointestinal (GI) obstruction, which was induced by extensive abdominal metastasis of the tumor. Considering his poor condition, we chose the targeted drug, cetuximab, as his further treatment. But after the application of cetuximab, the UGIB immediately happened twice in this patient. DIAGNOSIS: UGIB, as a rare complication of cetuximab, occured to the patient. INTERVENTIONS: We stopped the bleeding with thrombin, hemocoagulase and somatostatin and suspended the subsequent treatment plan of cetuximab. At the same time, anti-shock treatment was given immediately. OUTCOMES: He was died of respiratory and circulatory failure caused by UGIB and advanced tumor eventually. LESSONS: UGIB should be considered as a rare but severe complication of cetuximab. When cetuximab is applied for patients with advanced colon tumors, more cautions should be required if the patients are accompanied by upper gastrointestinal obstruction. In addition, for those patients who suffered from UGIB recently, cetuximab should be prohibited if the Rockall score ranged > 5 points.

Assembling global maps of cellular function through integrative analysis of physical and genetic networks.

To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.

Integration of biological networks and gene expression data using Cytoscape.

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.

A solution NMR molecular model for the aspartate-ligated, cubane cluster containing ferredoxin from the hyperthermophilic archeaon Pyrococcus furiosus.

A solution molecular model for the conformationally dynamically heterogeneous Pyrococcus furiosus ferredoxin with an intact disulfide bond has been constructed on the basis of reported (1)H NMR spectral parameters using distance geometry and simulated annealing protocols. Conventional long-mixing time NOESY and H-bonding constraints have been augmented by previously reported short-mixing time NOESY, steady-state NOE, and cluster paramagnetism-induced relaxation. The family of 15 structures with inconsequential violations exhibited low rms deviations for backbone atoms for the overwhelming majority of the residues, including the cluster ligating loop with the unprecedented ligated Asp14. Larger rms deviations were observed across the disulfide bond, but closer inspection revealed that the 15 structures can be factored into 10 substructures exhibiting an "S" or right-handed disulfide orientation and 5 exhibiting an "R" or left-handed disulfide orientation. The remainder of the structure is indistinguishable for the two disulfide orientations but confirms stabilizing extensions of secondary structural elements in the lengthening of the long helix and both the lengthening and incorporation of a third strand into the beta-sheet involving the termini, with these extensions interacting strongly in a modular fashion through the rings of Tyr46 and Trp2. These extensions of stabilizing interactions in Pyrococcus furiosus Fd, however, lead to strong destabilization of the disulfide bond and destabilization of the highly conserved first and last beta-turns in the sequence. It is concluded that the structural alternations in Pyrococcus Fd relative to other hyperthermostable Fds are not to increase thermostability but to place "stress" on the disulfide bond and render it more reducible. The possible physiological implications of this unique reducible disulfide bond are discussed.