Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Structural failure analysis with CMS-based ground motion selection using innovative cost function and weight factors

The selection and scaling of ground motion records is considered a primary and essential task in performing structural analysis and design.Conventional methods involve using ground motion models and a conditional spectrum to select ground motion records based on the target spectrum.This research demonstrates the influence of adopting different weighted factors for various period ranges during matching selected ground motions with the target hazard spectrum.The event data from the Next Generation Attenuation West 2(NGA-West 2)database is used as the basis for ground motion selection,and hazard de-aggregation is conducted to estimate the event parameters of interest,which are then used to construct the target intensity measure(IM).The target IMs are then used to select ground motion records with different weighted vector-valued objective functions.The weights are altered to account for the relative importance of IM in accordance with the structural analysis application of steel moment resisting frame(SMRF)buildings.Instead of an ordinary objective function for the matching spectrum,a novel model is introduced and compared with the conventional cost function.The results indicate that when applying the new cost function for ground motion selection,it places higher demands on structures compared to the conventional cost function.Moreover,submitting more weights to the first-mode period of structures increases engineering demand parameters.Findings demonstrate that weight factors allocated to different period ranges can successfully account for period elongation and higher mode effects.

Global research trends and hotspots in overweight/obese comorbid with depression among children and adolescents: A bibliometric analysis

BACKGROUND Overweight/obesity combined with depression among children and adolescents(ODCA)is a global concern.The bidirectional relationship between depression and overweight/obesity often leads to their comorbidity.Childhood and adolescence represent critical periods for physical and psychological development,during which the comorbidity of overweight/obesity and depression may increase the risk of adverse health outcomes.AIM To evaluate the relationship between ODCA,we conduct a bibliometric analysis to aid in formulating prevention and treatment strategies.METHODS From 2004 to 2023,articles related to ODCA were selected using the Science Citation Index Expanded from the Web of Science Core Collection.Bibliometric analysis of relevant publications,including countries/regions,institutions,authors,journals,references,and keywords,was conducted using the online bibliometric analysis platforms,CiteSpace,VOSviewer,and bibliometrix.RESULTS Between 2004 and 2023,a total of 1573 articles were published on ODCA.The United States has made leading contributions in this field,with Harvard University emerging as the leading contributor in terms of research output,and Tanofsky being the most prolific author.The J Adolescent Health has shown significant activity in this domain.Based on the results of the keyword and reference analyses,inequality,adverse childhood experiences,and comorbidities have become hot topics in ODCA.Moreover,the impact of balancedrelated behavior and exploration of the biological mechanisms,including the potential role of key adipocytokines and lipokines,as well as inflammation in ODCA,have emerged as frontier topics.CONCLUSION The trend of a significant increase in ODCA publications is expected to continue.The research findings will contribute to elucidating the pathogenic mechanisms of ODCA and its prevention and treatment.

Low Birth Weight in Cameroon: Research and Analysis of Factors Associated with Their Occurrence in Douala Maternity Wards

Introduction: Low birth weight (LBW) is defined by the World Health Organization (WHO) as a birth weight strictly below 2500 g, whatever the term of pregnancy. It constitutes a major public health problem, both in developed and developing countries, due to its magnitude and its strong association with infant morbidity and mortality. Main objective was to study the factors associated with the occurrence of small-for-gestational-age newborns in Douala. Methodology: We carried out a cross-sectional analytical study with prospective data collection using a technical pretested sheet in the maternity wards of the Douala General Hospital, the Laquintinie Hospital, and the District hospitals of Deido, Nylon and Bonassama over a period of 4 months (January to April 2020). We were interested in any newborn, born alive, vaginally or by cesarean section, of low weight, seen in the first 24 hours from a full-term single-fetal pregnancy whose mother had given her consent. Our sampling was consecutive and non-exhaustive. We excluded newborns whose term was unclear and those with congenital malformations or signs of embryo-foetopathy. Data collection was done using survey sheets. Statistical analyzes were carried out with CS Pro 7.3 and SPSS version 25.0 software. The Student, Chi-square and Fischer tests were used to compare the means of the variables, the percentages with a significance threshold P value Results: During the study period, 305 full-term newborns were included, divided into 172 boys and 133 girls. The percentage of small-for-gestational-age newborns was 9.8%;after multivariate analysis by logistic regression to eliminate confounding factors, we found maternal factors associated with small for gestational age newborns;maternal age less than 20 years, primiparity, gestational age (37 - 38), a delay in prenatal visits greater than 14 weeks, anemia in pregnancy, positive toxoplasmosis serology in pregnancy, a body mass index of Conclusion: Our study revealed the potential determinants of low birth weight at term in the Cameroonian urban context and specifically in Douala.

Algorithms and statistical analysis for linear structured weighted total least squares problem

Weighted total least squares(WTLS)have been regarded as the standard tool for the errors-in-variables(EIV)model in which all the elements in the observation vector and the coefficient matrix are contaminated with random errors.However,in many geodetic applications,some elements are error-free and some random observations appear repeatedly in different positions in the augmented coefficient matrix.It is called the linear structured EIV(LSEIV)model.Two kinds of methods are proposed for the LSEIV model from functional and stochastic modifications.On the one hand,the functional part of the LSEIV model is modified into the errors-in-observations(EIO)model.On the other hand,the stochastic model is modified by applying the Moore-Penrose inverse of the cofactor matrix.The algorithms are derived through the Lagrange multipliers method and linear approximation.The estimation principles and iterative formula of the parameters are proven to be consistent.The first-order approximate variance-covariance matrix(VCM)of the parameters is also derived.A numerical example is given to compare the performances of our proposed three algorithms with the STLS approach.Afterwards,the least squares(LS),total least squares(TLS)and linear structured weighted total least squares(LSWTLS)solutions are compared and the accuracy evaluation formula is proven to be feasible and effective.Finally,the LSWTLS is applied to the field of deformation analysis,which yields a better result than the traditional LS and TLS estimations.

Contribution of GIS to Soil Landscape Mapping by Multi-Criteria Analysis Using Weighting: The Case of the Square Degrees of M’Bahiakro (Centre) and Daloa (Centre-West) in Ivory Coast

As part of the drive to improve coffee and cocoa production in Ivory Coast, studies are carried out to identify soils that are favourable for these crops. It is therefore necessary to orientate soil investigations based on reliable criteria that best discriminate soil cover. With this in mind, this study is being carried out to help improve survey methods by mapping soil landscapes. It uses GIS and weighted multicriteria analysis. To do this, satellite images were processed and the geological map of the square degrees of M’Bahiakro and Daloa was reclassified. The results show that relief is the main factor in soil landscape differentiation, with respective weights of 0.58 and 0.67 for the forest and pre-forest zones. In contrast, the weight of geological formation in soil landscape differentiation remains low (0.05 for the forest zone and 0.07 for the pre-forest zone). The criteria used on the base of aggregation sum methods have made it possible to formulate soil landscape mapping prediction functions according to agro-ecological environments in the humid intertropical zone. This is essential for the orientation of soil survey work. Nevertheless, other comparative methods, such as the coding mapping method, could provide elements for discussion to validate the models.

Improving Badminton Action Recognition Using Spatio-Temporal Analysis and a Weighted Ensemble Learning Model

Incredible progress has been made in human action recognition(HAR),significantly impacting computer vision applications in sports analytics.However,identifying dynamic and complex movements in sports like badminton remains challenging due to the need for precise recognition accuracy and better management of complex motion patterns.Deep learning techniques like convolutional neural networks(CNNs),long short-term memory(LSTM),and graph convolutional networks(GCNs)improve recognition in large datasets,while the traditional machine learning methods like SVM(support vector machines),RF(random forest),and LR(logistic regression),combined with handcrafted features and ensemble approaches,perform well but struggle with the complexity of fast-paced sports like badminton.We proposed an ensemble learning model combining support vector machines(SVM),logistic regression(LR),random forest(RF),and adaptive boosting(AdaBoost)for badminton action recognition.The data in this study consist of video recordings of badminton stroke techniques,which have been extracted into spatiotemporal data.The three-dimensional distance between each skeleton point and the right hip represents the spatial features.The temporal features are the results of Fast Dynamic Time Warping(FDTW)calculations applied to 15 frames of each video sequence.The weighted ensemble model employs soft voting classifiers from SVM,LR,RF,and AdaBoost to enhance the accuracy of badminton action recognition.The E2 ensemble model,which combines SVM,LR,and AdaBoost,achieves the highest accuracy of 95.38%.

Depression weights in patients with gastric cancer:Bibliometric analysis as a weapon to chart the future of research

Bibliometric analyses are increasing in the field of gastric cancer.This letter discusses a recently published analysis that focused on the bidirectional relationship between depression and gastric cancer and evaluated the types of papers published in this field and the changes in the direction of research.There is an increasing need for new,clinically relevant studies of this association.

Adjuvant chemotherapy for isolated resectable colorectal lung metastasis: A retrospective study using inverse probability treatment weighting propensity analysis

BACKGROUND The benefit of adjuvant chemotherapy(ACT)for patients with no evidence of disease after pulmonary metastasis resection(PM)from colorectal cancer(CRC)remains controversial.AIM To assess the efficacy of ACT in patients after PM resection for CRC.METHODS This study included 96 patients who underwent pulmonary metastasectomy for CRC at a single institution between April 2008 and July 2023.The primary end-point was overall survival(OS);secondary endpoints included cancer-specific survival(CSS)and disease-free survival(DFS).An inverse probability of treat-ment-weighting(IPTW)analysis was conducted to address indication bias.Sur-vival outcomes compared using Kaplan-Meier curves,log-rank test,Cox regre-ssion and confirmed by propensity score-matching(PSM).RESULTS With a median follow-up of 27.5 months(range,18.3-50.4 months),the 5-year OS,CSS and DFS were 72.0%,74.4%and 51.3%,respectively.ACT had no significant effect on OS after PM resection from CRC[original cohort:P=0.08;IPTW:P=0.15].No differences were observed for CSS(P=0.12)and DFS(P=0.68)between the ACT and non-ACT groups.Multivariate analysis showed no association of ACT with better survival,while sublobar resection(HR=0.45;95%CI:0.20-1.00,P=0.049)and longer disease-free interval(HR=0.45;95%CI:0.20-0.98,P=0.044)were associated with improved survival.CONCLUSION ACT does not improve survival after PM resection for CRC.Further well-designed randomized controlled trials are needed to determine the optimal ACT regimen and duration.

Evaluating the Influence of the Prostate Weight on the Morbidity and Mortality of Transvesical Open Prostatectomy: Prospective Analysis of 108 Cases in the Urology-Andrology Department of the Ignace Deen National Hospital in Conakry

Introduction: Open transvesical prostatectomy remains today one of the most effective approaches for the management of benign prostatic hyperplasia despite the fact that, this method is associated with multiple complications. The objective of this study was to evaluate the influence of prostate weight on the morbidity and mortality of transvesical prostatectomy for adenoma in the urology-andrology department of the Ignace Deen National Hospital. Materials and Methods: This was a prospective, longitudinal and analytical study lasting 6 months, from March 1, 2022 to August 31, 2022 including patients admitted and operated on by open transvesical prostatectomy by assessing the influence of prostate weight on the morbidity and mortality of transvesical adenomectomies. Results: 108 patients were included in our study, the average age of our patients was 70 ± 7.7 years, cultivators were the most represented profession with 38.89%, and hypertension was the most represented comorbidity with 75%. 33.06% of cases became complicated and surgical wound infection was the main complication with a frequency of 17.40%. Statistical analysis did not conclude that, the prostate weight does not have a statistically significant influence on the morbidity and mortality of transvesical open prostatectomy for benign prostatic hyperplasia. Conclusion: Prostate weight has no influence on the morbidity and mortality of transvesical prostate adenoma.

A reweighted damped singular spectrum analysis method for robust seismic noise suppression

(Multichannel)Singular spectrum analysis is considered as one of the most effective methods for seismic incoherent noise suppression.It utilizes the low-rank feature of seismic signal and regards the noise suppression as a low-rank reconstruction problem.However,in some cases the seismic geophones receive some erratic disturbances and the amplitudes are dramatically larger than other receivers.The presence of this kind of noise,called erratic noise,makes singular spectrum analysis(SSA)reconstruction unstable and has undesirable effects on the final results.We robustify the low-rank reconstruction of seismic data by a reweighted damped SSA(RD-SSA)method.It incorporates the damped SSA,an improved version of SSA,into a reweighted framework.The damping operator is used to weaken the artificial disturbance introduced by the low-rank projection of both erratic and random noise.The central idea of the RD-SSA method is to iteratively approximate the observed data with the quadratic norm for the first iteration and the Tukeys bisquare norm for the rest iterations.The RD-SSA method can suppress seismic incoherent noise and keep the reconstruction process robust to the erratic disturbance.The feasibility of RD-SSA is validated via both synthetic and field data examples.

Weighted gene co-expression network analysis reveals similarities and differences of molecular features between dilated and ischemic cardiomyopathies

Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.

Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis

Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.

Multi-Criteria Group Decision-Making Method Based on an Improved Single-Valued Neutrosophic Hamacher Weighted Average Operator and Grey Relational Analysis

This paper proposes a multi-criteria decision-making (MCGDM) method based on the improved single-valued neutrosophic Hamacher weighted averaging (ISNHWA) operator and grey relational analysis (GRA) to overcome the limitations of present methods based on aggregation operators. First, the limitations of several existing single-valued neutrosophic weighted averaging aggregation operators (i.e. , the single-valued neutrosophic weighted averaging, single-valued neutrosophic weighted algebraic averaging, single-valued neutrosophic weighted Einstein averaging, single-valued neutrosophic Frank weighted averaging, and single-valued neutrosophic Hamacher weighted averaging operators), which can produce some indeterminate terms in the aggregation process, are discussed. Second, an ISNHWA operator was developed to overcome the limitations of existing operators. Third, the properties of the proposed operator, including idempotency, boundedness, monotonicity, and commutativity, were analyzed. Application examples confirmed that the ISNHWA operator and the proposed MCGDM method are rational and effective. The proposed improved ISNHWA operator and MCGDM method can overcome the indeterminate results in some special cases in existing single-valued neutrosophic weighted averaging aggregation operators and MCGDM methods.

Weight Analysis of the Influencing Factors of Homestay Competitiveness in Rural Guangzhou,China

At present,Guangzhou homestay industry is facing a bottleneck.Therefore,it is particularly important to analyze the factors that influence the competitiveness of rural homestays in Guangzhou,determine the evaluation system of competitiveness,and determine the weight of each factor.Based on Porter’s diamond theory,this paper analyzes and summarizes the influencing factors of homestay competitiveness,and divides the influencing factors into 5 primary factors and 34 secondary factors.The analytic hierarchy process(AHP)was used to determine the judgment matrix to form the weight results of each factor,and the results show that product characteristics account for the largest proportion among first level factors.Secondary factors such as theme creativity,personalized brand and the overall score account for a large proportion.The research results can act as a reference for the construction of competitiveness evaluation mechanism and model of local rural quality homestays.

Temperature-Triggered Hardware Trojan Based Algebraic Fault Analysis of SKINNY-64-64 Lightweight Block Cipher

SKINNY-64-64 is a lightweight block cipher with a 64-bit block length and key length,and it is mainly used on the Internet of Things(IoT).Currently,faults can be injected into cryptographic devices by attackers in a variety of ways,but it is still difficult to achieve a precisely located fault attacks at a low cost,whereas a Hardware Trojan(HT)can realize this.Temperature,as a physical quantity incidental to the operation of a cryptographic device,is easily overlooked.In this paper,a temperature-triggered HT(THT)is designed,which,when activated,causes a specific bit of the intermediate state of the SKINNY-64-64 to be flipped.Further,in this paper,a THT-based algebraic fault analysis(THT-AFA)method is proposed.To demonstrate the effectiveness of the method,experiments on algebraic fault analysis(AFA)and THT-AFA have been carried out on SKINNY-64-64.In the THT-AFA for SKINNY-64-64,it is only required to activate the THT 3 times to obtain the master key with a 100%success rate,and the average time for the attack is 64.57 s.However,when performing AFA on this cipher,we provide a relation-ship between the number of different faults and the residual entropy of the key.In comparison,our proposed THT-AFA method has better performance in terms of attack efficiency.To the best of our knowledge,this is the first HT attack on SKINNY-64-64.

Enhanced Sentiment Analysis Algorithms for Multi-Weight Polarity Selection on Twitter Dataset

Sentiment analysis is based on the orientation of user attitudes and satisfaction towards services and subjects.Different methods and techniques have been introduced to analyze sentiments for obtaining high accuracy.The sentiment analysis accuracy depends mainly on supervised and unsupervised mechanisms.Supervised mechanisms are based on machine learning algorithms that achieve moderate or high accuracy but the manual annotation of data is considered a time-consuming process.In unsupervised mechanisms,a lexicon is constructed for storing polarity terms.The accuracy of analyzing data is considered moderate or low if the lexicon contains small terms.In addition,most research methodologies analyze datasets using only 3-weight polarity that can mainly affect the performance of the analysis process.Applying both methods for obtaining high accuracy and efficiency with low user intervention during the analysis process is considered a challenging process.This paper provides a comprehensive evaluation of polarity weights and mechanisms for recent sentiment analysis research.A semi-supervised framework is applied for processing data using both lexicon and machine learning algorithms.An interactive sentiment analysis algorithm is proposed for distributing multi-weight polarities on Arabic lexicons that contain high morphological and linguistic terms.An enhanced scaling algorithm is embedded in the multi-weight algorithm to assign recommended weight polarities automatically.The experimental results are conducted on two datasets to measure the over-all accuracy of proposed algorithms that achieved high results when compared to machine learning algorithms.

Functions of Uni- and Multi-citations： Implications for Weighted Citation Analysis

Purpose： （1） To test basic assumptions underlying frequency-weighted citation analysis： （a） Uni-citations correspond to citations that are nonessential to the citing papers; （b） The influence of a cited paper on the citing paper increases with the frequency with which it is cited in the citing paper. （2） To explore the degree to which citation location may be used to help identify nonessential citations. Design/methodology/approach： Each of the in-text citations in all research articles published in Issue 1 of the Journal of the Association for Information Science and Technology （JASIST） 2016 was manually classified into one of these five categories： Applied, Contrastive, Supportive, Reviewed, and Perfunctory. The distributions of citations at different in-text frequencies and in different locations in the text by these functions were analyzed. Findings： Filtering out nonessential citations before assigning weight is important for frequency-weighted citation analysis. For this purpose, removing citations by location is more effective than re-citation analysis that simply removes uni-citations. Removing all citation occurrences in the Background and Literature Review sections and uni-citations in the Introduction section appears to provide a good balance between filtration and error rates. Research limitations： This case study suffers from the limitation of scalability and generalizability. We took careful measures to reduce the impact of other limitations of the data collection approach used. Relying on the researcher＇s judgment to attribute citation functions, this approach is unobtrusive but speculative, and can suffer from a low degree of confidence, thus creating reliability concerns. Practical implications： Weighted citation analysis promises to improve citation analysis for research evaluation, knowledge network analysis, knowledge representation, and information retrieval. The present study showed the importance of filtering out nonessential citations before assigning weight in a weighted citation analysis, which may be a significant step forward to realizing these promises. Originality/value： Weighted citation analysis has long been proposed as a theoretical solution to the problem of citation analysis that treats all citations equally, and has attracted increasing research interest in recent years. The present study showed, for the first time, the importance of filtering out nonessential citations in weighted citation analysis, pointing research in this area in a new direction.

Weighted Gene Co-expression Network Analysis of Gene Modules for the Prognosis of Esophageal Cancer

Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.

Transcriptome and weighted gene co-expression network analysis of jujube(Ziziphus jujuba Mill.)fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation

Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated.Here,the profiling of PA,(+)-catechin and(–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed.The levels of total PAs and catechin exhibited a decreased trend over jujube ripening,and epicatechin content of two jujube cultivars increased first and then declined.Transcriptome analysis revealed that the differentially expressed genes(DEGs)were mainly enriched in ribosome,glycolysis/gluconeogenesis,fructose and mannose metabolism.17 DEGs encoding PAL,CHS,CHI,CHS,F3'H,LAR,ANR,C4Hs,4CLs,FLSs,DFRs and UFGTs involved in PA biosynthesis were relatively abundant.The highly transcribed LAR gene may greatly contribute to epicatechin accumulation.A weighted gene co-expression network analysis(WGCNA)was performed,and a network module including 1620 genes highly correlated with content of Pas and catechin was established.We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module.Sixteen genes encoding 9 families of transcriptional factors(i.e.,MYB,bHLH,ERF,bZIP,NAC,SBP,MIKC,HB,WRKY)were considered as hub genes.The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data.These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.