bluuebunny/crossref_metadata_2025 huggingface dataset:
TD‐WS: a threat detection tool of WebSocket and Web Storage in HTML5 websites
Authors: Bai Junyang , Wang Weiping , Lu Mingming , Wang Haodong , Wang Jianxin
Published: November 2016

The new features of HTML5 greatly increase the convenience for both web developers and users, but they also bring new security threats. Although the web‐security community has started to analyze the security threats brought by HTML5, little has been performed to address the security threats for the client‐side applications. This paper studies security issues of two popular client‐side primitives: WebSocket and Web Storage. The security threats concerned in this paper are private information stealth through WebSocket and cross‐site scripting vulnerabilities caused by lacking of sanitization for WebSocket messages and Web Storage data. We analyze the unsafe data flows of these two HTML5 primitives in detail. Based on that, we present a threat detection tool called TD‐WS, which can automatically detect the privacy leaks and the cross‐site scripting vulnerabilities in WebSocket and Web Storage applications. The results show that TD‐WS effectively detects the security threats of WebSocket and Web Storage applications. Copyright © 2016 John Wiley & Sons, Ltd.
A novel extreme learning machine‐based cryptography system
Authors: Atee Hayfaa Abdulzahra , Ahmad Robiah , Noor Norliza Mohd , Rahma Abdul Monem S. , Sallam Muhammad Samer
Published: November 2016

Extreme Learning Machine (ELM) is a well‐known algorithm for the training of neural networks for two modes of functionality: regression and classification. This paper presents a novel model using ELM in ciphering. The study begins with an investigation of the Real‐time Recurrent Neural Network (RRNN) derived from the gradient‐based learning for symmetric cipher. The weakness of this cipher is that the error converges to zero, and that the RRNN will not change regardless of how the plaintext is changed. Given the nature of the ELM, a technique with an ELM‐based cipher is proposed to provide the capability of performing the training independently from the input and the error gradient. Different simulation scenarios were used to evaluate and validate the effectiveness of the proposed cipher. Results revealed that the ELM‐based cipher performed better than RRNNs, especially in terms of security. Moreover, the ELM‐based cipher demonstrated significantly competing performance for a wide range of evaluation measures. Using an ELM‐based cipher instead of an AES or other type of ciphers has the added advantage of providing an addition level of security—by allowing the user to change the algorithmic core of the cipher by simply changing the weights of the neural network. This allows hardware programmed ciphers to be more secure while costing less compared to other ciphers. Copyright © 2016 John Wiley & Sons, Ltd.
Semiparametric Bayes conditional graphical models for imaging genetics applications
Authors: Kundu Suprateek , Kang Jian
Published: November 2016

Motivated by the need for understanding neurological disorders, large‐scale imaging genetic studies are being increasingly conducted. A salient objective in such studies is to identify important neuroimaging biomarkers such as the brain functional connectivity, as well as genetic biomarkers, which are predictive of disorders. However, typical approaches for estimating the group level brain functional connectivity do not account for potential variation, resulting from demographic and genetic factors, while usual methods for discovering genetic biomarkers do not factor in the influence of the brain network on the imaging phenotype. We propose a novel semiparametric Bayesian conditional graphical model for joint variable selection and graph estimation, which simultaneously estimates the brain network after accounting for heterogeneity, and infers significant genetic biomarkers. The proposed approach specifies priors on the regression coefficients, which clusters brain regions having similar activation patterns depending on covariates, leading to dimension reduction. A novel graphical prior is proposed, which encourages modularity in brain organization by specifying denser and sparse connections within and across clusters, respectively. The posterior computation proceeds via a Markov chain Monte Carlo. We apply the approach to data obtained from the Alzheimer's disease neuroimaging initiative and demonstrate numerical advantages via simulation studies. Copyright © 2016 John Wiley & Sons, Ltd.
Pasting, rheological, and retrogradation properties of starches from dual‐purpose sorghum lines
Authors: Ehtiati Ahmad , Koocheki Arash , Shahidi Fakhri , Razavi Seyed Mohammad Ali , Majzoobi Mahsa
Published: November 2016

In this study, we evaluated the functionality of starches extracted from dual‐purpose sorghum lines (KDFGS1, KDFGS6, KDFGS9, and KDFGS20). There were no significant differences in swelling factor, solubility, or paste clarity among the lines. Sorghum starches exhibited similar pasting patterns with differences in peak viscosity, breakdown, and setback. Starch pastes had similar consistency and had shear‐thinning behavior. Sorghum starches showed good gel setting ability, while hardness, cohesiveness, and springiness were not statistically different among the lines. Starch from KDFGS20 had lower retrogradation rate and syneresis during storage at 4°C. Starch pastes were highly susceptible to successive freeze‐thaw cycles. Approximately 80% water was separated after five freeze‐thaw cycles. Our findings revealed that sorghum starches from dual‐purpose lines had acceptable water binding, viscosifying, and gelling properties, making them suitable for food applications that do not require starches with high freezing stability.
China Speaks Out: How and Why Chinese Employees Use Their Voice toward German Managers
Authors: Metz Annette , Gunkel Marjaana
Published: November 2016

Existing management literature on voice has primarily focused on examining who uses their voice and when it is used, ignoring why employees speak out and how they do so. We examine the conditions under which Chinese employees use their voice toward their German managers at German companies in Mainland China. The findings from our empirical study emphasize the importance of Chinese employees' personal identification with their German managers as a precondition for voice behaviors. Our results suggest that Chinese employees utilize indirect voice behavior in addition to direct voice behavior when interacting with their German managers. This indirect guanxi‐voice behavior has neither been recognized nor investigated in the literature. The theoretical and managerial implications of the results are discussed. © 2016 Wiley Periodicals, Inc.
Evaluation of Rex Shunt on Cavernous Transformation of the Portal Vein in Children
Authors: Wang Ruo‐Yi , Wang Jun‐Feng , Sun Xiao‐Gang , Liu Qian , Xu Jia‐Long , Lv Qi‐Gang , Chen Wei‐Xiu , Li Jin‐Liang
Published: November 2016

Background

Children with cavernous transformation of the portal vein (CTPV) develop severe complications from prehepatic portal hypertension, such as recurrent variceal bleeding and thrombocytopenia. In this study, we reported the results of 30 children with symptomatic CTPV that were treated by a Rex shunt. The effectiveness of this surgical approach was evaluated.

Methods

A retrospective review was performed of 30 children aged between 3 and 18 years with CTPV, who underwent a Rex shunt between 2008 and 2015. All children were evaluated based on symptoms, complete blood count, portal system color‐flow Doppler ultrasound or computed tomography angiography portography and gastroscopy for gastroesophageal varices pre‐ and postoperatively. Children were also evaluated during follow‐up. Intraoperative evaluations included liver biopsy, portography and portal pressure.

Results

Twenty‐one patients demonstrated intermittent bleeding from gastroesophageal varices, 3 patients showed hypersplenism with varying degrees of leucopenia, anemia and thrombocytopenia, and in 6 patients both bleeding and hypersplenism were observed. Rex was successful in 28 patients (93.3%). The portal pressure immediately decreased significantly after placing of the shunt (P < 0.01). During the clinical follow‐up period within 2–82 months, transaminase levels were maintained in the normal range. Blood flow velocity and diameter of the left portal vein significantly increased after surgery (P < 0.01). In addition, leukocyte and platelet counts increased postoperatively and anemia improved significantly (P < 0.01). Gastroscopy results indicated that the degree of gastroesophageal varices significantly alleviated postoperatively within 3 months and 1 year (P < 0.01). In 2 patients who demonstrated nodular cirrhosis and chronic active hepatitis, success of the Rex shunt was not achieved after operation. We found that for Rex effectiveness hepatic pathology and patient age were major determinants.

Conclusion

Rex shunt is an effective approach for the treatment of children suffering from CTPV at an early stage that do not show additional liver lesions.
Low Incidence of Lymph Node Metastasis After Resection of Hepatitis Virus‐Related Intrahepatic Cholangiocarcinoma
Authors: Iida Hiroya , Kaibori Masaki , Tanaka Shogo , Takemura Shigekazu , Wada Hiroshi , Hirokawa Fumitoshi , Nakai Takuya , Hayashi Michihiro , Eguchi Hidetoshi , Kubo Shoji
Published: November 2016

Background and objectives

We determined the rates of initial lymph node metastasis following curative resection of mass‐forming type‐intrahepatic cholangiocarcinoma (ICC) in patients with and without hepatitis virus infection.

Methods

We enrolled 87 patients between January 2000 and December 2013 with ICC without preoperative lymph node metastasis and without lymph node dissection. Patients included 32 who were seropositive for hepatitis B or C virus (virus group) and 55 who had no evidence of hepatitis virus infection (nonvirus group). Postsurgical outcomes and initial recurrence of the groups were compared, and we identified the risk factors for lymph node metastasis as initial recurrence.

Results

Platelet counts and prothrombin activities were significantly lower in the virus group compared with those of the nonvirus group. The number of patients with chronic hepatitis or liver cirrhosis was significantly higher in the virus group compared with the nonvirus group as well as their respective rates of recurrence‐free survival. One patient (3%) in the virus group and 14 patients (25%) in the nonvirus group had lymph node metastasis as initial recurrence (p = 0.007). Multivariate analysis revealed that the absence of hepatitis virus infection as an independent risk factor (p = 0.047).

Conclusion

Hepatitis virus‐associated mass‐forming‐type ICC confers a low risk of lymph node metastasis as initial postoperative recurrence.
En Bloc Resection with Major Blood Vessel Reconstruction for Locally Invasive Retroperitoneal Paragangliomas: A 15‐Year Experience with Literature Review
Authors: Hu Hankui , Huang Bin , Zhao Jichun , Yuan Ding , Yang Yi , Xiong Fei
Published: November 2016

Background

Retroperitoneal paragangliomas (PGs) are a rare subgroup of neuroendocrine tumors that are commonly located alongside the abdominal aorta. Complete tumor resection is thought to be restricted in patients with major blood vessel involvement. However, no study has specifically focused on aggressive surgical treatment in such patients. We evaluated the value of en bloc resection with major blood vessel reconstruction for locally invasive retroperitoneal PGs.

Methods

Twenty‐nine patients with retroperitoneal PGs with major blood vessel involvement were included in this retrospective study. Survival was compared between patients who underwent en bloc resection with major blood vessel reconstruction and those who underwent medical treatment. Prognostic predictors were analyzed in patients who underwent en bloc resection with major blood vessel reconstruction.

Results

All 11 patients who underwent medical treatment obtained a pathological diagnosis by computed tomography‐guided percutaneous needle biopsy. All 18 patients who underwent en bloc resection with major blood vessel reconstruction achieved complete tumor resection. Overall survival was higher in patients who underwent complete tumor resection than in those who underwent medical treatment (p < 0.05). No perioperative mortality occurred in patients who underwent complete tumor resection. Patients with no metastasis, no organ invasion, R0 resection, a Ki‐67 index of ≤3%, and a tumor diameter of ≤11.7 cm showed better tumor‐free survival (p < 0.05).

Conclusions

En bloc resection with major blood vessel reconstruction can be successfully performed and provide satisfactory outcomes for patients with locally invasive retroperitoneal PGs. This technique may become a standard surgical strategy for properly selected patients.
Teaching Genetic Counseling Skills: Incorporating a Genetic Counseling Adaptation Continuum Model to Address Psychosocial Complexity
Authors: Shugar Andrea
Published: November 2016

Genetic counselors are trained health care professionals who effectively integrate both psychosocial counseling and information‐giving into their practice. Preparing genetic counseling students for clinical practice is a challenging task, particularly when helping them develop effective and active counseling skills. Resistance to incorporating these skills may stem from decreased confidence, fear of causing harm or a lack of clarity of psycho‐social goals. The author reflects on the personal challenges experienced in teaching genetic counselling students to work with psychological and social complexity, and proposes a Genetic Counseling Adaptation Continuum model and methodology to guide students in the use of advanced counseling skills.
Präimplantationsdiagnostik – methodische Aspekte
Authors: Hehr Andreas , Paulmann Bernd , Eichhammer Lisa , Gassner Claudia , Seifert Bernd , Hehr Ute
Published: November 2016

Die Präimplantationsdiagnostik erfordert eine enge und vertrauensvolle interdisziplinäre Zusammenarbeit zwischen hoch qualifizierten Fachärzten und Naturwissenschaftlern aus Humangenetik und Reproduktionsmedizin. In einem sehr engen Zeitfenster müssen komplexe Laborabläufe standardisiert und qualitätsgesichert umgesetzt werden. In diesem Beitrag sollen orientierende Empfehlungen zur Umsetzung kurz vorgestellt werden. Zentral haben wir häufigere Problemsituationen thematisiert, welche bereits bei der Indikationsstellung wie auch bei den nachfolgenden Schritten in der genetischen Analyse, Datenauswertung und Befunderstellung mögliche Fehlerquellen darstellen. Ziel unserer verantwortlichen Arbeit an den PID-Zentren sollte eine hohe Geburtenrate bei hoher Diagnosesicherheit mit möglichst wenigen schonenden Behandlungszyklen sein.
Performance measures in evaluating machine learning based bioinformatics predictors for classifications
Authors: Jiao Yasen , Du Pufeng
Published: November 2016

Background

Many existing bioinformatics predictors are based on machine learning technology. When applying these predictors in practical studies, their predictive performances should be well understood. Different performance measures are applied in various studies as well as different evaluation methods. Even for the same performance measure, different terms, nomenclatures or notations may appear in different context.

Results

We carried out a review on the most commonly used performance measures and the evaluation methods for bioinformatics predictors.

Conclusions

It is important in bioinformatics to correctly understand and interpret the performance, as it is the key to rigorously compare performances of different predictors and to choose the right predictor.
Partners or donors: The perceived roles of Global Fund Principal Recipient NGOs in HIV prevention programmes in Ukraine
Authors: McGill Svetlana
Published: November 2016

Ukraine has one of Europe's fastest growing HIV rates and in 2003–2012 was one of the largest recipients of funding from the Global Fund to Fight AIDS, Tuberculosis and Malaria (GF). Doctoral research recently completed by the author investigates the conduct and practice of international and national nongovernmental organisations (NGOs) as Principal Recipients (PRs) of GF grants in Ukraine from 2003 to 2012. An ethnographic enquiry including 50 participant interviews was conducted in three oblasts in Ukraine, and in its capital, Kyiv. The paper presents some of the findings that emerged from the analysis. Discussing the PR NGOs roles and practices in delivering HIV prevention programmes funded by GF, the author argues that the anticipated benefits of NGO partnerships between PR NGOs and their Sub-Recipients (SRs) have not been achieved. Rather, PRs acted as donors and ran highly discretionary policies in channelling GF funding to SRs that installed competition and vertical relations between NGO-grantors and NGO-grantees. The outcome was a servile civil society that is dependent on external funding and is unable to genuinely represent their communities. With an anticipated GF phasing out from Ukraine, there is a critical lack of advocacy potential of the civil society to articulate and defend the needs of PLHIV when transferring HIV services into state funding.
Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes
Authors: van der Spek Peter J. , Kremer Andreas , Murry Lynn , Walker Michael G.
Published: November 2016

Microarray analyses of gene expression are widely used, but reports of the same analyses by different groups give widely divergent results, and raise questions regarding reproducibility and reliability. We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes. These reports show substantial differences in their results. In this article, we review the methodology, results, and potential causes of differences in these applications of microarrays. Finally, we suggest practices to improve the reliability and reproducibility of microarray experiments.
Gene Identification and Expression Analysis of 86,136 Expressed Sequence Tags (EST) from the Rice Genome
Authors: Zhou Yan , Tang Jiabin , Walker Michael G. , Zhang Xiuqing , Wang Jun , Hu Songnian , Xu Huayong , Deng Yajun , Dong Jianhai , Ye Lin , Lin Li , Li Jun , Wang Xuegang , Xu Hao , Pan Yibin , Lin Wei , Tian Wei , Liu Jing , Wei Liping , Liu Siqi , Yang Huanming , Yu Jun , Wang Jian
Published: November 2016

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to the existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.
Gene Expression Versus Sequence for Predicting Function: Glia Maturation Factor Gamma is not a Glia Maturation Factor
Authors: Walker Michael G.
Published: November 2016

It is standard practice, whenever a researcher finds a new gene, to search databases for genes that have a similar sequence. It is not standard practice, whenever a researcher finds a new gene, to search for genes that have similar expression (co-expression). Failure to perform co-expression searches has lead to incorrect conclusions about the likely function of new genes, and has lead to wasted laboratory attempts to confirm functions incorrectly predicted. We present here the example of Glia Maturation Factor gamma (GMF-gamma). Despite its name, it has not been shown to participate in glia maturation. It is a gene of unknown function that is similar in sequence to GMF-beta. The sequence homology and chromosomal location led to an unsuccessful search for GMF-gamma mutations in glioma. We examined GMF-gamma expression in 1432 human cDNA libraries. Highest expression occurs in phagocytic, antigen-presenting and other hematopoietic cells. We found GMF-gamma mRNA in almost every tissue examined, with expression in nervous tissue no higher than in any other tissue. Our evidence indicates that GMF-gamma participates in phagocytosis in antigen presenting cells. Searches for genes with similar sequences should be supplemented with searches for genes with similar expression to avoid incorrect predictions.
Proteomic Comparison of Two-Dimensional Gel Electrophoresis Profiles from Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Tissues
Authors: Li Cui , Zhan Xianquan , Li Maoyu , Wu Xiaoying , Li Feng , Li Jianling , Xiao Zhiqiang , Chen Zhuchu , Feng Xueping , Chen Ping , Xie Jingyun , Liang Songping
Published: November 2016

Differential proteome profiles of human lung squamous carcinoma tissue compared to paired tumor-adjacent normal bronchial epithelial tissue were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). The results showed that well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained under the condition of 0.75-mg protein-load. The average deviation of spot position was 0.733±0.101 mm in IEF direction, and 0.925±0.207 mm in SDS-PAGE direction. For tumor tissue, a total of 1241±88 spots were detected, 987±65 spots were matched with an average matching rate of 79.5%. For control, a total of 1190±72 spots were detected, and 875±48 spots were matched with an average matching rate of 73.5%. A total of 864±34 spots were matched between tumors and controls. Forty-three differential proteins were characterized: some proteins were related to oncogenes, and others involved in the regulation of cell cycle and signal transduction. It is suggested that the differential proteomic approach is valuable for mass identification of differentially expressed proteins involved in lung carcinogenesis. These data will be used to establish human lung cancer proteome database to further study human lung squamous carcinoma.
Finding Signals for Plant Promoters
Authors: Zheng Weimou
Published: November 2016

The strongest signal of plant promoter is searched with the model of single motif with two types. It turns out that the dominant type is the TATA-box. The other type may be called TATA-less signal, and may be used in gene finders for promoter recognition. While the TATA signals are very close for the monocot and the dicot, their TATA-less signals are significantly different. A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching signals in plant promoters.
A Genome Sequence of Novel SARS-CoV Isolates: The Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China
Authors: Qin E’de , He Xionglei , Tian Wei , Liu Yong , Li Wei , Wen Jie , Wang Jingqiang , Fan Baochang , Wu Qingfa , Chang Guohui , Cao Wuchun , Xu Zuyuan , Yang Ruifu , Wang Jing , Yu Man , Li Yan , Xu Jing , Si Bingyin , Hu Yongwu , Peng Wenming , Tang Lin , Jiang Tao , Shi Jianping , Ji Jia , Zhang Yu , Ye Jia , Wang Cui’e , Han Yujun , Zhou Jun , Deng Yajun , Li Xiaoyu , Hu Jianfei , Wang Caiping , Yan Chunxia , Zhang Qingrun , Bao Jingyue , Li Guoqing , Chen Weijun , Fang Lin , Li Changfeng , Lei Meng , Li Dawei , Tong Wei , Tian Xiangjun , Wang Jin , Zhang Bo , Zhang Haiqing , Zhang Yilin , Zhao Hui , Zhang Xiaowei , Li Shuangli , Cheng Xiaojie , Zhang Xiuqing , Liu Bin , Zeng Changqing , Li Songgang , Tan Xuehai , Liu Siqi , Dong Wei , Wang Jun , Wong Gane Ka-Shu , Yu Jun , Wang Jian , Zhu Qingyu , Yang Huanming
Published: November 2016

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral genome replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.
The M Protein of SARS-CoV: Basic Structural and Immunological Properties
Authors: Hu Yongwu , Wen Jie , Tang Lin , Zhang Haijun , Zhang Xiaowei , Li Yan , Wang Jing , Han Yujun , Li Guoqing , Shi Jianping , Tian Xiangjun , Jiang Feng , Zhao Xiaoqian , Wang Jun , Liu Siqi , Zeng Changqing , Wang Jian , Yang Huanming
Published: November 2016

We studied structural and immunological properties of the SARS-CoV M (membrane) protein, based on comparative analyses of sequence features, phylogenetic investigation, and experimental results. The M protein is predicted to contain a triple-spanning transmembrane (TM) region, a single N-glycosylation site near its N-terminus that is in the exterior of the virion, and a long C-terminal region in the interior. The M protein harbors a higher substitution rate (0.6% correlated to its size) among viral open reading frames (ORFs) from published data. The four substitutions detected in the M protein, which cause non-synonymous changes, can be classified into three types. One of them results in changes of pI (isoelectric point) and charge, affecting antigenicity. The second changes hydrophobicity of the TM region, and the third one relates to hydrophilicity of the interior structure. Phylogenetic tree building based on the variations of the M protein appears to support the non-human origin of SARS-CoV. To investigate its immunogenicity, we synthesized eight oligopeptides covering 69.2% of the entire ORF and screened them by using ELISA (enzyme-linked immunosorbent assay) with sera from SARS patients. The results confirmed our predictions on antigenic sites.
The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04
Authors: Xu Zuyuan , Zhang Haiqing , Tian Xiangjun , Ji Jia , Li Wei , Li Yan , Tian Wei , Han Yujun , Wang Lili , Zhang Zizhang , Xu Jing , Wei Wei , Zhu Jingui , Sun Haiyan , Zhang Xiaowei , Zhou Jun , Li Songgang , Wang Jun , Wang Jian , Bi Shengli , Yang Huanming
Published: November 2016

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS.
Complete Genome Sequences of the SARS-CoV: The BJ Group (Isolates BJ01-BJ04)
Authors: Bi Shengli , Qin E’de , Xu Zuyuan , Li Wei , Wang Jing , Hu Yongwu , Liu Yong , Duan Shumin , Hu Jianfei , Han Yujun , Xu Jing , Li Yan , Yi Yao , Zhou Yongdong , Lin Wei , Wen Jie , Xu Hong , Li Ruan , Zhang Zizhang , Sun Haiyan , Zhu Jingui , Yu Man , Fan Baochang , Wu Qingfa , Lin Wei , Tang Lin , Yang Bao’an , Li Guoqing , Peng Wenming , Li Wenjie , Jiang Tao , Deng Yajun , Liu Bohua , Shi Jianping , Deng Yongqiang , Wei Wei , Liu Hong , Tong Zongzhong , Zhang Feng , Zhang Yu , Wang Cui’e , Li Yuquan , Ye Jia , Gan Yonghua , Ji Jia , Li Xiaoyu , Tian Xiangjun , Lu Fushuang , Tan Gang , Yang Ruifu , Liu Bin , Liu Siqi , Li Songgang , Wang Jun , Wang Jian , Cao Wuchun , Yu Jun , Dong Xiaoping , Yang Huanming
Published: November 2016

Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city’s hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.
The C-Terminal Portion of the Nucleocapsid Protein Demonstrates SARS-CoV Antigenicity
Authors: Liu Guozhen , Hu Shaohui , Hu Yongwu , Chen Peng , Yin Jianning , Wen Jie , Wang Jingqiang , Lin Liang , Liu Jinxiu , You Bo , Yin Ye , Li Shuting , Wang Hao , Ren Yan , Ji Jia , Zhao Xiaoqian , Sun Yongqiao , Zhang Xiaowei , Fang Jianqiu , Wang Jian , Liu Siqi , Yu Jun , Zhu Heng , Yang Huanming
Published: November 2016

In order to develop clinical diagnostic tools for rapid detection of SARS-CoV (severe acute respiratory syndrome-associated coronavirus) and to identify candidate proteins for vaccine development, the C-terminal portion of the nucleocapsid (NC) gene was amplified using RT-PCR from the SARS-CoV genome, cloned into a yeast expression vector (pEGH), and expressed as a glutathione S-transferase (GST) and Hisx6 double-tagged fusion protein under the control of an inducible promoter. Western analysis on the purified protein confirmed the expression and purification of the NC fusion proteins from yeast. To determine its antigenicity, the fusion protein was challenged with serum samples from SARS patients and normal controls. The NC fusion protein demonstrated high antigenicity with high specificity, and therefore, it should have great potential in designing clinical diagnostic tools and provide useful information for vaccine development.
A Strategy for Searching Antigenic Regions in the SARS-CoV Spike Protein
Authors: Ren Yan , Zhou Zhengfeng , Liu Jinxiu , Lin Liang , Li Shuting , Wang Hao , Xia Ji , Zhao Zhe , Wen Jie , Zhou Cuiqi , Wang Jingqiang , Yin Jianning , Xu Ningzhi , Liu Siqi
Published: November 2016

In the face of the worldwide threat of severe acute respiratory syndrome (SARS) to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA), these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469–882 in the S protein, and one epitope site was located at Codons 599–620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis.
EST Pipeline System: Detailed and Automated EST Data Processing and Mining
Authors: Xu Hao , He Ling , Zhu Yuanzhong , Huang Wei , Fang Lijun , Tao Lin , Zhu Yuedong , Cai Lin , Xu Huayong , Zhang Liang , Yu Hong , Zhou Yan
Published: November 2016

Expressed sequence tags (ESTs) are widely used in gene survey research these years. The EST Pipeline System, software developed by Hangzhou Genomics Institute (HGI), can automatically analyze different scalar EST sequences by suitable methods. All the analysis reports, including those of vector masking, sequence assembly, gene annotation, Gene Ontology classification, and some other analyses, can be browsed and searched as well as downloaded in the Excel format from the web interface, saving research efforts from routine data processing for biological rules embedded in the data.
Genetic Algorithms Applied to Multi-Class Clustering for Gene Expression Data
Authors: Pan Haiyan , Zhu Jun , Han Danfu
Published: November 2016

A hybrid GA (genetic algorithm)-based clustering (HGACLUS) schema, combining merits of the Simulated Annealing, was described for finding an optimal or near-optimal set of medoids. This schema maximized the clustering success by achieving internal cluster cohesion and external cluster isolation. The performance of HGACLUS and other methods was compared by using simulated data and open microarray gene-expression datasets. HGACLUS was generally found to be more accurate and robust than other methods discussed in this paper by the exact validation strategy and the explicit cluster number.
Bioinformatics-Based Identification of Chemosensory Proteins in African Malaria Mosquito, Anopheles Gambiae
Authors: Li Zhengxi , Shen Zuorui , Zhou Jingjiang , Field Lin
Published: November 2016

Chemosensory proteins (CSPs) are identifiable by four spatially conserved Cysteine residues in their primary structure or by two disulfide bridges in their tertiary structure according to the previously identified olfactory specific-D related proteins. A genomics- and bioinformatics-based approach is taken in the present study to identify the putative CSPs in the malaria-carrying mosquito, Anopheles gambiae. The results show that five out of the nine annotated candidates are the most possible Anopheles CSPs of A. gambiae. This study lays the foundation for further functional identification of Anopheles CSPs, though all of these candidates need additional experimental verification.
Dexamethasone-Inducible Green Fluorescent Protein Gene Expression in Transgenic Plant Cells
Authors: Tang Wei , Collver Hilary , Kinken Katherine
Published: November 2016

Genomic research has made a large number of sequences of novel genes or expressed sequence tags available. To investigate functions of these genes, a system for conditional control of gene expression would be a useful tool. Inducible transgene expression that uses green fluorescent protein gene (gfp) as a reporter gene has been investigated in transgenic cell lines of cotton (COT; Gossypium hirsutum L.), Fraser fir [FRA; Abies fraseri (Pursh) Poir], Nordmann fir (NOR; Abies nordmanniana Lk.), and rice (RIC; Oryza sativa L. cv. Radon). Transgenic cell lines were used to test the function of the chemical inducer dexamethasone. Inducible transgene expression was observed with fluorescence and confocal microscopy, and was confirmed by northern blot analyses. Dexamethasone at 5 mg/L induced gfp expression to the nearly highest level 48 h after treatment in COT, FRA, NOR, and RIC. Dexamethasone at 10 mg/L inhibited the growth of transgenic cells in FRA and NOR, but not COT and RIC. These results demonstrated that concentrations of inducer for optimum inducible gene expression system varied among transgenic cell lines. The inducible gene expression system described here was very effective and could be valuable in evaluating the function of novel gene.
Preliminary Study on Detecting the SARS-CoV Specific Target cDNA Fragments by Multiplex PCR
Authors: Chen Wenbing , Li Shousong , Shao Biying , Zheng Teng , Jiang Shuxun , Huang Xiaorong , Cai Kaizhen , Zhang Zhideng
Published: November 2016

The multiplex polymerase chain reaction (PCR) technique was applied to detect the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) specific target cDNA fragments in the present study. The target cDNA fragments of SARS-CoV were synthesized artificially according to the genome sequence of SARS-CoV in GenBank submitted by The Chinese University of Hong Kong, and were used as simulated positive samples. Five primers recommended by World Health Organization (WHO) were used to amplify the fragments by single PCR and multiplex PCR. Three target cDNA fragments (121, 182 and 302 bp), as well as the three different combinations of any two of these fragments, were amplified by single PCR. The combination of these three fragments was amplified by multiplex PCR. The results indicated that the multiplex PCR technique could be applied to detect the SARS-CoV specific target cDNA fragments successfully.
Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms
Authors: Stiller John W.
Published: November 2016

Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.
Microarray and Proteomic Analysis of Brassinosteroid- and Gibberellin-Regulated Gene and Protein Expression in Rice
Authors: Yang Guangxiao , Komatsu Setsuko
Published: November 2016

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.
Recent Applications of Hidden Markov Models in Computational Biology
Authors: Choo Khar Heng , Tong Joo Chuan , Zhang Louxin
Published: November 2016

This paper examines recent developments and applications of Hidden Markov Models (HMMs) to various problems in computational biology, including multiple sequence alignment, homology detection, protein sequences classification, and genomic annotation.
Post-Transcriptional Gene Silencing Induced by Short Interfering RNAs in Cultured Transgenic Plant Cells
Authors: Tang Wei , Samuels Vanessa , Whitley Nicki , Bloom Nicole , DeLaGarza Tinya , Newton Ronald J.
Published: November 2016

Short interfering RNA (siRNA) is widely used for studying post-transcriptional gene silencing and holds great promise as a tool for both identifying function of novel genes and validating drug targets. Two siRNA fragments (siRNA-a and -b), which were designed against different specific areas of coding region of the same target green fluorescent protein (GFP) gene, were used to silence GFP expression in cultured gfp transgenic cells of rice (Oryza sativa L.; OS), cotton (Gossypium hirsutum L.; GH), Fraser fir [Abies fraseri (Pursh) Poir; AF], and Virginia pine (Pinus virginiana Mill.; PV). Differential gene silencing was observed in the bombarded transgenic cells between two siRNAs, and these results were consistent with the inactivation of GFP confirmed by laser scanning microscopy, Northern blot, and siRNA analysis in tested transgenic cell cultures. These data suggest that siRNA-mediated gene inactivation can be the siRNA specific in different plant species. These results indicate that siRNA is a highly specific tool for targeted gene knockdown and for establishing siRNA-mediated gene silencing, which could be a reliable approach for large-scale screening of gene function and drug target validation.
The Path to Enlightenment: Making Sense of Genomic and Proteomic Information
Authors: Maurer Martin H.
Published: November 2016

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.
Application of Proteomics in the Study of Tumor Metastasis
Authors: Cai Zhen , Chiu Jen-Fu , He Qing-Yu
Published: November 2016

Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive. The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer. Proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing methodologies will continue to extend its application in studying cancer metastasis.
A Systematical Analysis of Tryptic Peptide Identification with Reverse Phase Liquid Chromatography and Electrospray Ion Trap Mass Spectrometry
Authors: Sun Wei , Wu Shuzhen , Wang Xiaorong , Zheng Dexian , Gao Youhe
Published: November 2016

In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identified peptides in reverse phase liquid chromatography and electrospray tandem mass spectrometry (RPLC-MS/MS) analysis. Following protein digestion with trypsin, the peptide mixture was analyzed by on-line RPLC-MS/MS. Bovine serum albumin (BSA) was used to optimize acetonitrile (ACN) elution gradient for tryptic peptides, and Cytochrome C was used to retest the gradient and the sensitivity of LC-MS/MS. The characteristics of identified peptides were also analyzed. In our experiments, the suitable ACN gradient is 5% to 30% for tryptic peptide elution and the sensitivity of LC-MS/MS is 50 fmol. Analysis of the tryptic peptides demonstrated that longer (more than 10 amino acids) and multi-charge state (+2, +3) peptides are likely to be identified, and the hydropathicity of the peptides might not be related to whether it is more likely to be identified or not. The number of identified peptides for a protein might be used to estimate its loading amount under the same sample background. Moreover, in this study the identified peptides present three types of redundancy, namely identification, charge, and sequence redundancy, which may repress low abundance protein identification.
Predicting Protein Subcellular Localization: Past, Present, and Future
Authors: Dönnes Pierre , Höglund Annette
Published: November 2016

Functional characterization of every single protein is a major challenge of the post-genomic era. The large-scale analysis of a cell’s proteins, proteomics, seeks to provide these proteins with reliable annotations regarding their interaction partners and functions in the cellular machinery. An important step on this way is to determine the subcellular localization of each protein. Eukaryotic cells are divided into subcellular compartments, or organelles. Transport across the membrane into the organelles is a highly regulated and complex cellular process. Predicting the subcellular localization by computational means has been an area of vivid activity during recent years. The publicly available prediction methods differ mainly in four aspects: the underlying biological motivation, the computational method used, localization coverage, and reliability, which are of importance to the user. This review provides a short description of the main events in the protein sorting process and an overview of the most commonly used methods in this field.