bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractBackgroundChildren 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.MethodsA 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.ResultsTwenty‐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.ConclusionRex 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

AbstractBackground and objectivesWe 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.MethodsWe 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.ResultsPlatelet 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).ConclusionHepatitis 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

AbstractBackgroundRetroperitoneal 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.MethodsTwenty‐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.ResultsAll 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).ConclusionsEn 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

AbstractGenetic 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

Zusammenfassung
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

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.