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Sample records for cancer alliance bioinformatics

  1. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  2. NCI Alliance for Nanotechnology in Cancer

    Science.gov (United States)

    The NCI Alliance for Nanotechnology in Cancer funds the Cancer Nanotechnology Training Centers collectively with the NCI Cancer Training Center. Find out about the funded Centers, to date, that train our next generation of scientists in the field of Canc

  3. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

  4. Published Research - NCI Alliance for Nanotechnology in Cancer

    Science.gov (United States)

    The NCI Alliance for Nanotechnology in Cancer has published much exciting and impactful research over the years. Find here a list of all of these listed in PubMed and others across the field of Cancer Nanotechnology.

  5. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  6. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  7. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  8. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  9. Bioinformatics in cancer therapy and drug design

    Energy Technology Data Exchange (ETDEWEB)

    Horbach, D Y [International A. Sakharov environmental univ., Minsk (Belarus); Usanov, S A [Inst. of bioorganic chemistry, National academy of sciences of Belarus, Minsk (Belarus)

    2005-05-15

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  10. Bioinformatics Interpretation of Exome Sequencing: Blood Cancer

    Directory of Open Access Journals (Sweden)

    Jiwoong Kim

    2013-03-01

    Full Text Available We had analyzed 10 exome sequencing data and single nucleotide polymorphism chips for blood cancer provided by the PGM21 (The National Project for Personalized Genomic Medicine Award program. We had removed sample G06 because the pair is not correct and G10 because of possible contamination. In-house software somatic copy-number and heterozygosity alteration estimation (SCHALE was used to detect one loss of heterozygosity region in G05. We had discovered 27 functionally important mutations. Network and pathway analyses gave us clues that NPM1, GATA2, and CEBPA were major driver genes. By comparing with previous somatic mutation profiles, we had concluded that the provided data originated from acute myeloid leukemia. Protein structure modeling showed that somatic mutations in IDH2, RASGEF1B, and MSH4 can affect protein structures.

  11. Patient-oncologist alliance as protection against suicidal ideation in young adults with advanced cancer.

    Science.gov (United States)

    Trevino, Kelly M; Abbott, Caroline H; Fisch, Michael J; Friedlander, Robert J; Duberstein, Paul R; Prigerson, Holly G

    2014-08-01

    Young adults with cancer are at an increased risk of suicidal ideation. To the authors' knowledge, the impact of the patient-oncologist alliance on suicidal ideation has not been examined to date. The current study examined the relationship between the patient-oncologist therapeutic alliance and suicidal ideation in young adults with advanced cancer. A total of 93 young adult patients (aged 20 years-40 years) with incurable, recurrent, or metastatic cancer were evaluated by trained interviewers. Suicidal ideation was assessed with the Yale Evaluation of Suicidality scale, dichotomized into a positive and negative score. Predictors included diagnoses of major depressive disorder and posttraumatic stress disorder, physical quality of life, social support, and use of mental health and supportive care services. The Human Connection Scale, dichotomized into a strong (upper third) and weak (lower two-thirds) therapeutic alliance, assessed the strength of the patients' perceived oncologist alliance. Approximately 22.6% of patients screened positive for suicidal ideation. Patients with a strong therapeutic alliance were found to be at reduced risk of suicidal ideation after controlling for confounding influences of cancer diagnosis, Karnofsky performance status, number of physical symptoms, physical quality of life, major depressive disorder, posttraumatic stress disorder, and social support. A strong therapeutic alliance was also associated with a reduced risk of suicidal ideation after controlling for mental health discussions with health care providers and use of mental health interventions. The patient-oncologist alliance was found to be a robust predictor of suicidal ideation and provided better protection against suicidal ideation than mental health interventions, including psychotropic medications. Oncologists may significantly influence patients' mental health and may benefit from training and guidance in building strong alliances with their young adult patients.

  12. Working Alliance and Vocational Outcomes for Cancer Survivors: An Initial Analysis

    Science.gov (United States)

    Strauser, David R.

    2010-01-01

    This study examines the sex differences in the perception of working alliance and the perceptions of optimism regarding future employment and job satisfaction with adult cancer survivors receiving vocational rehabilitation services. No significant differences were found between males and females in terms of the three components of the working…

  13. Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment

    Science.gov (United States)

    Phan, John H.; Moffitt, Richard A.; Stokes, Todd H.; Liu, Jian; Young, Andrew N.; Nie, Shuming; Wang, May D.

    2013-01-01

    Recent advances in biomarker discovery, biocomputing, and nanotechnology have raised new opportunities for the emerging field of personalized medicine in which disease detection, diagnosis, and therapy are tailored to each individual’s molecular profile, and also for predictive medicine that uses genetic/molecular information to predict disease development, progression, and clinical outcome. Here we discuss advanced biocomputing tools for cancer biomarker discovery and multiplexed nanoparticle probes for cancer biomarker profiling, together with prospects and challenges in correlating biomolecular signatures with clinical outcome. This bio-nano-info convergence holds great promise for molecular diagnosis and individualized therapy of cancer and other human diseases. PMID:19409634

  14. A Virtual Bioinformatics Knowledge Environment for Early Cancer Detection

    Science.gov (United States)

    Crichton, Daniel; Srivastava, Sudhir; Johnsey, Donald

    2003-01-01

    Discovery of disease biomarkers for cancer is a leading focus of early detection. The National Cancer Institute created a network of collaborating institutions focused on the discovery and validation of cancer biomarkers called the Early Detection Research Network (EDRN). Informatics plays a key role in enabling a virtual knowledge environment that provides scientists real time access to distributed data sets located at research institutions across the nation. The distributed and heterogeneous nature of the collaboration makes data sharing across institutions very difficult. EDRN has developed a comprehensive informatics effort focused on developing a national infrastructure enabling seamless access, sharing and discovery of science data resources across all EDRN sites. This paper will discuss the EDRN knowledge system architecture, its objectives and its accomplishments.

  15. Therapist and Patient Perceptions of Alliance and Progress in Psychological Therapy for Women Diagnosed with Gynecological Cancers

    Science.gov (United States)

    Manne, Sharon L.; Kashy, Deborah A.; Rubin, Stephen; Hernandez, Enrique; Bergman, Cynthia

    2012-01-01

    Objective: The goal was to understand both therapist and patient perspectives on alliance and session progress for women in treatment for gynecological cancer. We used a longitudinal version of the one-with-many design to partition variation in alliance and progress ratings into therapist, patient/dyad, and time-specific components. We also…

  16. Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

    Directory of Open Access Journals (Sweden)

    Yang X

    2018-03-01

    Full Text Available Xiao Yang,1 Shaoming Zhu,2 Li Li,3 Li Zhang,1 Shu Xian,1 Yanqing Wang,1 Yanxiang Cheng1 1Department of Obstetrics and Gynecology, 2Department of Urology, Renmin Hospital of Wuhan University, 3Department of Pharmacology, Wuhan University Health Science Center, Wuhan, Hubei, People’s Republic of China Background: The mortality rate associated with ovarian cancer ranks the highest among gynecological malignancies. However, the cause and underlying molecular events of ovarian cancer are not clear. Here, we applied integrated bioinformatics to identify key pathogenic genes involved in ovarian cancer and reveal potential molecular mechanisms. Results: The expression profiles of GDS3592, GSE54388, and GSE66957 were downloaded from the Gene Expression Omnibus (GEO database, which contained 115 samples, including 85 cases of ovarian cancer samples and 30 cases of normal ovarian samples. The three microarray datasets were integrated to obtain differentially expressed genes (DEGs and were deeply analyzed by bioinformatics methods. The gene ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathway enrichments of DEGs were performed by DAVID and KOBAS online analyses, respectively. The protein–protein interaction (PPI networks of the DEGs were constructed from the STRING database. A total of 190 DEGs were identified in the three GEO datasets, of which 99 genes were upregulated and 91 genes were downregulated. GO analysis showed that the biological functions of DEGs focused primarily on regulating cell proliferation, adhesion, and differentiation and intracellular signal cascades. The main cellular components include cell membranes, exosomes, the cytoskeleton, and the extracellular matrix. The molecular functions include growth factor activity, protein kinase regulation, DNA binding, and oxygen transport activity. KEGG pathway analysis showed that these DEGs were mainly involved in the Wnt signaling pathway, amino acid metabolism, and the

  17. Highlights of recent developments and trends in cancer nanotechnology research--view from NCI Alliance for Nanotechnology in Cancer.

    Science.gov (United States)

    Hull, L C; Farrell, D; Grodzinski, P

    2014-01-01

    Although the incidence of cancer and cancer related deaths in the United States has decreased over the past two decades due to improvements in early detection and treatment, cancer still is responsible for a quarter of the deaths in this country. There is much room for improvement on the standard treatments currently available and the National Cancer Institute (NCI) has recognized the potential for nanotechnology and nanomaterials in this area. The NCI Alliance for Nanotechnology in Cancer was formed in 2004 to support multidisciplinary researchers in the application of nanotechnology to cancer diagnosis and treatment. The researchers in the Alliance have been productive in generating innovative solutions to some of the central issues of cancer treatment including how to detect tumors earlier, how to target cancer cells specifically, and how to improve the therapeutic index of existing chemotherapies and radiotherapy treatments. Highly creative ideas are being pursued where novelty in nanomaterial development enables new modalities of detection or therapy. This review highlights some of the innovative materials approaches being pursued by researchers funded by the NCI Alliance. Their discoveries to improve the functionality of nanoparticles for medical applications includes the generation of new platforms, improvements in the manufacturing of nanoparticles and determining the underlying reasons for the movement of nanoparticles in the blood. © 2013.

  18. Bioinformatics analysis of breast cancer bone metastasis related gene-CXCR4

    Institute of Scientific and Technical Information of China (English)

    Heng-Wei Zhang; Xian-Fu Sun; Ya-Ning He; Jun-Tao Li; Xu-Hui Guo; Hui Liu

    2013-01-01

    Objective: To analyze breast cancer bone metastasis related gene-CXCR4. Methods: This research screened breast cancer bone metastasis related genes by high-flux gene chip. Results:It was found that the expressions of 396 genes were different including 165 up-regulations and 231 down-regulations. The expression of chemokine receptor CXCR4 was obviously up-regulated in the tissue with breast cancer bone metastasis. Compared with the tissue without bone metastasis, there was significant difference, which indicated that CXCR4 played a vital role in breast cancer bone metastasis. Conclusions: The bioinformatics analysis of CXCR4 can provide a certain basis for the occurrence and diagnosis of breast cancer bone metastasis, target gene therapy and evaluation of prognosis.

  19. U.S. and Peru Formalize Alliance in Cancer Research

    Science.gov (United States)

    The National Cancer Institute (NCI) Center for Global Health (CGH) had the pleasure of welcoming a delegation of health officials from the Government of Peru for the signing of a memorandum of understanding (MOU) between the U.S. and Peru.

  20. Expression and Bioinformatic Analysis of Ornithine Aminotransferase 
in Non-small Cell Lung Cancer

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    Danfei ZHOU

    2012-09-01

    Full Text Available Background and objective It has been proven that ornithine aminotransferase (OAT might play an important role in the oncogenesis and progression of numerous malignant tumors. The aim of this study is to detect the mRNA and protein expression of OAT in non-small cell lung cancer (NSCLC, as well as to analyze the bioinformatic features and binary interactions. Methods OAT mRNA expression was detected in A549 and 16HBE cell lines by reverse transcription-polymerase chain reaction. OAT protein expression was determined in 55 cases of NSCLC and 17 cases of adjacent non-tumor lung tissues by immunohistochemical staining. The bioinformatic features and binary interactions of OAT were analyzed. Gene ontology annotation and signal pathway analysis were performed. Results OAT mRNA expression in A549 cells was 2.85-fold lower than that in 16HBE cells. OAT protein expression was significantly higher in NSCLC tissues than that in adjacent non-tumor lung tissues. A significant difference of OAT protein expression was existed between squamous cell lung cancer and adenocarcinoma (P<0.05, but was not correlated with the gender, age, lymph node metastasis, tumor size, and TNM stages. Bioinformatic analysis suggested that OAT was a highly homologous and stable protein located in the mitochondria. An aminotran-3 domain and several sites of phosphorylation, which may function in signal transduction, gene transcription, and molecular transit, were found. In the 54 selected binary interactions of OAT, TNF and TRAF6 play roles in the NF-κB pathway. Conclusion OAT may play an important role in the oncogenesis and progression of NSCLC. Thus, OAT may be a novel biomarker for the diagnosis of NSCLC or a new target for its treatment.

  1. The NCI Alliance for Nanotechnology in Cancer: achievement and path forward.

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    Ptak, Krzysztof; Farrell, Dorothy; Panaro, Nicholas J; Grodzinski, Piotr; Barker, Anna D

    2010-01-01

    Nanotechnology is a 'disruptive technology', which can lead to a generation of new diagnostic and therapeutic products, resulting in dramatically improved cancer outcomes. The National Cancer Institute (NCI) of National Institutes of Health explores innovative approaches to multidisciplinary research allowing for a convergence of molecular biology, oncology, physics, chemistry, and engineering and leading to the development of clinically worthy technological approaches. These initiatives include programmatic efforts to enable nanotechnology as a driver of advances in clinical oncology and cancer research, known collectively as the NCI Alliance for Nanotechnology in Cancer (ANC). Over the last 5 years, ANC has demonstrated that multidisciplinary approach catalyzes scientific developments and advances clinical translation in cancer nanotechnology. The research conducted by ANC members has improved diagnostic assays and imaging agents, leading to the development of point-of-care diagnostics, identification and validation of numerous biomarkers for novel diagnostic assays, and the development of multifunctional agents for imaging and therapy. Numerous nanotechnology-based technologies developed by ANC researchers are entering clinical trials. NCI has re-issued ANC program for next 5 years signaling that it continues to have high expectations for cancer nanotechnology's impact on clinical practice. The goals of the next phase will be to broaden access to cancer nanotechnology research through greater clinical translation and outreach to the patient and clinical communities and to support development of entirely new models of cancer care.

  2. Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

    Directory of Open Access Journals (Sweden)

    Jiajia Chen

    2013-01-01

    Full Text Available The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS technologies. Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer. Here we review the recent developments in prostate cancer biomarkers by high throughput sequencing technologies. We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.

  3. Bioinformatics analysis of differentially expressed proteins in prostate cancer based on proteomics data

    Directory of Open Access Journals (Sweden)

    Chen C

    2016-03-01

    Full Text Available Chen Chen,1 Li-Guo Zhang,1 Jian Liu,1 Hui Han,1 Ning Chen,1 An-Liang Yao,1 Shao-San Kang,1 Wei-Xing Gao,1 Hong Shen,2 Long-Jun Zhang,1 Ya-Peng Li,1 Feng-Hong Cao,1 Zhi-Guo Li3 1Department of Urology, North China University of Science and Technology Affiliated Hospital, 2Department of Modern Technology and Education Center, 3Department of Medical Research Center, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, People’s Republic of China Abstract: We mined the literature for proteomics data to examine the occurrence and metastasis of prostate cancer (PCa through a bioinformatics analysis. We divided the differentially expressed proteins (DEPs into two groups: the group consisting of PCa and benign tissues (P&b and the group presenting both high and low PCa metastatic tendencies (H&L. In the P&b group, we found 320 DEPs, 20 of which were reported more than three times, and DES was the most commonly reported. Among these DEPs, the expression levels of FGG, GSN, SERPINC1, TPM1, and TUBB4B have not yet been correlated with PCa. In the H&L group, we identified 353 DEPs, 13 of which were reported more than three times. Among these DEPs, MDH2 and MYH9 have not yet been correlated with PCa metastasis. We further confirmed that DES was differentially expressed between 30 cancer and 30 benign tissues. In addition, DEPs associated with protein transport, regulation of actin cytoskeleton, and the extracellular matrix (ECM–receptor interaction pathway were prevalent in the H&L group and have not yet been studied in detail in this context. Proteins related to homeostasis, the wound-healing response, focal adhesions, and the complement and coagulation pathways were overrepresented in both groups. Our findings suggest that the repeatedly reported DEPs in the two groups may function as potential biomarkers for detecting PCa and predicting its aggressiveness. Furthermore

  4. ANLN functions as a key candidate gene in cervical cancer as determined by integrated bioinformatic analysis

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    Xia L

    2018-04-01

    DEGs PPI network complex, contained 305 nodes and 4,962 edges, and 8 clusters were calculated according to k-core =2. Among them, cluster 1, which had 65 nodes and 1,780 edges, had the highest score in these clusters. In coexpression analysis, there were 86 hubgenes from the Brown modules that were chosen for further analysis. Sixty-one key genes were identified as the intersecting genes of the Brown module of WGCNA and DEGs. In survival analysis, only ANLN was a prognostic factor, and the survival was significantly better in the low-expression ANLN group.Conclusion: Our study suggested that ANLN may be a potential tumor oncogene and could serve as a biomarker for predicting the prognosis of cervical cancer patients. Keywords: bioinformatics analysis, cervical cancer, WGCNA, ANLN 

  5. Expanding Local Cancer Clinical Trial Options: Analysis of the Economic Impact of the Midwest Cancer Alliance in Kansas.

    Science.gov (United States)

    Gafford, J Atlee; Gurley-Calvez, Tami; Krebill, Hope; Lai, Sue Min; Christiadi; Doolittle, Gary C

    2017-09-01

    Patients benefit from receiving cancer treatment closer to home when possible and at high-volume regional centers when specialized care is required. The purpose of this analysis was to estimate the economic impact of retaining more patients in-state for cancer clinical trials and care, which might offset some of the costs of establishing broader cancer trial and treatment networks. Kansas Cancer Registry data were used to estimate the number of patients retained in-state for cancer care following the expansion of local cancer clinical trial options through the Midwest Cancer Alliance based at the University of Kansas Medical Center. The 2014 economic impact of this enhanced local clinical trial network was estimated in four parts: Medical spending was estimated on the basis of National Cancer Institute cost-of-care estimates. Household travel cost savings were estimated as the difference between in-state and out-of-state travel costs. Trial-related grant income was calculated from administrative records. Indirect and induced economic benefits to the state were estimated using an economic impact model. The authors estimated that the enhanced local cancer clinical trial network resulted in approximately $6.9 million in additional economic activity in the state in 2014, or $362,000 per patient retained in-state. This estimate includes $3.6 million in direct spending and $3.3 million in indirect economic activity. The enhanced trial network also resulted in 45 additional jobs. Retaining patients in-state for cancer care and clinical trial participation allows patients to remain closer to home for care and enhances the state economy.

  6. Performance of screening mammography: A report of the alliance for breast cancer screening in Korea

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun Hye [Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon (Korea, Republic of); Kim, Keum Woo [Konyang University Hospital, Konyang University College of Medicine, Daejeon (Korea, Republic of); Kim, Young Joong [Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung (Korea, Republic of); and others

    2016-07-15

    To analyze the diagnostic accuracy and trend in screening mammography in Korea. We retrospectively linked the information from hospitals participating in the Alliance of Breast Cancer Screening in Korea (ABCS-K) and the database of the National Cancer Screening Program. We calculated performance indicators, including the recall rate, cancer detection rate (CDR), positive predictive value (PPV), sensitivity, specificity, false-positive rate (FPR), and interval cancer rate (ICR). Changes in the performance indicators were calculated as the annual percent change with 95% confidence interval (CI). We enrolled 128756 cases from 10 hospitals from 2005 to 2010. The recall rate was 19.1% with a downward trend over time (-12.1% per year; 95% CI, -15.9 to -8.2). The CDR was 2.69 per 1000 examinations, without a significant trend. The PPV was 1.4% with an upward trend (20.8% per year; 95% CI, 15.2 to 26.7). The sensitivity was 86.5% without a significant trend, whereas the specificity was 81.1% with an upward trend (3.3% per year; 95% CI, 2.1 to 4.5). The FPR was 18.9% with a downward trend (-12.4% per year; 95% CI, -16.2 to -8.4). The ICR was 0.5 per 1000 negative examinations without a significant trend. There were institutional variations in the diagnostic accuracy and trend except for the CDR, sensitivity, and ICR. The sensitivity and CDR of screening mammography in the ABCS-K from 2005 to 2010 were compatible with those for Western women. The recall rate, PPV and specificity, however, were suboptimal, although they showed significant improvements over this period. A further analysis is required to explain institutional variations.

  7. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  8. Cognitive function and discontinuation of adjuvant hormonal therapy in older breast cancer survivors: CALGB 369901 (Alliance).

    Science.gov (United States)

    Bluethmann, Shirley M; Alfano, Catherine M; Clapp, Jonathan D; Luta, George; Small, Brent J; Hurria, Arti; Cohen, Harvey J; Sugarman, Steven; B Muss, Hyman; Isaacs, Claudine; Mandelblatt, Jeanne S

    2017-10-01

    To investigate the effects of cognitive function on discontinuation of hormonal therapy in breast cancer survivors ages 65+ ("older"). Older breast cancer survivors with invasive, non-metastatic disease, and no reported cognitive difficulties were recruited from 78 Alliance sites between 2004 and 2011. Eligible survivors (n = 1280) completed baseline interviews; follow-up was conducted annually for up to 7 years. Survivors with estrogen-receptor-positive (ER+) cancers who initiated hormonal therapy (n = 990) were included. Self-reported cognitive function was measured using the EORTC-QLQ30 scale; a difference of eight points on the 0-100 scale was considered clinically significant. Based on varying rates of discontinuation over time, discontinuation was evaluated separately for three time periods: early (3-5 years). Cox models for each time period were used to evaluate the effects of cognition immediately preceding discontinuation, controlling for age, chemotherapy, and other covariates. Survivors were 65-91 years old (mean 72.6 years), and 79% had stages 1 or 2A disease. Overall, 43% discontinued hormonal therapy before 5 years. Survivors who reported lower cognitive function in the period before discontinuation had greater hazards of discontinuing therapy at the treatment midpoint (HR 1.22 per 8-point difference, CI 1.09-1.40, p cognition was not related to discontinuation in the other periods. Self-reported cognitive problems were a significant risk factor for discontinuation of hormonal therapy 1-3 years post-initiation. Additional research is needed on the temporality of cognitive effects and hormonal therapy to support survivorship care needs of older survivors.

  9. [The Alliance for the Prevention of Colorectal Cancer in Spain. A civil commitment to society].

    Science.gov (United States)

    Morillas, Juan Diego; Castells, Antoni; Oriol, Isabel; Pastor, Ana; Pérez-Segura, Pedro; Echevarría, José Manuel; Caballero, Begoña; González-Navarro, Andrés; Bandrés, Fernando; Brullet, Enric; Iniesta, Antonio; Carballo, Fernando; Bouzas, Rosa; Ariza, Aurelio; Ibisate, Alfredo; García-Alfonso, Pilar; Escudero, Beatriz; Camacho, Silvia; Fernández-Marcos, Ana; González, Teresa; Quintero, Enrique; Lanas, Angel; Marzo, Mercè; Mascort, Juanjo; Andréu, Monserrat; Cerezo, Laura; Vázquez-Sequeiros, Enrique; Borrás, Josep María; Salas, Dolores; Ascunce, Nieves; Portillo, Isabel; Herráiz, Mayte; Valle, María Luisa; Sotoca, Amalia; Nieto, Santiago; Hué, Carlos; Paz-Ares, Luis

    2012-03-01

    Colorectal cancer (CRC) is the most common malignant tumor in Spain, when men and women are considered together, and the second leading cause of cancer death. Every week in Spain over 500 cases of CRC are diagnosed, and nearly 260 people die from the disease. Epidemiologic estimations for the coming years show a significant increase in the number of annual cases. CRC is a perfectly preventable tumor and can be cured in 90% of cases if detected in the early stages. Population-based screening programs have been shown to reduce the incidence of CRC and mortality from the disease. Unless early detection programs are established in Spain, it is estimated that in the coming years, 1 out of 20 men and 1 out of 30 women will develop CRC before the age of 75. The Alliance for the Prevention of Colorectal Cancer in Spain is an independent and non-profit organization created in 2008 that integrates patients' associations, altruistic non-governmental organizations and scientific societies. Its main objective is to raise awareness and disseminate information on the social and healthcare importance of CRC in Spain and to promote screening measures, early detection and prevention programs. Health professionals, scientific societies, healthcare institutions and civil society should be sensitized to this highly important health problem that requires the participation of all sectors of society. The early detection of CRC is an issue that affects the whole of society and therefore it is imperative for all sectors to work together. Copyright © 2012 Elsevier España, S.L. y AEEH y AEG. All rights reserved.

  10. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

    Full Text Available We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs, bisphenols (BPs, and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors.

  11. A bioinformatics approach for precision medicine off-label drug drug selection among triple negative breast cancer patients.

    Science.gov (United States)

    Cheng, Lijun; Schneider, Bryan P; Li, Lang

    2016-07-01

    Cancer has been extensively characterized on the basis of genomics. The integration of genetic information about cancers with data on how the cancers respond to target based therapy to help to optimum cancer treatment. The increasing usage of sequencing technology in cancer research and clinical practice has enormously advanced our understanding of cancer mechanisms. The cancer precision medicine is becoming a reality. Although off-label drug usage is a common practice in treating cancer, it suffers from the lack of knowledge base for proper cancer drug selections. This eminent need has become even more apparent considering the upcoming genomics data. In this paper, a personalized medicine knowledge base is constructed by integrating various cancer drugs, drug-target database, and knowledge sources for the proper cancer drugs and their target selections. Based on the knowledge base, a bioinformatics approach for cancer drugs selection in precision medicine is developed. It integrates personal molecular profile data, including copy number variation, mutation, and gene expression. By analyzing the 85 triple negative breast cancer (TNBC) patient data in the Cancer Genome Altar, we have shown that 71.7% of the TNBC patients have FDA approved drug targets, and 51.7% of the patients have more than one drug target. Sixty-five drug targets are identified as TNBC treatment targets and 85 candidate drugs are recommended. Many existing TNBC candidate targets, such as Poly (ADP-Ribose) Polymerase 1 (PARP1), Cell division protein kinase 6 (CDK6), epidermal growth factor receptor, etc., were identified. On the other hand, we found some additional targets that are not yet fully investigated in the TNBC, such as Gamma-Glutamyl Hydrolase (GGH), Thymidylate Synthetase (TYMS), Protein Tyrosine Kinase 6 (PTK6), Topoisomerase (DNA) I, Mitochondrial (TOP1MT), Smoothened, Frizzled Class Receptor (SMO), etc. Our additional analysis of target and drug selection strategy is also fully

  12. Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics

    Directory of Open Access Journals (Sweden)

    Kou YB

    2015-04-01

    Full Text Available Yubin Kou,1,2* Suya Zhang,3* Xiaoping Chen,2 Sanyuan Hu1 1Department of General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China; 2Department of General Surgery, 3Department of Neurology, Shuguang Hospital Baoshan Branch, Shanghai, People’s Republic of China *These authors contributed equally to this work Abstract: This study aimed to explore the underlying molecular mechanisms of colorectal cancer (CRC using bioinformatics analysis. Using GSE4107 datasets downloaded from the Gene Expression Omnibus, the differentially expressed genes (DEGs were screened by comparing the RNA expression from the colonic mucosa between 12 CRC patients and ten healthy controls using a paired t-test. The Gene Ontology (GO functional and pathway enrichment analyses of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID software followed by the construction of a protein–protein interaction (PPI network. In addition, hub gene identification and GO functional and pathway enrichment analyses of the modules were performed. A total of 612 up- and 639 downregulated genes were identified. The upregulated DEGs were mainly involved in the regulation of cell growth, migration, and the MAPK signaling pathway. The downregulated DEGs were significantly associated with oxidative phosphorylation, Alzheimer’s disease, and Parkinson’s disease. Moreover, FOS, FN1, PPP1CC, and CYP2B6 were selected as hub genes in the PPI networks. Two modules (up-A and up-B in the upregulated PPI network and three modules (d-A, d-B, and d-C in the downregulated PPI were identified with the threshold of Molecular Complex Detection (MCODE Molecular Complex Detection (MCODE score ≥4 and nodes ≥6. The genes in module up-A were significantly enriched in neuroactive ligand–receptor interactions and the calcium signaling pathway. The genes in module d-A were enriched in four pathways, including oxidative

  13. MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis.

    Science.gov (United States)

    Shen, Shixuan; Chen, Xiaohui; Li, Hao; Sun, Liping; Yuan, Yuan

    2018-01-01

    Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval. The Newcastle-Ottawa scale was used for quantity assessment . Subgroup and sensitivity analysis were conducted to explore sources of heterogeneity. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were employed for bioinformatics analysis on the correlation between MLH1 methylation and GC risk, clinicopathological behavior as well as prognosis. Results: 2365 GC and 1563 controls were included in the meta-analysis. The pooled OR of MLH1 methylation in GC was 4.895 (95% CI: 3.149-7.611, PMLH1 methylation enhanced GC risk but might not related with GC clinicopathological features and prognosis. Conclusion: MLH1 methylation is an alive biomarker for the prediction of GC and it might not affect GC behavior. Further study could be conducted to verify the impact of MLH1 methylation on GC prognosis.

  14. Patient satisfaction and alliance as a function of the physician's self-regulation, the physician's stress, and the content of consultation in cancer care.

    Science.gov (United States)

    De Vries, A M M; Gholamrezaee, M M; Verdonck-de Leeuw, I M; Passchier, J; Despland, J-N; Stiefel, F; de Roten, Y

    2017-07-01

    To investigate which characteristics of the physician and of the consultation are related to patient satisfaction with communication and working alliance. Real-life consultations (N = 134) between patients (n = 134) and their physicians (n = 24) were audiotaped. All of the patients were aware of their cancer diagnosis and consulted their physician to discuss the results of tests (CT scans, magnetic resonance imaging, or tumor markers) and the progression of their cancer. The consultations were transcribed and coded with the "Defense Mechanisms Rating Scale-Clinician." The patients and physicians completed questionnaires about stress, satisfaction, and alliance, and the data were analyzed using robust linear modeling. Patient satisfaction with communication and working alliance was high. Both were significantly (negatively) related to the physician's neurotic and action defenses-in particular to the defenses of displacement, self-devaluation, acting out, and hypochondriasis-as well as to the physician's stress level. The content of the consultation was not significantly related to the patient outcomes. Our study shows that patient satisfaction with communication and working alliance is not influenced by the content of the consultation but is significantly associated with the physician's self-regulation (defense mechanisms) and stress. The results of this study might contribute to optimizing communication skills training and to improving communication and working alliance in cancer care. Copyright © 2016 John Wiley & Sons, Ltd.

  15. All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health.

    Science.gov (United States)

    Lawler, Mark; Siu, Lillian L; Rehm, Heidi L; Chanock, Stephen J; Alterovitz, Gil; Burn, John; Calvo, Fabien; Lacombe, Denis; Teh, Bin Tean; North, Kathryn N; Sawyers, Charles L

    2015-11-01

    The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients. ©2015 American Association for Cancer Research.

  16. Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.

    Directory of Open Access Journals (Sweden)

    Bernd Timmermann

    Full Text Available BACKGROUND: Colorectal cancer (CRC is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS and microsatellite instable (MSI colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. CONCLUSIONS/SIGNIFICANCE: We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations.

  17. General Approach to Identifying Potential Targets for Cancer Imaging by Integrated Bioinformatics Analysis of Publicly Available Genomic Profiles

    Directory of Open Access Journals (Sweden)

    Yongliang Yang

    2011-03-01

    Full Text Available Molecular imaging has moved to the forefront of drug development and biomedical research. The identification of appropriate imaging targets has become the touchstone for the accurate diagnosis and prognosis of human cancer. Particularly, cell surface- or membrane-bound proteins are attractive imaging targets for their aberrant expression, easily accessible location, and unique biochemical functions in tumor cells. Previously, we published a literature mining of potential targets for our in-house enzyme-mediated cancer imaging and therapy technology. Here we present a simple and integrated bioinformatics analysis approach that assembles a public cancer microarray database with a pathway knowledge base for ascertaining and prioritizing upregulated genes encoding cell surface- or membrane-bound proteins, which could serve imaging targets. As examples, we obtained lists of potential hits for six common and lethal human tumors in the prostate, breast, lung, colon, ovary, and pancreas. As control tests, a number of well-known cancer imaging targets were detected and confirmed by our study. Further, by consulting gene-disease and protein-disease databases, we suggest a number of significantly upregulated genes as promising imaging targets, including cell surface-associated mucin-1, prostate-specific membrane antigen, hepsin, urokinase plasminogen activator receptor, and folate receptors. By integrating pathway analysis, we are able to organize and map “focused” interaction networks derived from significantly dysregulated entity pairs to reflect important cellular functions in disease processes. We provide herein an example of identifying a tumor cell growth and proliferation subnetwork for prostate cancer. This systematic mining approach can be broadly applied to identify imaging or therapeutic targets for other human diseases.

  18. Bioinformatics of non small cell lung cancer and the ras proto-oncogene

    CERN Document Server

    Kashyap, Amita; Babu M, Naresh

    2015-01-01

    Cancer is initiated by activation of oncogenes or inactivation of tumor suppressor genes. Mutations in the K-ras proto-oncogene are responsible for 10–30% of adenocarcinomas. Clinical Findings point to a wide variety of other cancers contributing to lung cancer incidence. Such a scenario makes identification of lung cancer difficult and thus identifying its mechanisms can contribute to the society. Identifying unique conserved patterns common to contributing proto-oncogenes may further be a boon to Pharmacogenomics and pharmacoinformatics. This calls for ab initio/de novo drug discovery that in turn will require a comprehensive in silico approach of Sequence, Domain, Phylogenetic and Structural analysis of the receptors, ligand screening and optimization and detailed Docking studies. This brief involves extensive role of the RAS subfamily that includes a set of proteins, which cause an over expression of cancer-causing genes like M-ras and initiate tumour formation in lungs. SNP Studies and Structure based ...

  19. Sugar-sweetened beverage intake and cancer recurrence and survival in CALGB 89803 (Alliance.

    Directory of Open Access Journals (Sweden)

    Michael A Fuchs

    Full Text Available In colon cancer patients, obesity, sedentary lifestyle, and high dietary glycemic load have been associated with increased risk of cancer recurrence. High sugar-sweetened beverage intake has been associated with obesity, diabetes, and cardio-metabolic diseases, but the influence on colon cancer survival is unknown.We assessed the association between sugar-sweetened beverage consumption on cancer recurrence and mortality in 1,011 stage III colon cancer patients who completed food frequency questionnaires as part of a U.S. National Cancer Institute-sponsored adjuvant chemotherapy trial. Hazard ratios (HRs and 95% confidence intervals (CIs were calculated with Cox proportional hazard models.Patients consuming ≥ 2 servings of sugar-sweetened beverages per day experienced an adjusted HR for disease recurrence or mortality of 1.67 (95% CI, 1.04-2.68, compared with those consuming <2 servings per month (P(trend = 0.02. The association of sugar-sweetened beverages on cancer recurrence or mortality appeared greater among patients who were both overweight (body mass index ≥ 2 5 kg/m(2 and less physically active (metabolic equivalent task-hours per week <18 (HR = 2.22; 95% CI, 1.29-3.81, P(trend = 0.0025.Higher sugar-sweetened beverage intake was associated with a significantly increased risk of cancer recurrence and mortality in stage III colon cancer patients.

  20. Cancer immunology, bioinformatics and chemokine evidence link vaccines contaminated with animal proteins to autoimmune disease: a detailed look at Crohn's disease and Vitiligo

    OpenAIRE

    Arumugham, Vinu

    2017-01-01

    Cancer research has demonstrated that immunization with homologous xenogeneic proteins (such as vaccines contaminated with animal proteins that resemble human proteins) results in autoimmunity. Bioinformatics analysis demonstrates that animal proteins have occasional amino acids differences compared to equivalent human proteins. So mutated human protein epitopes can be identical to animal protein derived epitopes. Low affinity self reactive T cells suited for detection of mutated human epitop...

  1. Predicted vitamin D status and colon cancer recurrence and mortality in CALGB 89803 (Alliance).

    Science.gov (United States)

    Fuchs, M A; Yuan, C; Sato, K; Niedzwiecki, D; Ye, X; Saltz, L B; Mayer, R J; Mowat, R B; Whittom, R; Hantel, A; Benson, A; Atienza, D; Messino, M; Kindler, H; Venook, A; Innocenti, F; Warren, R S; Bertagnolli, M M; Ogino, S; Giovannucci, E L; Horvath, E; Meyerhardt, J A; Ng, K

    2017-06-01

    Observational studies suggest that higher levels of 25-hydroxyvitamin D3 (25(OH)D) are associated with a reduced risk of colorectal cancer and improved survival of colorectal cancer patients. However, the influence of vitamin D status on cancer recurrence and survival of patients with stage III colon cancer is unknown. We prospectively examined the influence of post-diagnosis predicted plasma 25(OH)D on outcome among 1016 patients with stage III colon cancer who were enrolled in a National Cancer Institute-sponsored adjuvant therapy trial (CALGB 89803). Predicted 25(OH)D scores were computed using validated regression models. We examined the influence of predicted 25(OH)D scores on cancer recurrence and mortality (disease-free survival; DFS) using Cox proportional hazards. Patients in the highest quintile of predicted 25(OH)D score had an adjusted hazard ratio (HR) for colon cancer recurrence or mortality (DFS) of 0.62 (95% confidence interval [CI], 0.44-0.86), compared with those in the lowest quintile (Ptrend = 0.005). Higher predicted 25(OH)D score was also associated with a significant improvement in recurrence-free survival and overall survival (Ptrend = 0.01 and 0.0004, respectively). The benefit associated with higher predicted 25(OH)D score appeared consistent across predictors of cancer outcome and strata of molecular tumor characteristics, including microsatellite instability and KRAS, BRAF, PIK3CA, and TP53 mutation status. Higher predicted 25(OH)D levels after a diagnosis of stage III colon cancer may be associated with decreased recurrence and improved survival. Clinical trials assessing the benefit of vitamin D supplementation in the adjuvant setting are warranted. NCT00003835. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. [Factors affecting the adoption of ICT tools in experiments with bioinformatics in biopharmaceutical organizations: a case study in the Brazilian Cancer Institute].

    Science.gov (United States)

    Pitassi, Claudio; Gonçalves, Antonio Augusto; Moreno Júnior, Valter de Assis

    2014-01-01

    The scope of this article is to identify and analyze the factors that influence the adoption of ICT tools in experiments with bioinformatics at the Brazilian Cancer Institute (INCA). It involves a descriptive and exploratory qualitative field study. Evidence was collected mainly based on in-depth interviews with the management team at the Research Center and the IT Division. The answers were analyzed using the categorical content method. The categories were selected from the scientific literature and consolidated in the Technology-Organization-Environment (TOE) framework created for this study. The model proposed made it possible to demonstrate how the factors selected impacted INCA´s adoption of bioinformatics systems and tools, contributing to the investigation of two critical areas for the development of the health industry in Brazil, namely technological innovation and bioinformatics. Based on the evidence collected, a research question was posed: to what extent can the alignment of the factors related to the adoption of ICT tools in experiments with bioinformatics increase the innovation capacity of a Brazilian biopharmaceutical organization?

  3. Best Practices in Cancer Nanotechnology – Perspective from NCI Nanotechnology Alliance

    Science.gov (United States)

    Zamboni, William C.; Torchilin, Vladimir; Patri, Anil; Hrkach, Jeff; Stern, Stephen; Lee, Robert; Nel, Andre; Panaro, Nicholas J.; Grodzinski, Piotr

    2014-01-01

    Historically, treatment of patients with cancer using chemotherapeutic agents has been associated with debilitating and systemic toxicities, poor bioavailability, and unfavorable pharmacokinetics. Nanotechnology-based drug delivery systems, on the other hand, can specifically target cancer cells while avoiding their healthy neighbors, avoid rapid clearance from the body, and be administered without toxic solvents. They hold immense potential in addressing all of these issues which has hampered further development of chemotherapeutics. Furthermore, such drug delivery systems will lead to cancer therapeutic modalities which are not only less toxic to the patient but also significantly more efficacious. In addition to established therapeutic modes of action, nanomaterials are opening up entirely new modalities of cancer therapy, such as photodynamic and hyperthermia treatments. Furthermore, nanoparticle carriers are also capable of addressing several drug delivery problems which could not be effectively solved in the past and include overcoming formulation issues, multi-drug-resistance phenomenon and penetrating cellular barriers that may limit device accessibility to intended targets such as the blood-brain-barrier. The challenges in optimizing design of nanoparticles tailored to specific tumor indications still remain; however, it is clear that nanoscale devices carry a significant promise towards new ways of diagnosing and treating cancer. This review focuses on future prospects of using nanotechnology in cancer applications and discusses practices and methodologies used in the development and translation of nanotechnology-based therapeutics. PMID:22669131

  4. Bioinformatic analysis of cis-regulatory interactions between progesterone and estrogen receptors in breast cancer

    Directory of Open Access Journals (Sweden)

    Matloob Khushi

    2014-11-01

    Full Text Available Chromatin factors interact with each other in a cell and sequence-specific manner in order to regulate transcription and a wealth of publically available datasets exists describing the genomic locations of these interactions. Our recently published BiSA (Binding Sites Analyser database contains transcription factor binding locations and epigenetic modifications collected from published studies and provides tools to analyse stored and imported data. Using BiSA we investigated the overlapping cis-regulatory role of estrogen receptor alpha (ERα and progesterone receptor (PR in the T-47D breast cancer cell line. We found that ERα binding sites overlap with a subset of PR binding sites. To investigate further, we re-analysed raw data to remove any biases introduced by the use of distinct tools in the original publications. We identified 22,152 PR and 18,560 ERα binding sites (<5% false discovery rate with 4,358 overlapping regions among the two datasets. BiSA statistical analysis revealed a non-significant overall overlap correlation between the two factors, suggesting that ERα and PR are not partner factors and do not require each other for binding to occur. However, Monte Carlo simulation by Binary Interval Search (BITS, Relevant Distance, Absolute Distance, Jaccard and Projection tests by Genometricorr revealed a statistically significant spatial correlation of binding regions on chromosome between the two factors. Motif analysis revealed that the shared binding regions were enriched with binding motifs for ERα, PR and a number of other transcription and pioneer factors. Some of these factors are known to co-locate with ERα and PR binding. Therefore spatially close proximity of ERα binding sites with PR binding sites suggests that ERα and PR, in general function independently at the molecular level, but that their activities converge on a specific subset of transcriptional targets.

  5. Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer.

    Science.gov (United States)

    Wang, Yuzhi; Zhang, Yi; Huang, Qian; Li, Chengwen

    2018-04-19

    Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non‑tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t‑tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein‑protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in 'cell division', the 'proteinaceous extracellular matrix (ECM)', 'ECM structural constituents' and 'ECM‑receptor interaction', whereas downregulated genes were mainly enriched in 'response to drugs', 'extracellular space', 'transcriptional activator activity' and the 'peroxisome proliferator‑activated receptor signaling pathway'. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2‑a, baculoviral inhibitor of apoptosis repeat‑containing protein 5, cyclin‑dependent kinase 1, G2/mitotic‑specific cyclin‑B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in 'mitotic nuclear division', 'mid‑body', 'protein binding' and 'cell cycle'. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide

  6. Bioinformatics analysis for evaluation of the diagnostic potentialities of miR-19b, -125b and -205 as liquid biopsy markers of prostate cancer

    Science.gov (United States)

    Bryzgunova, O. E.; Lekchnov, E. A.; Zaripov, M. M.; Yurchenko, Yu. B.; Yarmoschuk, S. V.; Pashkovskaya, O. A.; Rykova, E. Yu.; Zheravin, A. A.; Laktionov, P. P.

    2017-09-01

    Presence of tumor-derived cell-free miRNA in biological fluids as well as simplicity and robustness of cell-free miRNA quantification makes them suitable markers for cancer diagnostics. Based on previously published data demonstrating diagnostic potentialities of miR-205 in blood and miR-19b as well as miR-125b in urine of prostate cancer patients, bioinformatics analysis was carried out to follow their involvement in prostate cancer development and select additional miRNA-markers for prostate cancer diagnostics. Studied miRNAs are involved in different signaling pathways and regulate a number of genes involved in cancer development. Five of their targets (CCND1, BRAF, CCNE1, CCNE2, RAF1), according to the STRING database, act as part of the same signaling pathway. RAF1 is regulated by miR-19b and miR-125b, and it was shown to be involved in prostate cancer development by DIANA and STRING databases. Thus, other microRNAs regulating RAF1 expression such as miR-16, -195, -497, and -7 (suggested by DIANA, TargetScan, MiRTarBase and miRDB databases) can potentially be regarded as prostate cancer markers.

  7. An audit comparing the reporting of staging MRI scans for rectal cancer with the London Cancer Alliance (LCA) guidelines.

    Science.gov (United States)

    Siddiqui, M R S; Shanmuganandan, A P; Rasheed, S; Tekkis, P; Brown, G; Abulafi, A M

    2017-11-01

    This article focuses on the audit and assessment of clinical practice before and after introduction of MRI reporting guidelines. Standardised proforma based reporting may improve quality of MRI reports. Uptake of the use may be facilitated by endorsement from regional and national cancer organisations. This audit was divided into 2 phases. MRI reports issued between April 2014 and June 2014 were included in the first part of our audit. Phase II included MRI reports issued between April 2015 and June 2015. 14 out of 15 hospitals that report MRI scans in the LCA responded to our audit proposal. The completion rate of key MRI metrics/metrics was better in proforma compared to prose reports both before (98% vs 73%; p < 0.05) and after introduction of the guidelines (98% vs 71%; p < 0.05). There was an approximate doubling of proforma reporting after the introduction of guidelines and workshop interventions (39% vs 65%; p < 0.05). Evaluation of locally advanced cancers (tumours extending to or beyond the circumferential resection margin) for beyond TME surgery was reported in 3% of prose reports vs. 42% in proformas. Incorporation of standardised reporting in official guidelines improved the uptake of proforma based reporting. Proforma based reporting captured more MRI reportable items compared to prose summaries, before and after the implementation of guidelines. MRI reporting of advanced cancers for beyond TME surgery falls short of acceptable standards but is more detailed in proforma based reports. Further work to improve completion especially in beyond TME reporting is required. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

  8. Alliance in Youth Care

    NARCIS (Netherlands)

    Linda Rothman; H. Pijnenburg; Rinie van Rijsingen

    2015-01-01

    This article introduces the concept of alliance in youth care. The concept of (therapeutic) alliance originates in adult psychotherapy and related research. Alliance refers to the working relationship between youth care workers and their clients. Within this concept, personal (emotional) and task

  9. The Cytotoxicity Mechanism of 6-Shogaol-Treated HeLa Human Cervical Cancer Cells Revealed by Label-Free Shotgun Proteomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Qun Liu

    2012-01-01

    Full Text Available Cervical cancer is one of the most common cancers among women in the world. 6-Shogaol is a natural compound isolated from the rhizome of ginger (Zingiber officinale. In this paper, we demonstrated that 6-shogaol induced apoptosis and G2/M phase arrest in human cervical cancer HeLa cells. Endoplasmic reticulum stress and mitochondrial pathway were involved in 6-shogaol-mediated apoptosis. Proteomic analysis based on label-free strategy by liquid chromatography chip quadrupole time-of-flight mass spectrometry was subsequently proposed to identify, in a non-target-biased manner, the molecular changes in cellular proteins in response to 6-shogaol treatment. A total of 287 proteins were differentially expressed in response to 24 h treatment with 15 μM 6-shogaol in HeLa cells. Significantly changed proteins were subjected to functional pathway analysis by multiple analyzing software. Ingenuity pathway analysis (IPA suggested that 14-3-3 signaling is a predominant canonical pathway involved in networks which may be significantly associated with the process of apoptosis and G2/M cell cycle arrest induced by 6-shogaol. In conclusion, this work developed an unbiased protein analysis strategy by shotgun proteomics and bioinformatics analysis. Data observed provide a comprehensive analysis of the 6-shogaol-treated HeLa cell proteome and reveal protein alterations that are associated with its anticancer mechanism.

  10. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Greater Philadelphia Bioinformatics Alliance (GPBA) 3rd Annual Retreat 2005

    Science.gov (United States)

    2005-11-01

    Biotech in recent days. The start of Biotech from the Agriculture ie rural side will be discussed and advancement will be discussed in detail towards...such advances in the food and Agricultural aspect. The significant results which not only makes the advancements of the understanding the public but...authored journal publications in human genetics, bioethics for industry and genetics education. Karl V. Steiner, Dr. Ing., Associate Director, Delaware

  12. Greater Philadelphia Bioinformatics Alliance (GPBA) 3rd Annual Retreat 2005

    National Research Council Canada - National Science Library

    Russell, David W

    2005-01-01

    .... Our experimental results show strong structural and functional relationships among member proteins within each of the communities identified by our approach, as verified by MIPS complex catalogue...

  13. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  14. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  15. A multifactorial likelihood model for MMR gene variant classification incorporating probabilities based on sequence bioinformatics and tumor characteristics: a report from the Colon Cancer Family Registry.

    Science.gov (United States)

    Thompson, Bryony A; Goldgar, David E; Paterson, Carol; Clendenning, Mark; Walters, Rhiannon; Arnold, Sven; Parsons, Michael T; Michael D, Walsh; Gallinger, Steven; Haile, Robert W; Hopper, John L; Jenkins, Mark A; Lemarchand, Loic; Lindor, Noralane M; Newcomb, Polly A; Thibodeau, Stephen N; Young, Joanne P; Buchanan, Daniel D; Tavtigian, Sean V; Spurdle, Amanda B

    2013-01-01

    Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ~12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing. © 2012 Wiley Periodicals, Inc.

  16. THE ALLIANCE FORMATION PROCESS

    OpenAIRE

    Whipple, Judith M.; Frankel, Robert

    1998-01-01

    While interest in developing strategic alliances within the food system continues to increase, there remains considerable risk when firms adopt such a cooperative strategy. The risk is due in part to the lack of concrete guidelines that illustrate the steps or stages of alliance development and the important strategic and operational decisions required at each stage. The existence of such guidelines would facilitate alliance formation and enable managers and researchers to better understand a...

  17. The winning alliance

    CERN Multimedia

    Antonella Del Rosso

    2012-01-01

    The ICTR-PHE 2012 conference, which closed its doors today after five busy days, sealed the alliance between the physics and medical communities. We have come a long way since 1977, when physicist David Townsend took the first PET images of a small mouse. Today, physicists are developing new detector techniques that medical doctors can transfer to the clinic in fields that are no longer confined to cancer treatment. Several powerful and innovative solutions for better healthcare are on their way.   An overwhelming number of proposals for improving virtually all aspects of cancer treatment was presented at the ICTR-PHE 2012: from new detectors and read-out solutions for implementation in the next generation of imaging instrumentation to accelerator-based facilities for the production of new isotopes for use both as radio-tracers and as drugs. And this is not all, because the issues that were discussed at the joint conference also included new uses of enhanced PET-CT imaging for cardiovascular...

  18. Understanding Cancer Prognosis

    Medline Plus

    Full Text Available ... Role in Cancer Research Intramural Research Extramural Research Bioinformatics and Cancer NCI-Designated Cancer Centers Frederick National ... Role in Cancer Research Intramural Research Extramural Research Bioinformatics and Cancer NCI-Designated Cancer Centers Frederick National ...

  19. Alliance capability as a mediator between experience and alliance performance

    DEFF Research Database (Denmark)

    Heimeriks, Koen; Duysters, Geert

    This study centers around the way in which firms can enhance alliance performance through the development of alliance capabilities. Whereas most research has focused on inter-firm antecedents of alliance performance, research on intra-firm antecedents pointing to prior experience and internal...... alliance managers and Vice-Presidents of 151 firms. The survey covers over 2600 alliances for the period 1997-2001. This study not only finds that alliance capabilities partially mediate between alliance experience and alliance performance, but also yields novel insights into the micro-level building...

  20. Developing Alliance Capabilities

    DEFF Research Database (Denmark)

    Heimeriks, Koen H.; Duysters, Geert; Vanhaverbeke, Wim

    This paper assesses the differential performance effects of learning mechanisms on the development of alliance capabilities. Prior research has suggested that different capability levels could be identified in which specific intra-firm learning mechanisms are used to enhance a firm's alliance...

  1. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Understanding Cancer Prognosis

    Medline Plus

    Full Text Available ... Adult Cancers Metastatic Cancer Recurrent Cancer Research NCI’s Role in Cancer Research Intramural Research Extramural Research Bioinformatics ... Terminology Resources NCI Data Catalog Cryo-EM NCI's Role in Cancer Research Intramural Research Extramural Research Bioinformatics ...

  3. Understanding Cancer Prognosis

    Medline Plus

    Full Text Available ... Extramural Research Bioinformatics and Cancer NCI-Designated Cancer Centers Frederick National Laboratory for Cancer Research Partners & Collaborators ... Extramural Research Bioinformatics and Cancer NCI-Designated Cancer Centers Frederick National Lab Partners & Collaborators Spotlight on Scientists ...

  4. Bioinformatics Analyses of the Role of Vascular Endothelial Growth Factor in Patients with Non-Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available This study was aimed to identify the expression pattern of vascular endothelial growth factor (VEGF in non-small cell lung cancer (NSCLC and to explore its potential correlation with the progression of NSCLC.Gene expression profile GSE39345 was downloaded from the Gene Expression Omnibus database. Twenty healthy controls and 32 NSCLC samples before chemotherapy were analyzed to identify the differentially expressed genes (DEGs. Then pathway enrichment analysis of the DEGs was performed and protein-protein interaction networks were constructed. Particularly, VEGF genes and the VEGF signaling pathway were analyzed. The sub-network was constructed followed by functional enrichment analysis.Total 1666 up-regulated and 1542 down-regulated DEGs were identified. The down-regulated DEGs were mainly enriched in the pathways associated with cancer. VEGFA and VEGFB were found to be the initiating factor of VEGF signaling pathway. In addition, in the epidermal growth factor receptor (EGFR, VEGFA and VEGFB associated sub-network, kinase insert domain receptor (KDR, fibronectin 1 (FN1, transforming growth factor beta induced (TGFBI and proliferating cell nuclear antigen (PCNA were found to interact with at least two of the three hub genes. The DEGs in this sub-network were mainly enriched in Gene Ontology terms related to cell proliferation.EGFR, KDR, FN1, TGFBI and PCNA may interact with VEGFA to play important roles in NSCLC tumorigenesis. These genes and corresponding proteins may have the potential to be used as the targets for either diagnosis or treatment of patients with NSCLC.

  5. Alliances in "The Hunger Games"

    Science.gov (United States)

    Painter, Judith

    2012-01-01

    This lesson plan is based on "The Hunger Games" by Suzanne Collins. Characters in "The Hunger Games" form alliances both inside and outside the arena. Katniss and Gale form alliances within District 12. Katniss, Peeta, and the other tributes form alliances for a variety of reasons during the Games. An alliance means that "someone's got your back"…

  6. Trust in Strategic Alliances

    DEFF Research Database (Denmark)

    Nielsen, Bo

    2011-01-01

    This article examines the dynamic and multi-dimensional nature of trust in strategic alliances. Adopting a co-evolutionary approach, I developed a framework to show how trust, conceptualised in different forms, plays distinct roles at various evolutionary stages of the alliance relationship....... Emphasising the multi-dimensional and dynamic role of trust, the framework illustrates how initial levels of a particular type of trust may co-evolve with the alliance and influence subsequent phases of the relationship – either on its own or in combination with other types or dimensions of trust....... The theoretical distinction between trust as antecedent, moderator and outcome during the evolution of the alliance relationship leads to research questions that may guide future empirical research....

  7. Alliances: Are they effective?

    International Nuclear Information System (INIS)

    Wardt, J. de

    1997-01-01

    Concern is growing in the oil field that alliances are not doing as well as they should be. Have they been adopted as a panacea without sufficient understanding of what they are and how to implement them? That question is answered in this analysis, which is organized as follows: a changing industry--two key trend drivers; entering a new era of organizing and managing systems; types of contracts--alliances vs. fixed and incentive contracts, limitations of discounting; oilfield alliances--new solutions are needed to improve the system; change/commitments--how changes are being implemented by the innovators, how many really support it; and alliances take effort and time--why it isn't easy to do it right

  8. Family Caregiver Alliance

    Science.gov (United States)

    ... on your schedule. Look for our launch soon! FAMILY CARE NAVIGATOR ─ Click on Your State AL AK ... AiA18 Smart Patients Caregivers Community In partnership with Family Caregiver Alliance Learn more Caregiver Research Studies show ...

  9. Construction of possible integrated predictive index based on EGFR and ANXA3 polymorphisms for chemotherapy response in fluoropyrimidine-treated Japanese gastric cancer patients using a bioinformatic method

    International Nuclear Information System (INIS)

    Takahashi, Hiro; Kaniwa, Nahoko; Saito, Yoshiro; Sai, Kimie; Hamaguchi, Tetsuya; Shirao, Kuniaki; Shimada, Yasuhiro; Matsumura, Yasuhiro; Ohtsu, Atsushi; Yoshino, Takayuki; Doi, Toshihiko; Takahashi, Anna; Odaka, Yoko; Okuyama, Misuzu; Sawada, Jun-ichi; Sakamoto, Hiromi; Yoshida, Teruhiko

    2015-01-01

    Variability in drug response between individual patients is a serious concern in medicine. To identify single-nucleotide polymorphisms (SNPs) related to drug response variability, many genome-wide association studies have been conducted. We previously applied a knowledge-based bioinformatic approach to a pharmacogenomics study in which 119 fluoropyrimidine-treated gastric cancer patients were genotyped at 109,365 SNPs using the Illumina Human-1 BeadChip. We identified the SNP rs2293347 in the human epidermal growth factor receptor (EGFR) gene as a novel genetic factor related to chemotherapeutic response. In the present study, we reanalyzed these hypothesis-free genomic data using extended knowledge. We identified rs2867461 in annexin A3 (ANXA3) gene as another candidate. Using logistic regression, we confirmed that the performance of the rs2867461 + rs2293347 model was superior to those of the single factor models. Furthermore, we propose a novel integrated predictive index (iEA) based on these two polymorphisms in EGFR and ANXA3. The p value for iEA was 1.47 × 10 −8 by Fisher’s exact test. Recent studies showed that the mutations in EGFR is associated with high expression of dihydropyrimidine dehydrogenase, which is an inactivating and rate-limiting enzyme for fluoropyrimidine, and suggested that the combination of chemotherapy with fluoropyrimidine and EGFR-targeting agents is effective against EGFR-overexpressing gastric tumors, while ANXA3 overexpression confers resistance to tyrosine kinase inhibitors targeting the EGFR pathway. These results suggest that the iEA index or a combination of polymorphisms in EGFR and ANXA3 may serve as predictive factors of drug response, and therefore could be useful for optimal selection of chemotherapy regimens. The online version of this article (doi:10.1186/s12885-015-1721-z) contains supplementary material, which is available to authorized users

  10. Learning in Strategic Technology Alliances

    OpenAIRE

    SCHOENMAKERS, Wilfred; DUYSTERS, Geert

    2003-01-01

    In this paper we examine the influence of strategic technology alliances on organisational learning. From an empirical perspective we examined the pre- and post- alliance knowledge bases of allying firms. We found that the pre- alliance knowledge base overlap of the allying firms has an inverted U-shaped relationship with the degree of learning taking place in the alliance. Alliances established for the purpose of learning also show a significantly greater increase in knowledge base overlap f...

  11. Patient and tumor characteristics and BRAF and KRAS mutations in colon cancer, NCCTG/Alliance N0147.

    Science.gov (United States)

    Gonsalves, Wilson I; Mahoney, Michelle R; Sargent, Daniel J; Nelson, Garth D; Alberts, Steven R; Sinicrope, Frank A; Goldberg, Richard M; Limburg, Paul J; Thibodeau, Stephen N; Grothey, Axel; Hubbard, Joleen M; Chan, Emily; Nair, Suresh; Berenberg, Jeffrey L; McWilliams, Robert R

    2014-07-01

    KRAS and BRAF (V600E) mutations are important predictive and prognostic markers, respectively, in colon cancer, but little is known about patient and clinical factors associated with them. Two thousand three hundred twenty-six of 3397 patients in the N0147 phase III adjuvant trial for stage III colon cancer completed a patient questionnaire. Primary tumors were assessed for KRAS and BRAF (V600E) mutations and defective mismatch repair (dMMR) status. Logistic regression models and categorical data analysis were used to identify associations of patient and tumor characteristics with mutation status. All statistical tests were two-sided. KRAS (35%) and BRAF (V600E) (14%) mutations were nearly mutually exclusive. KRAS mutations were more likely to be present in patients without a family history of colon cancer and never smokers. Tumors with KRAS mutations were less likely to have dMMR (odds ratio [OR] = 0.21; 95% confidence interval [CI] = 0.15 to 0.31; P characteristics are associated with KRAS and BRAF (V600E) mutations. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  13. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  14. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  15. Strategic alliance development : a study on alliances between competing firms

    NARCIS (Netherlands)

    Wahyuni, S.

    2003-01-01

    The objective of this study was to reveal the development of lSAs (International Strategic Alliances) and the important factors for every phase of an alliance relationship. Since there are a great number of variables that can be assessed throughout the whole process of an alliance life, we decided

  16. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  17. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  18. The History and Accomplishments of the LIVESTRONG Young Adult Alliance.

    Science.gov (United States)

    Mathews-Bradshaw, Beth; Johnson, Rebecca; Kaplan, Stuart; Craddock, Kelli; Hayes-Lattin, Brandon

    2011-03-01

    This article outlines the history, background, and accomplishments of the LIVESTRONG Young Adult Alliance. The LIVESTRONG Young Adult Alliance, a program of the Lance Armstrong Foundation, was developed as a vehicle for a strategic plan designed to implement the Adolescent and Young Adult Oncology Progress Review Group (AYAO PRG) recommendations. The AYAO PRG was co-sponsored by Lance Armstrong Foundation and the National Cancer Institute (NCI); both LIVESTRONG and NCI provide strategic oversight and guidance to the Alliance. Highlights and accomplishments: The Alliance accomplishments include the publication of disease-specific retrospective analyses, funding of an AYA cohort study and biorepository proposal, publication of two position statements on guidelines for care of AYAs with cancer and training for AYA oncology health professionals, promotion of an international charter of rights for AYA cancer patients, creation and distribution of a survey to college health professionals, creation and implementation of a Cancer Centers Working Group and Institutional Review Board Toolkit, and continued growth and collaboration through an annual meeting. The growth and success of the Alliance has coincided with the growth of AYA oncology as a field. The collaborative environment of the Alliance draws together a diverse group of individuals united in the effort to increase survival rates and improve the quality of life for adolescents and young adults diagnosed with cancer.

  19. Patterns of Local-Regional Management Following Neoadjuvant Chemotherapy in Breast Cancer: Results From ACOSOG Z1071 (Alliance)

    Energy Technology Data Exchange (ETDEWEB)

    Haffty, Bruce G., E-mail: hafftybg@cinj.rutgers.edu [Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey (United States); McCall, Linda M. [Alliance Statistics and Data Center, Duke University, Durham, North Carolina (United States); Ballman, Karla V. [Weill Medical College of Cornell University, New York, New York (United States); McLaughlin, Sarah [Mayo Clinic, Jacksonville, Florida (United States); Jagsi, Reshma [University of Michigan, Ann Arbor, Michigan (United States); Ollila, David W. [University of North Carolina, Chapel Hill, North Carolina (United States); Hunt, Kelly K. [Department of Breast Surgical Oncology, MD Anderson Cancer Center, Houston, Texas (United States); Buchholz, Thomas A. [MD Anderson Cancer Center, Houston, Texas (United States); Boughey, Judy C. [Mayo Clinic, Rochester, Minnesota (United States)

    2016-03-01

    Purpose: American College of Surgeons Oncology Group Z1071 was a prospective trial evaluating the false negative rate of sentinel lymph node (SLN) surgery after neoadjuvant chemotherapy (NAC) in breast cancer patients with initial node-positive disease. Radiation therapy (RT) decisions were made at the discretion of treating physicians, providing an opportunity to evaluate variability in practice patterns following NAC. Methods and Materials: Of 756 patients enrolled from July 2009 to June 2011, 685 met all eligibility requirements. Surgical approach, RT, and radiation field design were analyzed based on presenting clinical and pathologic factors. Results: Of 401 node-positive patients, mastectomy was performed in 148 (36.9%), mastectomy with immediate reconstruction in 107 (26.7%), and breast-conserving surgery (BCS) in 146 patients (36.4%). Of the 284 pathologically node-negative patients, mastectomy was performed in 84 (29.6%), mastectomy with immediate reconstruction in 69 (24.3%), and BCS in 131 patients (46.1%). Bilateral mastectomy rates were higher in women undergoing reconstruction than in those without (66.5% vs 32.2%, respectively, P<.0001). Use of internal mammary RT was low (7.8%-11.2%) and did not differ between surgical approaches. Supraclavicular RT rate ranged from 46.6% to 52.2% and did not differ between surgical approaches but was omitted in 193 or 408 node-positive patients (47.3%). Rate of axillary RT was more frequent in patients who remained node-positive (P=.002). However, 22% of patients who converted to node-negative still received axillary RT. Post-mastectomy RT was more frequently omitted after reconstruction than mastectomy (23.9% vs 12.1%, respectively, P=.002) and was omitted in 19 of 107 patients (17.8%) with residual node-positive disease in the reconstruction group. Conclusions: Most clinically node-positive patients treated with NAC undergoing mastectomy receive RT. RT is less common in patients undergoing reconstruction. There

  20. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  1. Sustaining alliances for integrity.

    Science.gov (United States)

    Werhane, P H

    2000-01-01

    Research in business ethics has shown that value-grounded organizations outperform their counterparts in business terms and that industries can successfully regulate themselves. The market in health care, systems theory, and stakeholder analysis are used to generate a set of five potential core values to sustain an Ethics Alliance of Oral Health Organizations.

  2. Learning in strategic technology alliances

    NARCIS (Netherlands)

    Schoenmakers, W.W.M.E.; Duysters, G.M.

    2006-01-01

    In this paper we examine the influence of strategic technology alliances on organisational learning. From an empirical perspective we examine the pre- and post-alliance knowledge bases of allying firms. We find that the pre-alliance knowledge base overlap of the allying firms has an inverted

  3. BARRIERS OF STRATEGIC ALLIANCES ORGANIZATION

    Directory of Open Access Journals (Sweden)

    Vladislav M. Sannikov

    2014-01-01

    Full Text Available General barriers of organization of different types of strategic alliances have beenconsidered in the article. There are several recommendations for overcoming themin cases of international alliances, and in case of work in one state. The article also identified goals and tasks of single coordination center of alliance to overcome organization barriers.

  4. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  5. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  6. Understanding Alliance Formation Patterns

    Science.gov (United States)

    2015-12-01

    military, transportation, and communications technologies, which caused every place in the world to be politically significant. Second, “divisions of power...test a similar claim about the association between distance and dyadic alliance formation. In their first model, in which they use the complete data...1885 to 1990] are positively related to dyadic trade levels, and that their non- defense-pact counterparts are not significantly related to trade in

  7. Velvet Creative Alliance

    Index Scriptorium Estoniae

    2007-01-01

    Tallinnas Niine t. 11 asuva disainibüroo Velvet Creative Alliance sisekujundus, mille eest sisearhitekt Taavi Aunre (Boom) pälvis Eesti Sisearhitektide Liidu 2006. a. büroointerjööri preemia. Osa mööblist on valmistatud T. Aunre jooniste järgi. Graafilise disaini osa kavandas disainibüroo ise. T. Aunrest, tema tähtsamad tööd. Plaan, 9 värv. vaadet, foto T. Aunrest

  8. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  9. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  10. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  11. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  12. Interpartner Legitimacy in the Alliance Development Process

    DEFF Research Database (Denmark)

    Kumar, Rajesh; Das, T.K.

    2007-01-01

    We propose a framework to understand interpartner legitimacy in strategic alliances. Interpartner legitimacy is the mutual acknowledgment by the alliance partners that their actions are proper in the developmental processes of the alliance. We argue that interpartner legitimacy is needed...... legitimacy in different alliance types. Finally, we derive propositions for further research, and discuss strategies that alliance managers can adopt to develop interpartner legitimacy....

  13. Building Alliance Capability: Management Techniques for Superior Alliance Performance

    NARCIS (Netherlands)

    J.A.J. Draulans (Johan); A-P. de Man (Ard-Pieter); H.W. Volberda (Henk)

    2003-01-01

    textabstractDespite the fact that they represent a growing element of business strategy, alliances between organisations quite often result in failure. This is partly due to the fact that firms have not built up adequate capabilities to manage alliances. Special management techniques have to be

  14. Building alliance capability : management techniques for superior alliance performance

    NARCIS (Netherlands)

    Draulans, J.; Man, de A.P.; Volberda, H.W.

    2003-01-01

    Despite the fact that they represent a growing element of business strategy, alliances between organisations quite often result in failure. This is partly due to the fact that firms have not built up adequate capabilities to manage alliances. Special management techniques have to be implemented in

  15. SU-D-204-06: Integration of Machine Learning and Bioinformatics Methods to Analyze Genome-Wide Association Study Data for Rectal Bleeding and Erectile Dysfunction Following Radiotherapy in Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Oh, J; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States); Kerns, S [University of Rochester Medical Center, Rochester, NY (United States); Ostrer, H [Albert Einstein College of Medicine, Bronx, NY (United States); Rosenstein, B [Mount Sinai School of Medicine, New York, NY (United States)

    2016-06-15

    Purpose: We investigated whether integration of machine learning and bioinformatics techniques on genome-wide association study (GWAS) data can improve the performance of predictive models in predicting the risk of developing radiation-induced late rectal bleeding and erectile dysfunction in prostate cancer patients. Methods: We analyzed a GWAS dataset generated from 385 prostate cancer patients treated with radiotherapy. Using genotype information from these patients, we designed a machine learning-based predictive model of late radiation-induced toxicities: rectal bleeding and erectile dysfunction. The model building process was performed using 2/3 of samples (training) and the predictive model was tested with 1/3 of samples (validation). To identify important single nucleotide polymorphisms (SNPs), we computed the SNP importance score, resulting from our random forest regression model. We performed gene ontology (GO) enrichment analysis for nearby genes of the important SNPs. Results: After univariate analysis on the training dataset, we filtered out many SNPs with p>0.001, resulting in 749 and 367 SNPs that were used in the model building process for rectal bleeding and erectile dysfunction, respectively. On the validation dataset, our random forest regression model achieved the area under the curve (AUC)=0.70 and 0.62 for rectal bleeding and erectile dysfunction, respectively. We performed GO enrichment analysis for the top 25%, 50%, 75%, and 100% SNPs out of the select SNPs in the univariate analysis. When we used the top 50% SNPs, more plausible biological processes were obtained for both toxicities. An additional test with the top 50% SNPs improved predictive power with AUC=0.71 and 0.65 for rectal bleeding and erectile dysfunction. A better performance was achieved with AUC=0.67 when age and androgen deprivation therapy were added to the model for erectile dysfunction. Conclusion: Our approach that combines machine learning and bioinformatics techniques

  16. SU-D-204-06: Integration of Machine Learning and Bioinformatics Methods to Analyze Genome-Wide Association Study Data for Rectal Bleeding and Erectile Dysfunction Following Radiotherapy in Prostate Cancer

    International Nuclear Information System (INIS)

    Oh, J; Deasy, J; Kerns, S; Ostrer, H; Rosenstein, B

    2016-01-01

    Purpose: We investigated whether integration of machine learning and bioinformatics techniques on genome-wide association study (GWAS) data can improve the performance of predictive models in predicting the risk of developing radiation-induced late rectal bleeding and erectile dysfunction in prostate cancer patients. Methods: We analyzed a GWAS dataset generated from 385 prostate cancer patients treated with radiotherapy. Using genotype information from these patients, we designed a machine learning-based predictive model of late radiation-induced toxicities: rectal bleeding and erectile dysfunction. The model building process was performed using 2/3 of samples (training) and the predictive model was tested with 1/3 of samples (validation). To identify important single nucleotide polymorphisms (SNPs), we computed the SNP importance score, resulting from our random forest regression model. We performed gene ontology (GO) enrichment analysis for nearby genes of the important SNPs. Results: After univariate analysis on the training dataset, we filtered out many SNPs with p>0.001, resulting in 749 and 367 SNPs that were used in the model building process for rectal bleeding and erectile dysfunction, respectively. On the validation dataset, our random forest regression model achieved the area under the curve (AUC)=0.70 and 0.62 for rectal bleeding and erectile dysfunction, respectively. We performed GO enrichment analysis for the top 25%, 50%, 75%, and 100% SNPs out of the select SNPs in the univariate analysis. When we used the top 50% SNPs, more plausible biological processes were obtained for both toxicities. An additional test with the top 50% SNPs improved predictive power with AUC=0.71 and 0.65 for rectal bleeding and erectile dysfunction. A better performance was achieved with AUC=0.67 when age and androgen deprivation therapy were added to the model for erectile dysfunction. Conclusion: Our approach that combines machine learning and bioinformatics techniques

  17. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Understanding organizational change for alliancing

    NARCIS (Netherlands)

    B.M. Keers, Bianca; van Fenema, Paul C.; Zijm, Henk

    2017-01-01

    Purpose: The purpose of this paper is to examine an organization’s operational alignment in the process of alliance formation. Design/methodology/approach: A literature study was conducted on the strategic importance of assessing and aligning organizations’ operations for alliancing. Furthermore, an

  19. Crafting successful strategic technology alliances

    NARCIS (Netherlands)

    Duysters, G.M.; Kok, G.; Vaandrager, M.

    1999-01-01

    Despite the trend towards an increasing use of strategic technology alliances, mortality rates of cooperative agreements have always been extremely high. In this paper we argue that rapid economic and technological developments have overthrown traditional thinking about alliances and that firms

  20. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  1. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  2. Strategic alliances and market risk.

    Science.gov (United States)

    Havenaar, Matthias; Hiscocks, Peter

    2012-08-01

    Strategic alliances in product development and marketing are crucial to the biotechnology industry. Many alliances, however, are terminated before the drug reaches the market. In this article we make the case that strategic alliances can fail because of how they are negotiated. Alliance contracts are often inflexible and do not allow for changes in market conditions. We propose a model for contract valuation that can assist biotech and/or pharma deal makers in negotiating alliances that have a higher chance of survival in uncertain market conditions. The model makes use of variable royalties and milestone payments. Because licensing is key to the biotech and/or pharma business model this article will be of interest not only to professionals in licensing, but to all professionals active in the industry. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Association of mRNA expression of TP53 and the TP53 codon 72 Arg/Pro gene polymorphism with colorectal cancer risk in Asian population: a bioinformatics analysis and meta-analysis.

    Science.gov (United States)

    Dong, Zhiyong; Zheng, Longzhi; Liu, Weimin; Wang, Cunchuan

    2018-01-01

    The relationship between TP53 codon 72 Pro/Arg gene polymorphism and colorectal cancer risk in Asians is still controversial, and this bioinformatics analysis and meta-analysis was performed to assess the associations. The association studies were identified from PubMed, and eligible reports were included. RevMan 5.3.1 software, Oncolnc, cBioPortal, and Oncomine online tools were used for statistical analysis. A random/fixed effects model was used in meta-analysis. The data were reported as risk ratios or mean differences with corresponding 95% CI. We confirmed that TP53 was associated with colorectal cancer, the alteration frequency of TP53 was 53% mutation and 7% deep deletion, and TP53 mRNA expression was different in different types of colorectal cancer based on The Cancer Genome Atlas database. Then, 18 studies were included that examine the association of TP53 codon 72 gene polymorphism with colorectal cancer risk in Asians. The meta-analysis indicated that TP53 Pro allele and Pro/Pro genotype were associated with colorectal cancer risk in Asian population, but Arg/Arg genotype was not (Pro allele: odds ratios [OR]=1.20, 95% CI: 1.06 to 1.35, P =0.003; Pro/Pro genotype: OR=1.39, 95% CI: 1.15 to 1.69, P =0.0007; Arg/Arg genotype: OR=0.86, 95% CI: 0.74 to 1.00, P =0.05). Interestingly, in the meta-analysis of the controls from the population-based studies, we found that TP53 codon 72 Pro/Arg gene polymorphism was associated with colorectal cancer risk (Pro allele: OR=1.33, 95% CI: 1.15 to 1.55, P =0.0002; Pro/Pro genotype: OR=1.61, 95% CI: 1.28 to 2.02, P colorectal cancer, but the different value levels of mRNA expression were not associated with survival rate of colon and rectal cancer. TP53 Pro allele and Pro/Pro genotype were associated with colorectal cancer risk in Asians.

  4. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  5. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  6. The Research Data Alliance

    Science.gov (United States)

    Fontaine, K. S.

    2015-12-01

    The Research Data Alliance (RDA) is an international organization created in 2012 to provide researchers with a forum for identifying and removing barriers to data sharing. Since then, RDA has gained over 3000 individual members, over three dozen organizational members, 47 Interest Groups, and 17 Working Groups, all focused on research data sharing. Interoperability is one instantiation of data sharing, but is not the only barrier to overcome. Technology limitations, discipline-specific cultures that do not support sharing, lack of best-practices, or lack of good definitions, are only three of a long list of situations preventing researchers from sharing their data. This presentation will cover how RDA has grown, some details on how the first eight solutions contribute to interoperability and sharing, and a sneak peek at what's in the pipeline.

  7. Therapeutic Alliance in Telephone-Administered Cognitive-Behavioral Therapy for Hematopoietic Stem Cell Transplant Survivors

    Science.gov (United States)

    Applebaum, Allison J.; DuHamel, Katherine N.; Winkel, Gary; Rini, Christine; Greene, Paul B.; Mosher, Catherine E.; Redd, William H.

    2012-01-01

    Objective: A strong therapeutic alliance has been found to predict psychotherapeutic treatment success across a variety of therapeutic modalities and patient populations. However, only a few studies have examined therapeutic alliance as a predictor of psychotherapy outcome among cancer survivors, and none have examined this relation in…

  8. Clinical value and potential pathways of miR-183-5p in bladder cancer: A study based on miRNA-seq data and bioinformatics analysis.

    Science.gov (United States)

    Gao, Jia-Min; Huang, Lin-Zhen; Huang, Zhi-Guang; He, Rong-Quan

    2018-04-01

    The clinicopathological value and exploration of the potential molecular mechanism of microRNA-183-5p (miR-183-5p) have been investigated in various cancers; however, to the best of the author's knowledge, no similar research has been reported for bladder cancer. In the present study, it was revealed that the expression level of miR-183-5p was notably increased in bladder cancer tissues compared with adjacent non-cancerous tissues (P=0.001) and was markedly increased in the tissue samples of papillary, pathological T stage (T0-T2) and pathological stage (I-II) compared with tissue samples of their counterparts (P=0.05), according to data from The Cancer Genome Atlas. Receiver operating characteristic analysis revealed the robust diagnostic value of miR-183-5p for distinguishing bladder cancer from non-cancerous bladder tissues (area under curve=0.948; 95% confidence interval: 0.919-0.977). Amplification and deep deletion of miR-183-5p were indicated by cBioPortal, accounting for 1% (4/412) of bladder cancer cases. Data from YM500v3 demonstrated that compared with other cancers, bladder cancer exhibited high expression levels of miR-183-5p, and miR-183-5p expression in primary solid tumors was much higher compared with solid normal tissues. A meta-analysis indicated that miR-183-5p was more highly expressed in bladder cancer samples compared with normal counterparts. A total of 88 potential target genes of miR-183-5p were identified, 13 of which were discerned as hub genes by protein-protein interaction. The epithelial-to-mesenchymal transition pathway was the most significantly enriched pathway by FunRich (P=0.0001). In summary, miR-183-5p may participate in the tumorigenesis and development of bladder cancer via certain signaling pathways, particularly the epithelial-to-mesenchymal transition pathway. However, the exact molecular mechanism of miR-183-5p in bladder cancer must be validated by in vitro and in vivo experiments.

  9. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  10. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  11. The evolution of alliance capabilities

    NARCIS (Netherlands)

    Heimeriks, K.H.; Duysters, G.M.; Vanhaverbeke, W.P.M.

    2004-01-01

    This paper assesses the effectiveness and differential performance effects of learning mechanisms on the evolution of alliance capabilities. Relying on the concept of capability lifecycles, prior research has suggested that different capability levels could be identified in which different

  12. Depression and Bipolar Support Alliance

    Science.gov (United States)

    Depression and Bipolar Support Alliance Crisis Hotline Information Coping with a Crisis Suicide Prevention Information Psychiatric Hospitalization ... sign-up Education info, training, events Mood Disorders Depression Bipolar Disorder Anxiety Screening Center Co-occurring Illnesses/ ...

  13. TinyOS Alliance Structure

    DEFF Research Database (Denmark)

    Bonnet, Philippe; Culler, David; Estrin, Deborah

    2006-01-01

    This memo describes the goals and organization structure of the TinyOS Alliance. It covers membership, the working group forums for contribution, intellectual property, source licensing, and the TinyOS Steering Committee (TSC)....

  14. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  15. Western Nuclear Science Alliance

    International Nuclear Information System (INIS)

    Reese, Steve; Miller, George; Frantz, Stephen; Beller, Denis; Morse, Ed; Krahenbuhl, Melinda; Flocchini, Bob; Elliston, Jim

    2010-01-01

    The Western Nuclear Science Alliance (WNSA) was formed at Oregon State University (OSU) under the DOE Innovations in Nuclear Infrastructure and Education (INIE) program in 2002. The primary objective of the INIE program is to strengthen nuclear science and engineering programs at the member institutions and to address the long term goal of the University Reactor Infrastructure and Education Assistance Program. WNSA has been very effective in meeting these goals. The infrastructure at several of the WNSA university nuclear reactors has been upgraded significantly, as have classroom and laboratory facilities for Nuclear Engineering, Health Physics, and Radiochemistry students and faculty. Major nuclear-related education programs have been inaugurated, including considerable assistance by WNSA universities to other university nuclear programs. Research has also been enhanced under WNSA, as has outreach to pre-college and college students and faculty. The INIE program under WNSA has been an exceptional boost to the nuclear programs at the eight funded WNSA universities. In subsequent years under INIE these programs have expanded even further in terms of new research facilities, research reactor renovations, expanded educational opportunities, and extended cooperation and collaboration between universities, national laboratories, and nuclear utilities.

  16. A calculating alliance.

    Science.gov (United States)

    Alanis, M; Sippel, S

    1999-01-01

    This article discusses the effects of the alliance between the Church and the Argentine state on women's reproductive rights. Several commentators have criticized how President Carlos Menem used the campaign against abortion for his own political interest. He issued a presidential decree on antiabortion campaign--the Day of the Unborn Child. This decree was announced on December 8, 1998, and the day of observance is March 25 of every coming year. Although the Argentine government does not have a law that explicitly regulates family planning method for the last two decades, many Argentines find the action of the president selfish. The initiation of this presidential decree was the culmination of Menem's manipulation of church and state to secure clerical support for his political regime. Even if statistics is providing him with data concerning the effects of unclear reproductive health laws, he and the church still has chosen not to focus on reproductive rights exclusively, but have concerned themselves primarily with other social and economic issues. While Menem uses the Vatican's pro-life rhetoric and his presidential power to protect fetal life, Argentines will have to contend with the existing Menem policies, which compromise the health of women and children.

  17. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  18. Expression profile analysis of long noncoding RNA in HER-2-enriched subtype breast cancer by next-generation sequencing and bioinformatics

    Directory of Open Access Journals (Sweden)

    Yang F

    2016-02-01

    Full Text Available Fan Yang, Shixu Lyu, Siyang Dong, Yehuan Liu, Xiaohua Zhang, Ouchen Wang Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China Background: Human epidermal growth factor receptor 2 (HER-2-enriched subtype breast cancer is associated with a more aggressive phenotype and shorter survival time. Long noncoding RNAs (LncRNAs have essential roles in tumorigenesis and occupy a central place in cancer progression. Notably, few studies have focused on the dysregulation of LncRNAs in the HER-2-enriched subtype breast cancer. In this study, we analyzed the expression profile of LncRNAs and mRNAs in this particular subtype of breast cancer. Methods: Seven pairs of HER-2-enriched subtype breast cancer and normal tissue were sequenced. We screened out differently expressed genes and measured the correlation of the expression levels of dysregulated LncRNAs and HER-2 by Pearson’s correlation coefficient analysis. Gene ontology analysis and pathway analysis were used to understand the biological roles of these differently expressed genes. Pathway act network and coexpression network were constructed. Results: More than 1,300 LncRNAs and 2,800 mRNAs, which were significantly differently expressed, were identified. Among these LncRNAs, AFAP1-AS1 was the most dysregulated LncRNA, while ORM2 was the most dysregulated mRNA. LOC100288637 had the highest positive correlation coefficient of 0.93 with HER-2, while RPL13P5 had the highest negative correlation coefficient of -0.87. The pathway act network showed that MAPK signaling pathway, PI3K-Akt signaling pathway, metabolic pathways, cell cycle, and regulation of actin cytoskeleton were highly related with HER-2-enriched subtype breast cancer. Coexpression network recognized LINC00636, LINC01405, ADARB2-AS1, ST8SIA6-AS1, LINC00511, and DPP10-AS1 as core genes. Conclusion: These results analyze the functions of LncRNAs and provide

  19. Differential effects of selective frankincense (Ru Xiang) essential oil versus non-selective sandalwood (Tan Xiang) essential oil on cultured bladder cancer cells: a microarray and bioinformatics study

    Science.gov (United States)

    2014-01-01

    Background Frankincense (Boswellia carterii, known as Ru Xiang in Chinese) and sandalwood (Santalum album, known as Tan Xiang in Chinese) are cancer preventive and therapeutic agents in Chinese medicine. Their biologically active ingredients are usually extracted from frankincense by hydrodistillation and sandalwood by distillation. This study aims to investigate the anti-proliferative and pro-apoptotic activities of frankincense and sandalwood essential oils in cultured human bladder cancer cells. Methods The effects of frankincense (1,400–600 dilutions) (v/v) and sandalwood (16,000–7,000 dilutions) (v/v) essential oils on cell viability were studied in established human bladder cancer J82 cells and immortalized normal human bladder urothelial UROtsa cells using a colorimetric XTT cell viability assay. Genes that responded to essential oil treatments in human bladder cancer J82 cells were identified using the Illumina Expression BeadChip platform and analyzed for enriched functions and pathways. The chemical compositions of the essential oils were determined by gas chromatography–mass spectrometry. Results Human bladder cancer J82 cells were more sensitive to the pro-apoptotic effects of frankincense essential oil than the immortalized normal bladder UROtsa cells. In contrast, sandalwood essential oil exhibited a similar potency in suppressing the viability of both J82 and UROtsa cells. Although frankincense and sandalwood essential oils activated common pathways such as inflammatory interleukins (IL-6 signaling), each essential oil had a unique molecular action on the bladder cancer cells. Heat shock proteins and histone core proteins were activated by frankincense essential oil, whereas negative regulation of protein kinase activity and G protein-coupled receptors were activated by sandalwood essential oil treatment. Conclusion The effects of frankincense and sandalwood essential oils on J82 cells and UROtsa cells involved different mechanisms leading to

  20. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...

  1. Knowledge acquisition and complementary specialization in alliances : The impact of technological overlap and alliance experience

    NARCIS (Netherlands)

    Kavusan, Korcan; Noorderhaven, Niels G.; Duysters, Geert M.

    2016-01-01

    While alliances are widely acknowledged to facilitate knowledge transfers across firms, alliances also allow partnering firms to combine technological capabilities toward joint innovation outcomes through complementary specialization. We examine how technological overlap and alliance experience -

  2. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  3. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  4. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  5. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  6. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  7. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  8. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  9. Your alliances are too stable.

    Science.gov (United States)

    Ernst, David; Bamford, James

    2005-06-01

    A 2004 McKinsey survey of more than 30 companies reveals that at least 70% of them have major alliances that are underperforming and in need of restructuring. Moreover, JVs that broaden or otherwise adjust their scope have a 79% success rate, versus 33% for ventures that remain essentially unchanged. Yet most firms don't routinely evaluate the need to overhaul their alliances or intervene to correct performance problems. That means corporations are missing huge opportunities: By revamping just one large alliance, a company can generate 100 million dololars to 300 million dollars in extra income a year. Here's how to unlock more value from alliances: (1) Launch the process. Don't wait until your venture is in the middle of a crisis; regularly scan your major alliances to determine which need restructuring. Once you've targeted one, designate a restructuring team and find a senior sponsor to push the process along. Then delineate the scope of the team's work. (2) Diagnose performance. Evaluate the venture on the following performance dimensions: ownership and financials, strategy, operations, governance, and organization and talent. Identify the root causes of the venture's problems, not just the symptoms, and estimate how much each problem is costing the company. (3) Generate restructuring options. Based on the diagnosis, decide whether to fix, grow, or exit the alliance. Assuming the answer is fix or grow, determine whether fundamental or incremental changes are needed, using the five performance dimensions above as a framework. Then assemble three or four packages of restructuring options, test them with shareholders, and gain parents' approval. (4) Execute the changes. Embark on a widespread and consistent communication effort, building support among executives in the JV and the parent companies. So the process stays on track, assign accountability to certain groups or individuals.

  10. Strategic alliances : Alliance contracting and trust in an evolutionary perspective

    NARCIS (Netherlands)

    Gerard Berendsen; Ineke Pieters; Ben Alders

    2009-01-01

    In this paper we will identify the contract dimensions of alliance contracts directed at joint development of new products or services. We will determine to what extent these contract dimensions are adaptable to future needs and insights. We will also provide insight into the contingency of these

  11. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  12. Learning and specialization in strategic alliances

    NARCIS (Netherlands)

    Kavusan, K.; Noorderhaven, Niels; Duijsters, Geert

    2017-01-01

    We explore the conditions enabling partners in strategic alliances to acquire valuable technological knowledge from each other, and to specialize in complementary areas. Our findings show that knowledge acquisition across alliance partners is maximized when the technological knowledge bases of

  13. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  14. The evidence base for successful alliancing

    OpenAIRE

    Hutchinson, Linda; Spalburg, Nadine

    2016-01-01

    Introduction: There is increasing recognition that collaborative and integrated working is needed to meet the challenges faced in UK health and care and other public funded services. Alliances and alliance contracts have generated interest as a possible tool that commissioners can use to drive collaboration. There are examples in healthcare from New Zealand and recent alliance developments in services in England.In adopting alliance methodologies for the context of public sector commissioning...

  15. The Relationship between Supervisee Stress, Coping Resources, the Working Alliance, and the Supervisory Working Alliance

    Science.gov (United States)

    Gnilka, Philip B.; Chang, Catherine Y.; Dew, Brian J.

    2012-01-01

    The authors examined the relationship of perceived stress, specific types of coping resources, the working alliance, and the supervisory working alliance among 232 counselor supervisees. The working alliance and the supervisory working alliance were negatively related to perceived stress and positively related to multiple coping resources. Two…

  16. Working Alliances in College Classrooms

    Science.gov (United States)

    Meyers, Steven A.

    2008-01-01

    I explain how professors can establish working alliances with students to cultivate a climate conducive to learning. This process involves (a) attending to the emotional bonds that exist in the college classroom, (b) developing shared educational goals and tasks to promote a common sense of purpose, and (c) addressing classroom conflict to repair…

  17. Novozymes-Monsanto bioag alliance

    DEFF Research Database (Denmark)

    Hansen, Henning Otte

    2017-01-01

    er begge drevet af globale udfordringer med hensyn til den fremtidige fødevaresituation og -forsyning. På imagefronten er der dog tale om meget forskellige virksomheder, hvilket dog ikke ser ud til at have været afgørende. Begge partnere har individuelle styrker og svagheder i alliance...

  18. Strategic technology alliance termination : an empirical investigation

    NARCIS (Netherlands)

    Sadowski, B.M.; Duysters, G.M.

    2008-01-01

    There is growing consensus that overall alliance termination rates are high. However, despite this track record of termination and despite unsurpassed growth rates of strategic technology alliances, little is known about the reasons for their termination. Typically strategic alliances have been

  19. Alliances and Bisection Width for Planar Graphs

    DEFF Research Database (Denmark)

    Olsen, Martin; Revsbæk, Morten

    2013-01-01

    An alliance in a graph is a set of vertices (allies) such that each vertex in the alliance has at least as many allies (counting the vertex itself) as non-allies in its neighborhood of the graph. We show that any planar graph with minimum degree at least 4 can be split into two alliances in polyn...

  20. Bioinformatics functional analysis of let-7a, miR-34a, and miR-199a/b reveals novel insights into immune system pathways and cancer hallmarks for hepatocellular carcinoma.

    Science.gov (United States)

    Soliman, Bangly; Salem, Ahmed; Ghazy, Mohamed; Abu-Shahba, Nourhan; El Hefnawi, Mahmoud

    2018-05-01

    Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression. There were 87 common target messenger RNAs (p ≤ 0.05) that were predicted to be regulated by the three micro-RNAs using miRror 2.0 target prediction tool. In addition, the functional enrichment analysis of these targets that was performed by DAVID functional annotation and REACTOME tools revealed two major immune-related pathways, eight hepatocellular carcinoma hallmarks-linked pathways, and two pathways that mediate interconnected processes between immune system and hepatocellular carcinoma hallmarks. Moreover, protein-protein interaction network for the predicted common targets was obtained by using STRING database. The individual analysis of target genes and pathways for the three micro-RNAs of interest using miRGator V3.0 and GeneTrail servers revealed some novel predicted target oncogenes such as SOX4, which we validated experimentally, in addition to some regulated pathways of immune system and hepatocarcinogenesis such as insulin signaling pathway and adipocytokine signaling pathway. In general, our results demonstrate that let-7a, miR-34a, and miR-199 a/b have novel interactions in different immune system pathways and major hepatocellular carcinoma hallmarks. Thus, our findings shed more light on the roles of these miRNAs as cancer silencers.

  1. Strategic Alliance Development - A Process Model A Case Study Integrating Elements of Strategic Alliances

    OpenAIRE

    Mohd Yunos, Mohd Bulkiah

    2007-01-01

    There has been enormous increase in the formation of strategic alliance and the research efforts devoted to understanding alliance development process over the last few decades. However, the critical elements that influence the each stage of alliance development are yet unexplored. This dissertation aims to fill this gap and to supplement it by introducing an integrated process model of strategic alliance development and its critical elements. The process model for strategic alliance developm...

  2. DETERMINING INTERNATIONAL STRATEGIC ALLIANCE PER-FORMANCE

    OpenAIRE

    Nielsen, Bo Bernhard

    2002-01-01

    This paper considers the relationship between subjective measures of international al-liance performance and a set of variables, which may act as predictors of success before the alliance is formed (pre-alliance formation factors), and a set of variables which emerge during the operation of the alliance (post-alliance formation factors). The empiri-cal study, based on a web-survey, investigates a sample of Danish partner firms engaged in 48 equity joint ventures and 70 non-equity joint ventur...

  3. A double-blind, placebo-controlled randomized trial of creatine for the cancer anorexia/weight loss syndrome (N02C4): an Alliance trial.

    Science.gov (United States)

    Jatoi, A; Steen, P D; Atherton, P J; Moore, D F; Rowland, K M; Le-Lindqwister, N A; Adonizio, C S; Jaslowski, A J; Sloan, J; Loprinzi, C

    2017-08-01

    Multiple pilot studies, including one in colorectal cancer patients, suggest that creatine, an amino acid derivative, augments muscle, improves strength, and thereby could palliate the cancer anorexia/weight loss syndrome. In this randomized, double-blind, placebo-controlled trial, incurable patients with this syndrome were assigned creatine (20 g/day load×5 days followed by 2 g/day orally) versus identical placebo. Patients were weighed once a week for 1 month and then monthly. Patients were also assessed over 1 month for appetite and quality of life (validated questionnaires), fist grip strength, body composition (bioelectrical impedance), and adverse events. The primary endpoint was 10% or greater weight gain from baseline during the first month. Within this combined cohort of 263 evaluable patients (134 received creatine and 129 placebo), only 3 gained ≥10% of their baseline weight by 1 month: two creatine-treated and the other placebo-exposed (P = 1.00). Questionnaire data on appetite, quality of life, and activities of daily living showed no statistically significant differences between groups. Similarly, no statistically significant differences between groups were observed for fist-grip strength or body composition. Rates and severity of adverse events were comparable between groups. Finally, a median survival of 230 and 239 days were observed in the creatine and placebo groups, respectively (P = 0.70). Creatine, as prescribed in this trial, had no effect on the cancer anorexia/weight loss syndrome. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  4. MicroRNA-671-3p inhibits the development of breast cancer: A study based on in vitro experiments, in-house quantitative polymerase chain reaction and bioinformatics analysis

    Science.gov (United States)

    He, Rong-Quan; Lan, Ai-Hua; Zhong, Jin-Cai; Chen, Gang; Feng, Zhen-Bo; Wei, Kang-Lai

    2018-01-01

    MicroRNAs (miRNAs or miRs) are highly conserved small noncoding RNA molecules involved in gene regulation. An increasing number of studies have demonstrated that miRNAs act as oncogenes or antioncogenes in various types of cancer, including breast cancer (BC). However, the exact role of miR-671-3p in BC has not yet been reported. In the present study, in vitro experiments were implemented to explore the effects of miR-671-3p on the proliferation and apoptosis of BC cells, and reverse transcription-quantitative polymerase chain reaction was conducted using in-house clinical BC samples to address the expression level and clinical value of miR-671-3p in BC. Simultaneously, miR-671-3p target genes were collected, and subsequent bioinformatics analyses were executed to probe the potential signaling pathway through which miR-671-3p influenced the occurrence and progression of BC. According to the results, the expression level of miR-671-3p was lower in BC tissues compared with that in adjacent non-tumorous tissues (P=0.048), and the area under the curve was 0.697 (95% confidence interval=0.538-0.856), with a sensitivity and specificity of 0.818 and 0.579, respectively. Forced miR-671-3p expression in the BC cell line MDA-MB-231 evidently arrested cell proliferation and induced cell apoptosis. Furthermore, in silico enrichment analyses suggested that miR-671-3p may be involved in the initiation and progression of BC through the targeting of genes associated with the Wnt signaling pathway. In conclusion, the present study findings suggested that miR-671-3p may function as a tumor suppressor in BC by influencing the Wnt signaling cascade, which provides a prospective molecular target for the therapy of BC. PMID:29620195

  5. Strategic alliances in engineering, technology and development

    International Nuclear Information System (INIS)

    Jazrawi, W.

    1991-01-01

    The role of strategic alliances in the development of heavy oil resources, both mineable and in-situ, is discussed. A strategic alliance is defined as a custom designed, long term collaborative working arrangement between two parties to pool, exchange, and integrate their resources to maximize mutual gain. A combination of one or more of the following success factors is seen as contributing to the unlocking of static heavy oil resources: sufficiently high and sustained crude oil prices; strategic intent to pursue heavy oil development regardless of short-term setbacks or economic downturns; technology breakthroughs that can reduce bitumen supply and upgrading costs; and strategic alliances. An idealized model for strategic alliances designed to help develop heavy oil resources is illustrated. The advantages and pitfalls involved in strategic alliances are listed along with the characteristics of viable contract agreements for such alliances. Some examples of strategic alliances in engineering and technology development are presented from Alberta experience. 2 figs., 1 tab

  6. Detection of Occult Micrometastases in Patients With Clinical Stage I Non-Small-Cell Lung Cancer: A Prospective Analysis of Mature Results of CALGB 9761 (Alliance).

    Science.gov (United States)

    Martin, Linda W; D'Cunha, Jonathan; Wang, Xiaofei; Herzan, Debra; Gu, Lin; Abraham, Naif; Demmy, Todd L; Detterbeck, Frank C; Groth, Shawn S; Harpole, David H; Krasna, Mark J; Kernstine, Kemp; Kohman, Leslie J; Patterson, G Alexander; Sugarbaker, David J; Vollmer, Robin T; Maddaus, Michael A; Kratzke, Robert A

    2016-05-01

    Outcomes after resection of stage I non-small-cell lung cancer (NSCLC) are variable, potentially due to undetected occult micrometastases (OM). Cancer and Leukemia Group B 9761 was a prospectively designed study aimed at determining the prognostic significance of OM. Between 1997 and 2002, 502 patients with suspected clinical stage I (T1-2N0M0) NSCLC were prospectively enrolled at 11 institutions. Primary tumor and lymph nodes (LNs) were collected and sent to a central site for molecular analysis. Both were assayed for OM using immunohistochemistry (IHC) for cytokeratin (AE1/AE3) and real-time reverse transcriptase polymerase chain reaction (RT-PCR) for carcinoembryonic antigen. Four hundred eighty-nine of the 502 enrolled patients underwent complete surgical staging. Three hundred four patients (61%) had pathologic stage I NSCLC (T1, 58%; T2, 42%) and were included in the final analysis. Fifty-six percent had adenocarcinomas, 34% had squamous cell carcinomas, and 10% had another histology. LNs from 298 patients were analyzed by IHC; 41 (14%) were IHC-positive (42% in N1 position, 58% in N2 position). Neither overall survival (OS) nor disease-free survival was associated with IHC positivity; however, patients who had IHC-positive N2 LNs had statistically significantly worse survival rates (hazard ratio, 2.04, P = .017). LNs from 256 patients were analyzed by RT-PCR; 176 (69%) were PCR-positive (52% in N1 position, 48% in N2 position). Neither OS nor disease-free survival was associated with PCR positivity. NSCLC tumor markers can be detected in histologically negative LNs by AE1/AE3 IHC and carcinoembryonic antigen RT-PCR. In this prospective, multi-institutional trial, the presence of OM by IHC staining in N2 LNs of patients with NSCLC correlated with decreased OS. The clinical significance of this warrants further investigation. © 2016 by American Society of Clinical Oncology.

  7. Detection of Occult Micrometastases in Patients With Clinical Stage I Non–Small-Cell Lung Cancer: A Prospective Analysis of Mature Results of CALGB 9761 (Alliance)

    Science.gov (United States)

    D’Cunha, Jonathan; Wang, Xiaofei; Herzan, Debra; Gu, Lin; Abraham, Naif; Demmy, Todd L.; Detterbeck, Frank C.; Groth, Shawn S.; Harpole, David H.; Krasna, Mark J.; Kernstine, Kemp; Kohman, Leslie J.; Patterson, G. Alexander; Sugarbaker, David J.; Vollmer, Robin T.; Maddaus, Michael A.; Kratzke, Robert A.

    2016-01-01

    Purpose Outcomes after resection of stage I non–small-cell lung cancer (NSCLC) are variable, potentially due to undetected occult micrometastases (OM). Cancer and Leukemia Group B 9761 was a prospectively designed study aimed at determining the prognostic significance of OM. Materials and Methods Between 1997 and 2002, 502 patients with suspected clinical stage I (T1-2N0M0) NSCLC were prospectively enrolled at 11 institutions. Primary tumor and lymph nodes (LNs) were collected and sent to a central site for molecular analysis. Both were assayed for OM using immunohistochemistry (IHC) for cytokeratin (AE1/AE3) and real-time reverse transcriptase polymerase chain reaction (RT-PCR) for carcinoembryonic antigen. Results Four hundred eighty-nine of the 502 enrolled patients underwent complete surgical staging. Three hundred four patients (61%) had pathologic stage I NSCLC (T1, 58%; T2, 42%) and were included in the final analysis. Fifty-six percent had adenocarcinomas, 34% had squamous cell carcinomas, and 10% had another histology. LNs from 298 patients were analyzed by IHC; 41 (14%) were IHC-positive (42% in N1 position, 58% in N2 position). Neither overall survival (OS) nor disease-free survival was associated with IHC positivity; however, patients who had IHC-positive N2 LNs had statistically significantly worse survival rates (hazard ratio, 2.04, P = .017). LNs from 256 patients were analyzed by RT-PCR; 176 (69%) were PCR-positive (52% in N1 position, 48% in N2 position). Neither OS nor disease-free survival was associated with PCR positivity. Conclusion NSCLC tumor markers can be detected in histologically negative LNs by AE1/AE3 IHC and carcinoembryonic antigen RT-PCR. In this prospective, multi-institutional trial, the presence of OM by IHC staining in N2 LNs of patients with NSCLC correlated with decreased OS. The clinical significance of this warrants further investigation. PMID:26926677

  8. Heartland Alliance for Regional Transmission

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Nancy [Climate and Energy Project, Inc., Hutchinson, KS (United States)

    2017-03-15

    The Heartland Alliance for Regional Transmission (HART) will foster a candid, productive conversation among stakeholders that identifies challenges to and benefits from a massive build out of wind generation and transmission across the Southwest Power Pool. Based on the outcomes of those deliberations, HART will develop and deliver an ambitious, coordinated, peer-to-peer outreach effort that spans the SPP to improve market acceptance for wind.

  9. Hsa-microRNA-181a is a regulator of a number of cancer genes and a biomarker for endometrial carcinoma in patients: a bioinformatic and clinical study and the therapeutic implication

    Directory of Open Access Journals (Sweden)

    He S

    2015-02-01

    Full Text Available Shuming He,1 Shumei Zeng,1 Zhi-Wei Zhou,2,3 Zhi-Xu He,3 Shu-Feng Zhou2,3 1Department of Obstetrics and Gynecology, Xiaolan People’s Hospital affiliated to Southern Medical University, Zhongshan, Guangdong, People’s Republic of China; 2Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA; 3Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center and Sino-US Joint Laboratory for Medical Sciences, Guiyang Medical University, Guiyang, Guizhou, People’s Republic of China Abstract: The aberrant expression of human microRNA-181a-1 (hsa-miR-181a has been implicated in the pathogenesis of various cancers, serving as an oncogene or a tumor suppressor. However, the role of hsa-miR-181a in the pathogenesis of endometrial carcinoma (EC and its clinical significance are unclear. This study aimed to search for the molecular targets of hsa-miR-181a using bioinformatic tools and then determine the expression levels of hsa-miR-181a in normal, hyperplasia, and EC samples from humans. To predict the targets of hsa-miR-181a, ten different algorithms were used, including miRanda-mirSVR, DIANA microT v5.0, miRDB, RNA22 v2, TargetMiner, TargetScan 6.2, PicTar, MicroCosm Targets v5, and miRWALK. Two algorithms, TarBase 6.0 and miRTarBase, were used to identify the validated targets of hsa-miR-181a-5p (a mature product of hsa-miR-181a, and the web-based Database for Annotation, Visualization and Integrated ­Discovery (DAVID 6.7 was used to provide biological functional interpretation of the validated targets of hsa-miR-181a-5p. A total of 78 formalin-fixed, paraffin-embedded tissue specimens from 65 patients and 13 healthy subjects were collected and examined, including normal endometrium (n=13, endometrial hyperplasia (n=18, and EC (37 type I and 10 type II EC cases. Our bioinformatic studies have showed that hsa-miR-181a might regulate a large number of

  10. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  11. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  12. Analysis of participant factors that affect the diagnostic performance of screening mammography: A report of the alliance for breast cancer screening in Korea

    International Nuclear Information System (INIS)

    Kim, Young Joong; Lee, Eu Hye

    2017-01-01

    To analyze participant factors that affect the diagnostic performance of screening mammography. We enrolled 128756 cases from 10 hospitals between 2005 and 2010. We analyzed recall rate, cancer detection rate (CDR) per 1000 examinations, positive predictive value (PPV), sensitivity, specificity, false positive rate (FPR), and interval cancer rate (ICR) per 1000 negative examinations according to participant factors including age, breast density, and number of visit to the same institution, and adjusted for confounding variables. Increasing age improved recall rates (27.4% in 40's, 17.5% in 50's, 11.1% in 60's, and 8.6% in 70's), CDR (2.7, 3.2, 2.0, and 2.4), PPV (1.0, 1.8, 1.8, and 2.8%), sensitivity (81.3, 88.8, 90.3, and 94.7%), specificity (72.7, 82.7, 89.0, and 91.7%), and FPR (27.3, 17.3, 11.0, and 8.4%) (p < 0.05). Higher breast density impaired recall rates (4.0% in P1, 9.0% in P2, 28.9% in P3, and 27.8% in P4), PPV (3.3, 2.3, 1.2, and 1.3%), specificity (96.1, 91.2, 71.4, and 72.5%), and FPR (3.9, 8.9, 28.6, and 27.6%) (p < 0.001). It also increased CDR (1.3, 2.1, 3.3, and 3.6) and ICR (0.2, 0.3, 0.6, and 1.6) (p < 0.05). Successive visits to the same institution improved recall rates (20.9% for one visit, 10.7% for two visits, 7.7% for more than three visits), PPV (1.6, 2.8, and 2.7%), specificity (79.4, 89.6, and 92.5%), and FPR (20.6, 10.4, and 7.5%) (p < 0.001). Young age and dense breasts negatively affected diagnostic performance in mammography screening, whereas successive visits to the same institution had a positive effect. Examinee education for successive visits to the same institution would improve the diagnostic performance

  13. Analysis of participant factors that affect the diagnostic performance of screening mammography: A report of the alliance for breast cancer screening in Korea

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Joong [Dept. of Radiology, Konyang University Hospital, Konyang University College of Medicine, Daejeon (Korea, Republic of); Lee, Eu Hye [Dept. of Radiology, Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon (Korea, Republic of); and others

    2017-08-01

    To analyze participant factors that affect the diagnostic performance of screening mammography. We enrolled 128756 cases from 10 hospitals between 2005 and 2010. We analyzed recall rate, cancer detection rate (CDR) per 1000 examinations, positive predictive value (PPV), sensitivity, specificity, false positive rate (FPR), and interval cancer rate (ICR) per 1000 negative examinations according to participant factors including age, breast density, and number of visit to the same institution, and adjusted for confounding variables. Increasing age improved recall rates (27.4% in 40's, 17.5% in 50's, 11.1% in 60's, and 8.6% in 70's), CDR (2.7, 3.2, 2.0, and 2.4), PPV (1.0, 1.8, 1.8, and 2.8%), sensitivity (81.3, 88.8, 90.3, and 94.7%), specificity (72.7, 82.7, 89.0, and 91.7%), and FPR (27.3, 17.3, 11.0, and 8.4%) (p < 0.05). Higher breast density impaired recall rates (4.0% in P1, 9.0% in P2, 28.9% in P3, and 27.8% in P4), PPV (3.3, 2.3, 1.2, and 1.3%), specificity (96.1, 91.2, 71.4, and 72.5%), and FPR (3.9, 8.9, 28.6, and 27.6%) (p < 0.001). It also increased CDR (1.3, 2.1, 3.3, and 3.6) and ICR (0.2, 0.3, 0.6, and 1.6) (p < 0.05). Successive visits to the same institution improved recall rates (20.9% for one visit, 10.7% for two visits, 7.7% for more than three visits), PPV (1.6, 2.8, and 2.7%), specificity (79.4, 89.6, and 92.5%), and FPR (20.6, 10.4, and 7.5%) (p < 0.001). Young age and dense breasts negatively affected diagnostic performance in mammography screening, whereas successive visits to the same institution had a positive effect. Examinee education for successive visits to the same institution would improve the diagnostic performance.

  14. Beef alliances: motivations, extent, and future prospects.

    Science.gov (United States)

    Schroeder, Ted C; Kovanda, Joseph

    2003-07-01

    With their growth, it is important to consider how alliances will impact the beef industry in the future. Alliances have the potential to make sweeping changes to cattle production, live and feeder cattle marketing, food safety protocols, use of government grades and standards, ownership structure, supply chain management, wholesale and retail product marketing, risk management, and many other industry activities. In an effort to address these issues, this article addresses the following questions: What is an alliance? What has motivated their proliferation? What have we learned from alliances? What aspects of alliances affect their likelihood of success or failure? What is the future of alliances? Are they a fad or a long-term evolving industry structural change?

  15. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  16. Collaborative Customer Management in Financial Services Alliances

    OpenAIRE

    Geib, Malte; Kolbe, Lutz; Brenner, Walter

    2004-01-01

    The integration of the financial services industry and many financial services companies' focus on core competencies have led to the emergence of financial services alliances. These alliances face a variety of challenges regarding an integrated approach to customer relationship management (CRM) by the partner companies.In this paper we describe the challenges derived from an analysis of five financial services companies that formed different financial services alliances. The main inhibitors o...

  17. Towards a dynamic concept of alliance capability

    OpenAIRE

    SLUYTS, Kim; MARTENS, Rudy; MATTHYSSENS, Paul

    2008-01-01

    This paper has a threefold purpose. First, we offer a literature review on alliance capability based on strategic and competence based management literature. Second, we extend existing literature on alliance capability by breaking this concept down into five sub capabilities, which are each linked to a stage of the alliance life cycle. Finally, we suggest how firms can support these capabilities through structural, technological and people-related tools and techniques. We argue that current l...

  18. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  19. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  20. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  1. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  2. Terra Nova breaks new ground for alliances

    International Nuclear Information System (INIS)

    Ghiselin, D.

    1996-01-01

    This paper reviews the development of alliances to help develop the Terra Nova oil and gas field in the offshore Atlantic areas of Canada. Largely attributed to BP, the strategic alliance concept got its start in the North Sea and on the North Slope of Alaska. BP saw it as the best way to take advantage of economy-of-scale, mitigate risk, and achieve outsourcing goals while retaining their core competencies. This paper reviews the methods of developing the alliances, the developing of a development plan for the Terra Nova field, and how the alliance plans to maximize the profittability of the operation for all involved

  3. A model of strategic marketing alliances for hospices: vertical, internal, osmotic alliances and the complete model.

    Science.gov (United States)

    Starnes, B J; Self, D R

    1999-01-01

    This article develops two previous research efforts. William J. Winston (1994, 1995) has proposed a set of strategies by which health care organizations can benefit from forging strategic alliances. Raadt and Self (1997) have proposed a classification model of alliances including horizontal, vertical, internal, and osmotic. In the second of two articles, this paper presents a model of vertical, internal, and osmotic alliances. Advantages and disadvantages of each are discussed. Finally, the complete alliance system model is presented.

  4. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  5. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  6. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  7. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  8. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  9. Lung Cancer: Glossary

    Science.gov (United States)

    ... professional support team today. Learn More . Find more lung cancer resources. Learn More Donate Today! What is Lung ... to Give How Your Support Helps Events Lung Cancer Awareness © Lung Cancer Alliance. The information presented in this website ...

  10. Cancer Nanotechnology Plan

    Science.gov (United States)

    The Cancer Nanotechnology Plan serves as a strategic document to the NCI Alliance for Nanotechnology in Cancer as well as a guiding document to the cancer nanotechnology and oncology fields, as a whole.

  11. Alliance Concentration in Multinational Companies : Examining Alliance Portfolios, Firm Structure, and Firm Performance

    NARCIS (Netherlands)

    Bos, Brenda; Faems, Dries; Noseleit, Florian

    Research summary: This article explores the distribution of alliances across firms' internal structure. Focusing on multinational companies, we examine the impact of alliance portfolio concentrationi.e., the extent to which alliances are concentrated within a limited number of geographic unitson

  12. Alliance Concentration in Multinational Companies : Examining Alliance Portfolios, Firm Structure, and Firm Performance

    NARCIS (Netherlands)

    Bos, Brenda; Faems, Dries; Noseleit, Florian

    2017-01-01

    Research summary: This article explores the distribution of alliances across firms' internal structure. Focusing on multinational companies, we examine the impact of alliance portfolio concentrationi.e., the extent to which alliances are concentrated within a limited number of geographic unitson

  13. Technology alliances in emerging economies : Persistence and interrelation in European firms’alliance formation

    NARCIS (Netherlands)

    Jacob, J.; Belderbos, R.; Gilsing, V.A.

    2013-01-01

    We analyse the patterns and determinants of technology alliance formation with partner firms from emerging economies with a focus on European firms' alliance strategies. We examine to what extent European firms' alliance formation with partners based in emerging economies is persistent – that is, to

  14. Northeast Waste Management Alliance (NEWMA)

    International Nuclear Information System (INIS)

    Goland, A.N.; Kaplan, E.

    1993-11-01

    Funding was provided to Brookhaven National Laboratory in the fourth quarter of FY93 to establish a regional alliance as defined by Dr. Clyde Frank during his visit to BNL on March 7, 1993. In collaboration with the Long Island Research Institute (LIRI), BNL developed a business plan for the Northeast Waste Management Alliance (NEWMA). Concurrently, informal discussions were initiated with representatives of the waste management industry, and meetings were held with local and state regulatory and governmental personnel to obtain their enthusiasm and involvement. A subcontract to LIRI was written to enable it to formalize interactions with companies offering new waste management technologies selected for their dual value to the DOE and local governments in the Northeast. LIRI was founded to develop and coordinate economic growth via introduction of new technologies. As a not-for-profit institution it is in an ideal position to manage the development of NEWMA through ready access to venture capital and strong interactions with the business community, universities, and BNL. Another subcontract was written with a professor at SUNY/Stony Brook to perform an evaluation of new pyrolitic processes, some of which may be appropriate for development by NEWMA. Independent endorsement of the business plan recently by another organization, GETF, with broad knowledge of DOE/EM-50 objectives, provides a further incentive for moving rapidly to implement the NEWMA strategy. This report describes progress made during the last quarter of FY93

  15. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  16. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  17. Peer Mentoring through eAlliances

    Science.gov (United States)

    Blaha, Cindy; Cunningham, Beth; Cox, Anne; Ramos, Idalia; Whitten, Barbara

    2018-06-01

    Being a woman in astronomy or physics can be a very isolating experience. Peer mentoring has been shown to help combat this isolation. eAlliance, an NSF ADVANCE PLAN-D program hosted by AAPT, is seeking to establish mutual mentoring networks of women faculty within the physics and astronomy community. The eAlliance program will reduce the isolation of participating faculty members and provide support to help members achieve their personal goals and enhance their career development. Participants register at the eAlliance website (ealliance.aapt.org) and complete a personal profile which is used to match them to other registered women faculty with similar mentoring goals. So far, 95 women have registered in the eAlliance database and 22 of the participants are astronomers. Currently the project has five sponsored eAlliances (with 4-5 members each) and several more in the process of forming. As of March 2018, 4 of the 22 sponsored eAlliance members are astronomers. The mentoring cohorts are holding regular electronic meetings and using project funds to support annual face-to-face meetings at national meetings of their own choosing. The first eAlliance Summit Meeting will be held in July 2018 and will bring all the cohorts together to share their peer mentoring experiences and gather advice for future cohorts just starting out. All women faculty in astronomy and physics are invited to join the eAlliance program.

  18. Essays on capability development through alliances

    NARCIS (Netherlands)

    Kavusan, K.

    2015-01-01

    As a result of the surging rate of technological innovation in the last decades, firms in high-technology industries increasingly rely on alliances to tap into external knowledge sources and to develop new products and services. While alliances are of vital importance to many firms to develop new

  19. Project alliancing in the offshore industry

    NARCIS (Netherlands)

    Halman, Johannes I.M.; Braks, B.F.M.

    In this paper the shift towards new types of project organisation within the Offshore Industry is explained and discussed. Special focus is given to the organisational concept of Project Alliancing. The principles, structure and culture of a Project Alliance as applied within the Offshore Industry

  20. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  1. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  2. Towards Alliance Performance Management in Service Logistics

    Directory of Open Access Journals (Sweden)

    Bianca Keers

    2015-04-01

    Full Text Available This study explores the management of stakeholder values for alliance success. A multiple-case study method is used to analyze – within six organizations attempting to form alliances – how the management of inter-organizational dimensions of stakeholder value adds to the success of an alliance business strategy. Our study focuses on the establishment of vertical service alliances within the Dutch maritime sector, including private-private as well as public-private initiatives. The findings point toward the usefulness of developing an inter-organizational success map. Because of its comprehensive multi-stakeholder orientation, a success map can be used by alliance managers to understand management’s considerations, including the trade-offs among an alliance’s various performance drivers. This new conceptual thinking can enhance research and best practices on inter-organizational design.

  3. Project alliancing in the offshore industry

    International Nuclear Information System (INIS)

    Halman, J.I.M.; Braks, B.F.M.

    1999-01-01

    In this paper the shift towards new types of project organisation within the offshore industry is explained and discussed. Special focus is given to the organisational concept of project alliancing. The principles, structure and culture of a project alliance as applied within the offshore industry are described. In the paper the organisational concept of project alliancing is discussed on its potential to reduce project costs and enhance profits, both for the operator (oil and gas company) as well as for participating contractors. A risk and reward mechanism developed to share project risks and rewards between allied parties is explained for an alliance case. Based upon an in-depth study carried out within a contractor company in the offshore industry the organisational and financial implications of project alliancing are presented. (author)

  4. Forging Industry-Academic Alliances

    Directory of Open Access Journals (Sweden)

    Joseph M. Woodside

    2014-08-01

    Full Text Available With ever increasing amounts of data, organizations are identifying the importance of Business Intelligence (BI and Analytics for decision making. However in order to realize the full potential of these technologies, organizations require well-trained and educated management and analytic subject matter experts to transform the data and results into actionable information for decisions. In order to meet this demand for analytical talent, a Center for Business Intelligence and Analytics (CBIA housed within the university seeks to develop knowledge and skills vital in the fast changing field of business, through developing the next generation of managers and analysts with skills in decision-making through use of analytical techniques. This presentation provides the strategic framework for the definition and development of a CBIA and framework for joint academic and industry collaboration to develop the next generation of industry experts. The core components including industry demand, alliance objectives including objectives, curriculum and talent requirements, and opportunities.

  5. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  6. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  7. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  8. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  9. Review and Support of the Relationship between Alliance Competence and Alliance Orientation

    Directory of Open Access Journals (Sweden)

    Gonzalo R. Llanos-Herrera

    2017-11-01

    Full Text Available This paper seeks to contribute to the understanding of the formation of strategic alliances among companies. Specifically, it seeks to understand the relationship between alliance competence (Lambe, Speakman & Hunt, 2002 and alliance orientation (Kandemir, Yaprak & Cavusgil, 2006, following some of the most important guidelines of the leading exponents of theories based on resources and dynamic capabilities. Once the concepts were developed we proceeded to establish a hypothesis that seeks to better understand the relationships between the constructs and how they interact to achieve alliances that are beneficial for the parties involved. In particular, the findings corroborate the proposed relationships, supporting a direct link between market orientation constructs and senior management commitment to the alliances, as well as the commitment of senior management and competencies for alliances. As a fundamental contribution to this work, a mediating role of the alliance orientation construct was also detected between the relationship of senior management commitment and alliance competence. Future research is proposed into the elements of the practical guidelines for alliances and the relationship of this construct with the others related to alliances and particularly to their performance.

  10. Fostering change within organizational participants of multisectoral health care alliances.

    Science.gov (United States)

    Hearld, Larry R; Alexander, Jeffrey A; Mittler, Jessica N

    2012-01-01

    A touted advantage of multisectoral health care alliances is their ability to coordinate diverse constituencies and pursue community health goals in ways that allow them to make greater progress than each constituency could independently. However, participating organizations may have goals that do not entirely overlap or necessarily align with the alliance's goals, which can weaken or undermine an alliance's efforts. Fostering changes within participating organizations in ways that are consistent with the alliance's goals (i.e., alliance-oriented change) may be one mechanism by which alliances can coordinate diverse activities and improve care in their local communities. We examined whether alliance-oriented change within participating organizations is associated with alliance decision-making and conflict management style, level of participation, perceptions of alliance participation benefits and costs, and awareness of alliance activities within participating organizations. The study used two rounds of survey data collected from organizational participants of 14 alliances participating in the Robert Wood Johnson Foundation's Aligning Forces for Quality program. Alliance participants generally reported low levels of alliance-oriented change within their organizations as a result of the alliance and its activities. However, participants reporting higher levels of internal change in response to alliance activities had more positive perceptions of alliance decision-making style, higher levels of participation in alliance activities, more positive perceptions of alliance participation benefits relative to costs, and greater awareness of alliance activities across multiple levels of their respective organizations. Despite relatively low levels of alliance-oriented change within participating organizations, alliances may still have the means to align the goal orientations of a diverse membership and foster change that may extend the reach of the alliance in the community.

  11. Collaborative innovation effort and size in alliances

    DEFF Research Database (Denmark)

    Asikainen, Anna-Leena; Radziwon, Agnieszka

    of organisational and marketing innovations. Additionally, small firms were more likely (than large) to engage into alliances as a part of their strategy. On more general level our data also confirm that factors such as: number of highly educated employees, foreign ownership of a firm and presence of firm......This study presents quantitative investigation of the factors that influence the process of forming strategic alliances with a special focus on the role of innovation strategies and firm’s size in alliance building process. The empirical sample is based on a large scale data from the Community...

  12. Review and Support of the Relationship between Alliance Competence and Alliance Orientation

    OpenAIRE

    Gonzalo R. Llanos-Herrera; Nelson A. Andrade-Valbuena

    2017-01-01

    This paper seeks to contribute to the understanding of the formation of strategic alliances among companies. Specifically, it seeks to understand the relationship between alliance competence (Lambe, Speakman & Hunt, 2002) and alliance orientation (Kandemir, Yaprak & Cavusgil, 2006), following some of the most important guidelines of the leading exponents of theories based on resources and dynamic capabilities. Once the concepts were developed we proceeded to establish a hypothesis that se...

  13. Managing multiple facets of risk in new product alliances

    NARCIS (Netherlands)

    Lee, R.P.; Johnson, J.L.

    2010-01-01

    The trend of forming alliances to develop new products continues; however, many of these new product alliances fail. As such we explore how key risk types intrinsic in new product alliances, performance, relational, and knowledge appropriation risks, influence alliance success. Further, we theorize

  14. Shaping the alliance management agenda: a capability approach

    NARCIS (Netherlands)

    Duysters, G.; Saebi, T.; de Man, A.P.

    2011-01-01

    Over the past years, the topic of alliance capability has captured the attention of numerous alliance scholars. This emerging research stream claims that a main cause for alliance success lies in the partner's individual capability to manage their alliances. This editorial paper reviews the main

  15. Managing strategic alliances in the power generation industry

    DEFF Research Database (Denmark)

    Kumar, Rajesh

    2003-01-01

    Highlights the challenges for power development developers in initiating alliances in the power generation industry. Importance of strategic alliances in the industry; Nature of the alliances in the independent power industry; Strategies for creating and sustaining value in global power development......; Management of tensions inherent in internal and external alliances....

  16. Navigating the changing learning landscape: perspective from bioinformatics.ca

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable...

  17. Creation of a European alliance in radioecology

    International Nuclear Information System (INIS)

    Real, A.; Mora, J. C.; Robles, B.; Cancio, D.

    2011-01-01

    Eight European organizations, including the CIEMAT, have created an Alliance Radioecology, pledging to integrate part of their R and D on a new Strategic Research Agenda, in order to integrate and sustain long-term research in this discipline.

  18. Successful alliances driven by processes, not discounts

    International Nuclear Information System (INIS)

    Brett, J.F.; Craig, V.B.; Pile, K.E.; Wadsworth, D.B.; Brett, K.V.; Aslakson, J.

    1996-01-01

    When alliances are executed properly and partners have a full understanding of true integration, drilling ventures can improve their potential to reduce costs and accelerate production by 12--30%. Many companies enter alliances without a full grasp of the economic potential such a relationship might offer. Many alliances rely too heavily on relationship issues and commercial terms instead of focusing on integrating their technical processes successfully. Process-driven alliance (PDA) is the term adopted by a new Gas Research Institute report prepared by OGCI Management Inc. to represent a fundamentally different way to plan, execute, and evaluate drilling projects. This paper discusses the findings of the GRI study, describing the stability of PDAs, value chain, successful PDAs, changed commercial terms, and characteristics of failure

  19. The Transition from Alliance Networks to Multilateral Alliances in the Global Airline Industry

    Directory of Open Access Journals (Sweden)

    Sergio G. Lazzarini

    2008-01-01

    Full Text Available This study examines conditions in which alliance networks (informal webs of bilateral entanglements between firms may or may not evolve into multilateral alliances (broad, formal multiple-firm arrangements. I offer a theory to explain the formation of multilateral alliances based on both the resource profile and the structure of existing interfirm networks, and provide an initial test of that theory in the context of the global airline industry. Using data from 75 global airlines and their alliances, I propose a methodology to retrieve samples of alliance networks and then use regression analysis to assess how the resource profile and the structure of these networks influence their formalization into multilateral alliances. I find that multilateral alliances are more likely to emerge when alliance networks exhibit high resource diversity and network structure characterized by moderate density and high centralization. Apparently, while highly sparse networks reduce actors’ awareness of their potential joint collaboration, highly dense or embedded networks substitute for the need for formal controls accompanying multilateral agreements. The effect of centralization suggests that the formation of multilateral alliances tends to be triggered by leading actors directly connected to other network members.

  20. Partner Capabilities and Alliance Time Frame: An Analysis of International Strategic Alliances from the CEE

    Directory of Open Access Journals (Sweden)

    S. Hossein Jalali

    2017-01-01

    Full Text Available Partner selecton is one of the most discussed issues in strategic alliances literature. However, the majority of research has typically focused on generic partner characteristcs and presented conceptual models for alliance partner selecton, addressing clan image but only limited pieces of the partner selecton puzzle. Rooted in the resource-based view, this paper suggests that partner selecton is contngent upon the intended tme frame of strategic alliances and presents a new and intensive conceptual framework that examines the appropriate partner capability for strategic alliances, in the case of short/medium-term alliances and long-term ones. Based on empirical evidences from 736 alliances in the CEE region, the fndings stress the differences between varied partner capabilites in short/medium-term and long-term alliances. Accordingly, the signifcance of technological capability increases with the number of year’s alliances endured. Moreover, the importance of market capability decreases signifcantly when alliances last for a longer tme frame.

  1. Clinical Value of miR-101-3p and Biological Analysis of its Prospective Targets in Breast Cancer: A Study Based on The Cancer Genome Atlas (TCGA) and Bioinformatics.

    Science.gov (United States)

    Li, Chun-Yao; Xiong, Dan-Dan; Huang, Chun-Qin; He, Rong-Quan; Liang, Hai-Wei; Pan, Deng-Hua; Wang, Han-Lin; Wang, Yi-Wen; Zhu, Hua-Wei; Chen, Gang

    2017-04-18

    BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified. The potential genes targeted by miR-101-3p were also predicted. Gene Ontology (GO) and pathway and network analyses were constructed for the DEGs and predicted genes. RESULTS In the TCGA data, a low level of miR-101-2 expression might represent a diagnostic (AUC: 0.63) marker, and the miR-101-1 was a prognostic (HR=1.79) marker. MiR-101-1 was linked to the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), and miR-101-2 was associated with the tumor (T), lymph node (N), and metastasis (M) stages of BC. Moreover, 427 genes were selected from the 921 DEGs in GEO and the 7924 potential target genes from the prediction databases. These genes were related to transcription, metabolism, biosynthesis, and proliferation. The results were also significantly enriched in the VEGF, mTOR, focal adhesion, Wnt, and chemokine signaling pathways. CONCLUSIONS MiR-101-1 and miR-101-2 may be prospective biomarkers for the prognosis and diagnosis of BC, respectively, and are associated with diverse clinical parameters. The target genes of miR-101-3p regulate the development and progression of BC. These results provide insight into the pathogenic mechanism and potential therapies for BC.

  2. Strategic Alliances in The Robotics Industry

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Bjørn

    2014-01-01

    The purpose of the master-thesis was to examine how Blue Ocean Robotics can structure its strategic alliances to gain a competitive advantage in the market development of robotics in international markets.......The purpose of the master-thesis was to examine how Blue Ocean Robotics can structure its strategic alliances to gain a competitive advantage in the market development of robotics in international markets....

  3. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  4. When and how to create strategic alliances

    International Nuclear Information System (INIS)

    Reinsvold, C.

    1994-01-01

    As oil prices remain flat and discoveries become more costly, the relationships between suppliers and operators are changing. Arms-length, unit pricing buying practices remain the norm for many buyers, but others have identified advantages of forming alliances that make greater use of the suppliers' capabilities. Recently, operators and the service industry have started to evolve a new culture that provides value-added solutions in an incentive environment. coupled with long-term risk-sharing or partnering arrangements, the potential advantages to both the operator and supplier are clear. An alliance is a long-term commitment between the operator and one or more supplier organizations, formed to achieve well-defined project objectives in a way that is beneficial to all alliance partners. Alliances take many forms and are adapted to meet the needs of the project. Successful alliances are characterized by trust, common goals and open communication. They build on the efficiencies, capabilities and strengths each partner brings to the relationship. The nine steps to creating a successful alliance are described

  5. Key state legislative provisions on purchasing alliances.

    Science.gov (United States)

    Wicks, E K; Curtis, R E; Haugh, K

    1994-01-01

    In order to function effectively in post-reform healthcare markets, behavioral healthcare professionals must understand and interact with health purchasing alliances. Healthcare reform initiatives based upon the principles of managed competition envision an important role for cooperative health purchasing organizations, or "health alliances," that collect premiums and contract with health plans for the provision of comprehensive health services delivered within the framework of a standardized benefit package. Health purchasing alliances have already been implemented in eight states, and this trend is expected to grow. The following article illustrates the structure and authority of the health alliances that are already in operation, and is presented here to give Behavioral Healthcare Tomorrow journal readers an up-to-date overview of reforming healthcare markets. This matrix arrays recent state laws which we identify as clearly including components of managed competition or purchasing alliances. Other states undoubtedly have elements of reform that include some aspects of these concepts. For example, under legislation, a Vermont health care authority was established and, among other things, charged with developing two comprehensive reform proposals, one of which will involve multipayors and the other a single-payor system. Options will likely embody many of the activities of alliances. Vermont is not included in this matrix because these provisions are still in the developmental stage.

  6. Strategic Alliances: the Potential for Russian Nanoindustry

    Directory of Open Access Journals (Sweden)

    Inshakova Elena Ivanovna

    2015-05-01

    Full Text Available Strategic alliances as a form of interfirm cooperation (including international cooperation increase the potential of solving large-scale problems of national nanoindustry development, providing synergy of participants resources united by the principle of complementarity and substitution in the process of joint implementation of complex R&D programs, mobilization and input of significant financial, material, technical and intellectual resources of the participants in nanotechnology projects. Strategic alliances in nanoindustry with national and international companies participation are defined as institutional and organizational form of interfirm cooperation. At this, the upper limit of its functioning is represented by hierarchical relations in transactions within the integrated structures, and the low limit by heterarchical relations in transactions among the detached firms. The paper identifies the main factors of successful functioning of strategic alliances in nanoindustry. At the same time, the participants pursuit of their own economic interests (including non-matching interests will inevitably become a source of origin and accumulation of contradictions in the alliance, which can cause its disintegration or acquisition of a weaker, passive participant by a stronger one. This determines the need for a thorough study of decisions on entering into a strategic alliance, on tactical and operational participation in its management in accordance with the contribution of partners to its creation, defining their authority and share in the results of operations. The article also studies the experience of strategic alliances formation in American and European nanoindustry, and exemplifies the potential of such interfirm cooperation in the realia of Russian economy.

  7. Validation of Progression‐Free Survival as a Surrogate Endpoint for Overall Survival in Malignant Mesothelioma: Analysis of Cancer and Leukemia Group B and North Central Cancer Treatment Group (Alliance) Trials

    Science.gov (United States)

    Wang, Xiaoyi; Hodgson, Lydia; George, Stephen L.; Sargent, Daniel J.; Foster, Nate R.; Ganti, Apar Kishor; Stinchcombe, Thomas E.; Crawford, Jeffrey; Kratzke, Robert; Adjei, Alex A.; Kindler, Hedy L.; Vokes, Everett E.; Pang, Herbert

    2017-01-01

    Abstract Purpose. The aim of this study was to investigate whether progression‐free survival (PFS) can be considered a surrogate endpoint for overall survival (OS) in malignant mesothelioma. Materials and Methods. Individual data were collected from 15 Cancer and Leukemia Group B (615 patients) and 2 North Central Cancer Treatment Group (101 patients) phase II trials. The effects of 5 risk factors for OS and PFS, including age, histology, performance status (PS), white blood cell count, and European Organisation for Research and Treatment of Cancer (EORTC) risk score, were used in the analysis. Individual‐level surrogacy was assessed by Kendall's tau through a Clayton bivariate Copula survival (CBCS) model. Summary‐level surrogacy was evaluated via the association between logarithms of the hazard ratio (log HR)—log HROS and log HRPFS—measured in R2 from a weighted least‐square (WLS) regression model and the CBCS model. Results. The median PFS for all patients was 3.0 months (95% confidence interval [CI], 2.8–3.5 months) and the median OS was 7.2 months (95% CI, 6.5–8.0 months). Moderate correlations between PFS and OS were observed across all risk factors at the individual level, with Kendall's tau ranging from 0.46 to 0.47. The summary‐level surrogacy varied among risk factors. The Copula R2 ranged from 0.51 for PS to 0.78 for histology. The WLS R2 ranged from 0.26 for EORTC and PS to 0.67 for age. Conclusions. The analyses demonstrated low to moderate individual‐level surrogacy between PFS and OS. At the summary level, the surrogacy between PFS and OS varied significantly across different risk factors. With a short postprogression survival and a moderate correlation between PFS and OS, there is no evidence that PFS is a valid surrogate endpoint for OS in malignant mesothelioma. Implications for Practice. For better disease management and for more efficient clinical trial designs, it is important to know if progression‐free survival (PFS) is

  8. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  9. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  10. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  11. The International Planetary Data Alliance

    Science.gov (United States)

    Stein, T.; Arviset, C.; Crichton, D. J.

    2017-12-01

    The International Planetary Data Alliance (IPDA) is an association of partners with the aim of improving the quality of planetary science data and services to the end users of space based instrumentation. The specific mission of the IPDA is to facilitate global access to, and exchange of, high quality scientific data products managed across international boundaries. Ensuring proper capture, accessibility and availability of the data is the task of the individual member space agencies. The IPDA was formed in 2006 with the purpose of adopting standards and developing collaborations across agencies to ensure data is captured in common formats. Member agencies include: Armenian Astronomical Society, China National Space Agency (CNSA), European Space Agency (ESA), German Aerospace Center (DLR), Indian Space Research Organization (ISRO), Italian Space Agency (ASI), Japanese Aerospace Exploration Agency (JAXA), National Air and Space Administration (NASA), National Centre for Space Studies (CNES), Space Research Institute (IKI), UAE Space Agency, and UK Space Agency. The IPDA Steering Committee oversees the execution of projects and coordinates international collaboration. The IPDA conducts a number of focused projects to enable interoperability, construction of compatible archives, and the operation of the IPDA as a whole. These projects have helped to establish the IPDA and to move the collaboration forward. A key project that is currently underway is the implementation of the PDS4 data standard. Given the international focus, it has been critical that the PDS and the IPDA collaborate on its development. Also, other projects have been conducted successfully, including developing the IPDA architecture and corresponding requirements, developing shared registries for data and tools across international boundaries, and common templates for supporting agreements for archiving and sharing data for international missions. Several projects demonstrating interoperability across

  12. Contractual Alliance Governance: Impact of Different Contract Functions on Alliance Performance

    NARCIS (Netherlands)

    Faems, D.L.M.; Alberink, Rutger; Groen, Arend J.; Klein Woolthuis, Rosalinde

    2010-01-01

    Recent research on alliance governance has emphasized that contracts can have both a control and coordination function. In this paper, we test the impact of these different contract functions on alliance performance. Conducting structural equation analyses on a sample of 270 Dutch technology

  13. Strategic Alliance Poker: Demonstrating the Importance of Complementary Resources and Trust in Strategic Alliance Management

    Science.gov (United States)

    Reutzel, Christopher R.; Worthington, William J.; Collins, Jamie D.

    2012-01-01

    Strategic Alliance Poker (SAP) provides instructors with an opportunity to integrate the resource based view with their discussion of strategic alliances in undergraduate Strategic Management courses. Specifically, SAP provides Strategic Management instructors with an experiential exercise that can be used to illustrate the value creation…

  14. Entrepreneurial Alliances: A Study of Entrepreneurship and Strategic Alliances in the Charter School Industry

    Science.gov (United States)

    Washington, Cheryl A.

    2012-01-01

    This study investigated the practices, processes, and success rates of 15 entrepreneurial alliances in the Texas charter school industry. The research involved interdisciplinary industries (business and education) and focused on how a specific type of alliance structure utilized social innovation to exploit opportunity and impact change in the…

  15. Enacting the alliance : towards a role-based theory of alliance implementation

    NARCIS (Netherlands)

    Noorderhaven, N.G.; Peeters, T.J.G.; Elst, van den J.; Das, T.K.

    2011-01-01

    Alliance research has tended to neglect the roles of individual managers and employees. However, firms are no unitary actors but complex social systems comprising individuals whose mindsets and interests influence an alliance. Building on organizational role theory we distinguish between three types

  16. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  17. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  18. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  19. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  20. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  1. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  2. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  3. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

  4. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  5. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  6. ENTREPRENEURIAL ECO-SYSTEMS & REGIONAL ALLIANCES

    Directory of Open Access Journals (Sweden)

    Joe ENGLISH

    2015-05-01

    Full Text Available The study of universities and their role in enterprise development, support and education is very mature. However when Isenberg coined the term ‘entrepreneurial ecosystem’ and suggested that higher education was one of the key foundation blocks of a regional eco-system it threw open the concept of the university having a wider role in the overall business, economic and civic life of a region. What is this wider role, and how do the universities themselves view their place in this evolving entrepreneurial eco-system? How do they fit into Regional Alliances set up to build regional economic development? This paper introduces two pilot Alliances that have been recently formed using both the education institutes and the wider eco-system to drive Innovation and Graduate Employability (The SHIP and REAL Alliances.

  7. Multinational Corporation and International Strategic Alliance

    Institute of Scientific and Technical Information of China (English)

    陆兮

    2015-01-01

    The world is now deeply into the second great wave of globalization, in which product, capital, and markets are becoming more and more integrated across countries. Multinational corporations are gaining their rapid growth around the globe and playing a significant role in the world economy. Meanwhile, the accelerated rate of globalization has also imposed pressures on MNCs, left them desperately seeking overseas alliances in order to remain competitive. International strategic alliances, which bring together large and commonly competitive firms for specific purposes, have gradual y shown its importance in the world market. And the form of international joint venture is now widely adopted. Then after the formation of alliances, selecting the right partner, formulating right strategies, establishing harmonious and effective partnership are generally the key to success.

  8. Do Strategic Alliances, Acquisitions, and R

    Directory of Open Access Journals (Sweden)

    Martynov Aleksey

    2016-01-01

    Full Text Available This paper studies possible complementarities and substitution effects between such strategic choices as alliances, acquisitions and internal R&D investments. The findings indicate that a firm’s absorptive capacity affects the presence of complementarities and substitution effects among those strategic choices. Firms with high absorptive capacity exhibit substitution effects between alliances and acquisitions and between alliances and internal R&D investments. Firms with high absorptive capacity also exhibit complementarities between acquisitions and additional R&D investments. These results were obtained from panel data of large and medium U.S. companies spanning the years 1998-2009. The results are robust to the use of different measures of performance: profitability, market-to-book value, and sales growth. This paper contributes to our understanding of the role of absorptive capacity for the optimal choice of inter-organizational strategy vs. greater internal R&D investments.

  9. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  10. Financial analysis for the infusion alliance.

    Science.gov (United States)

    Perucca, Roxanne

    2010-01-01

    Providing high-quality, cost-efficient care is a major strategic initiative of every health care organization. Today's health care environment is transparent; very competitive; and focused upon providing exceptional service, safety, and quality. Establishing an infusion alliance facilitates the achievement of organizational strategic initiatives, that is, increases patient throughput, decreases length of stay, prevents the occurrence of infusion-related complications, enhances customer satisfaction, and provides greater cost-efficiency. This article will discuss how to develop a financial analysis that promotes value and enhances the financial outcomes of an infusion alliance.

  11. New Actors and Alliances in Development

    DEFF Research Database (Denmark)

    Richey, Lisa Ann; Ponte, Stefano

    2014-01-01

    ‘New actors and alliances in development’ brings together an interdisciplinary group of scholars exploring how development financing and interventions are being shaped by a wider and more complex platform of actors than usually considered in the existing literature. The contributors also trace...... a changing set of key relations and alliances in development – those between business and consumers; ngos and celebrities; philanthropic organisations and the state; diaspora groups and transnational advocacy networks; ruling elites and productive capitalists; and ‘new donors’ and developing country...

  12. Strategic alliances fit pattern of industry innovation

    International Nuclear Information System (INIS)

    Crump, J.G.

    1997-01-01

    The strategic alliance, vitally important as an isolated practice in the oil and gas business, also fits a broad pattern of innovation by which the industry is redefining itself for prosperity in a new energy age. The industry is experiencing a renaissance in almost every aspect, from technological breakthroughs to innovative business practices to new products and markets. An inevitable outgrowth of such rapid and fundamental change is an evolution in business relationships. The strategic alliance is at the forefront of this trend. Development of new relationships capitalizes on, and partly results from, enormous advances in technology and finance. The paper discusses new relationships, the outsourcing rage, integrating work flows, and technological advances

  13. Coupling methodology within the software platform alliances

    Energy Technology Data Exchange (ETDEWEB)

    Montarnal, Ph; Deville, E; Adam, E; Bengaouer, A [CEA Saclay, Dept. de Modelisation des Systemes et Structures 91 - Gif-sur-Yvette (France); Dimier, A; Gaombalet, J; Loth, L [Agence Nationale pour la Gestion des Dechets Radioactifs (ANDRA), 92 - Chatenay Malabry (France); Chavant, C [Electricite de France (EDF), 92 - Clamart (France)

    2005-07-01

    CEA, ANDRA and EDF are jointly developing the software platform ALLIANCES which aim is to produce a tool for the simulation of nuclear waste storage and disposal repository. This type of simulations deals with highly coupled thermo-hydro-mechanical and chemical (T-H-M-C) processes. A key objective of Alliances is to give the capability for coupling algorithms development between existing codes. The aim of this paper is to present coupling methodology use in the context of this software platform. (author)

  14. Coupling methodology within the software platform alliances

    International Nuclear Information System (INIS)

    Montarnal, Ph.; Deville, E.; Adam, E.; Bengaouer, A.; Dimier, A.; Gaombalet, J.; Loth, L.; Chavant, C.

    2005-01-01

    CEA, ANDRA and EDF are jointly developing the software platform ALLIANCES which aim is to produce a tool for the simulation of nuclear waste storage and disposal repository. This type of simulations deals with highly coupled thermo-hydro-mechanical and chemical (T-H-M-C) processes. A key objective of Alliances is to give the capability for coupling algorithms development between existing codes. The aim of this paper is to present coupling methodology use in the context of this software platform. (author)

  15. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  16. Single-Cell Transcriptomics Bioinformatics and Computational Challenges

    Directory of Open Access Journals (Sweden)

    Lana Garmire

    2016-09-01

    Full Text Available The emerging single-cell RNA-Seq (scRNA-Seq technology holds the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. It opens the door to reveal the intercellular heterogeneity and has been employed to a variety of applications, ranging from characterizing cancer cells subpopulations to elucidating tumor resistance mechanisms. Parallel to improving experimental protocols to deal with technological issues, deriving new analytical methods to reveal the complexity in scRNA-Seq data is just as challenging. Here we review the current state-of-the-art bioinformatics tools and methods for scRNA-Seq analysis, as well as addressing some critical analytical challenges that the field faces.

  17. A bioinformatics roadmap for the human vaccines project.

    Science.gov (United States)

    Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

    2017-06-01

    Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

  18. The Alliance to Scale Digital Innovation and Entrepreneurship (Seed ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    The Alliance to Scale Digital Innovation and Entrepreneurship (Seed Alliance). This project will support digital innovations that solve development challenges. ... It combines three regional, competitive small grants and awards programs from ...

  19. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  20. USING THE SYNERGY OF ALLIANCES AND PARTNERSHIP FOR SUSTAINABLE GROWTH

    OpenAIRE

    Elena DOVAL; Oriana DOVAL

    2010-01-01

    The purpose of this research is to demonstrate by searching the literature that the synergy of different types of alliances and partnership brings much more opportunities for the sustainable growth of the companies. After a briefing about definitions, types and purpose of alliances and partnership the paper reminds the process of alliances and partnership formation and emphasises the main advantages and limits of alliances and partnership Finally, a new type of company is defined, i.e. ‘the s...

  1. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  2. ALLIANCES: simulation platform for radioactive waste disposal

    International Nuclear Information System (INIS)

    Deville, E.; Montarnal, Ph.; Loth, L.; Chavant, C.

    2009-01-01

    CEA, ANDRA and EDF are jointly developing the software platform ALLIANCES whose aim is to produce a tool for the simulation of nuclear waste storage and disposal. This type of simulations deals with highly coupled thermo-hydro-mechanical-chemical and radioactive (T-H-M-C-R) processes. ALLIANCES' aim is to accumulate within the same simulation environment the already acquired knowledge and to gradually integrate new knowledge. The current version of ALLIANCES contains the following modules: - Hydraulics and reactive transport in unsaturated and saturated media; - Multi-phase flow; - Mechanical thermal-hydraulics; - Thermo-Aeraulics; - Chemistry/Transport coupling in saturated media; - Alteration of waste package coupled with the environment; - Sensitivity analysis tools. The next releases will include more physical phenomena like: reactive transport in unsaturated flow and multicomponent multiphase flow; incorporation of responses surfaces in sensitivity analysis tools; integration of parallel numerical codes for flow and transport. Since the distribution of the first release of ALLIANCES (December 2003), the platform was used by ANDRA for his safety simulation program and by CEA for reactive transport simulations (migration of uranium in a soil, diffusion of different reactive species on laboratory samples, glass/iron/clay interaction). (authors)

  3. Alliances - Another Way to Access the Market

    International Nuclear Information System (INIS)

    Komarov, Yuri A.

    1999-01-01

    The late 1990s were a difficult period for the world economy: decreased economic growth rate, dropping prices for energy and other raw materials, dropping import prices of natural gas. Companies involved in the energy business are currently at the stage of survival. High-priced projects with increased risks are postponed until better times. Consequently, Gazprom had to cut investments by two thirds. For Gazprom, the problems have been aggravated by the transition from authoritatively planned economy to market economy. Alliances are one of the most effective current methods of operation in the natural gas market. Alliances between Gazprom and leading Western oil and gas companies are beneficial both to the participants and the consumers because such alliances will provide for creation of a service package of the 21th century. The importance for Gazprom of cooperation with its alliance partners is that it makes it possible to implement cost-cutting measures that benefit both producers and consumers. It also makes it possible to ensure reliable distribution of the gas

  4. Managing R&D Alliance Portfolios

    DEFF Research Database (Denmark)

    Engel Nielsen, Lars; Mahnke, Volker

    2003-01-01

    be observed in several companies engaged in the cross section of telecommunication and mobile technology where increased complexity magnifies managerial challenges. Drawing on modern portfolio theory, this paper offers a model for managing portfolios of R&D alliances. In particular, an analysis...

  5. Strategic alliances in oil and gas industry

    International Nuclear Information System (INIS)

    Crump, J.G.

    1998-01-01

    A competitor today is an ally tomorrow. A strategic partner in one market is an adversary in another. In this radically new way of doing business, the oil and gas industry seems quite at home. The trend to mergers is not unique to the oil industry, what is unique is the knack of petroleum companies to form strategic alliances [it

  6. Mergers and alliances the wider view

    CERN Document Server

    Woodsworth, Anne

    2013-01-01

    Volume 36 of Advances in Librarianship seeks to provide a broad review of the factors that lead to mergers and other alliances, the methods used to ensure effective and successful collaborations, and descriptions of the factors which contributed to less successful efforts at consolidation.

  7. Developing Strategic Alliances in Management Learning

    Science.gov (United States)

    Thorne, E. Ann; Wright, Gill

    2005-01-01

    Purpose: The notion of effective strategic alliances provides the basis on which this paper proposes a framework to manage the application and outcomes of management learning. The management of key partner collaboration emerges in this paper as a major success factor in determining effective management learning. A proactive structured approach to…

  8. Facilitating Economic Development through Strategic Alliances.

    Science.gov (United States)

    Noftsinger, John B., Jr.

    2002-01-01

    Discusses how colleges and universities are becoming increasingly involved in economic development, with the formation of strategic alliances that have led to programs that benefit business and higher education. Discusses example programs from the Valley of Virginia Partnership for Education, and the outreach program of James Madison University.…

  9. Black-Brown Relations: Are Alliances Possible?

    Science.gov (United States)

    Klor de Alva, J. Jorge; West, Cornel

    1997-01-01

    Dialogue between Cornel West and Jorge Klor de Alva explores the question of black-brown alliances, those between African Americans and Hispanic Americans. If minority groups can put aside the difference of skin color and join to combat economic and social racism, they can have far-reaching and meaningful impacts on society. (SLD)

  10. The therapeutic alliance: a psychoanalytic perspective.

    Science.gov (United States)

    Freebury, D R

    1989-11-01

    Psychoanalysis has long distinguished between the transference neurosis and that part of the communication between therapist and patient which depends upon a relatively intact part of the patient's ego. It has been proposed that it is this capacity of the patient that sustains the difficult work of dealing with communications which are the consequence of transference, and which often threaten the viability of the treatment. This quality has been referred to variously as the unobjectionable positive transference, rational transference, mature transference, therapeutic alliance and working alliance. The ever broadening scope of Psychoanalysis, along with our greater knowledge of early childhood development, has enhanced our understanding of the many influences affecting the treatment alliances. Newer views of the transference, which stress the significance of the therapists' contributions to the therapeutic dyad, make it clear that the therapeutic alliance can no longer be explained as some simple, reality based, conflict free, motivating force. It involves, rather, a complex interaction of several factors, to each of which one must add the therapists' reciprocal reactions. Psychotherapy outcome research will need to take all of these factors into consideration.

  11. Robustness of airline alliance route networks

    Science.gov (United States)

    Lordan, Oriol; Sallan, Jose M.; Simo, Pep; Gonzalez-Prieto, David

    2015-05-01

    The aim of this study is to analyze the robustness of the three major airline alliances' (i.e., Star Alliance, oneworld and SkyTeam) route networks. Firstly, the normalization of a multi-scale measure of vulnerability is proposed in order to perform the analysis in networks with different sizes, i.e., number of nodes. An alternative node selection criterion is also proposed in order to study robustness and vulnerability of such complex networks, based on network efficiency. And lastly, a new procedure - the inverted adaptive strategy - is presented to sort the nodes in order to anticipate network breakdown. Finally, the robustness of the three alliance networks are analyzed with (1) a normalized multi-scale measure of vulnerability, (2) an adaptive strategy based on four different criteria and (3) an inverted adaptive strategy based on the efficiency criterion. The results show that Star Alliance has the most resilient route network, followed by SkyTeam and then oneworld. It was also shown that the inverted adaptive strategy based on the efficiency criterion - inverted efficiency - shows a great success in quickly breaking networks similar to that found with betweenness criterion but with even better results.

  12. Rice postharvest learning alliance in Cambodia

    NARCIS (Netherlands)

    Flor, Rica Joy; Leeuwis, Cees; Maat, Harro; Gummert, Martin

    2016-01-01

    Research projects employ the learning alliance (LA) approach but there is scepticism that its rhetoric is not evident in practice. The authors examined a case of an implemented LA, comparing its outcomes with assumptions from the project and its conceptual design to evaluate the implementation of

  13. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  14. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

    Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Bioinformatics relies on nimble IT framework which can adapt to changing requirements. To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics. Use of the microservices framework is an effective methodology for the fabrication and

  15. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

    Objective: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework is an effective

  16. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

  18. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  19. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  20. 78 FR 35747 - Airworthiness Directives; Engine Alliance Turbofan Engines

    Science.gov (United States)

    2013-06-14

    ... Airworthiness Directives; Engine Alliance Turbofan Engines AGENCY: Federal Aviation Administration (FAA), DOT... Alliance GP7270 and GP7277 turbofan engines. This AD was prompted by damage to the high-pressure compressor... Alliance GP7270 and GP7277 turbofan engines with a high-pressure compressor (HPC) stage 6 disk, part number...

  1. 78 FR 5710 - Airworthiness Directives; Engine Alliance Turbofan Engines

    Science.gov (United States)

    2013-01-28

    ... Airworthiness Directives; Engine Alliance Turbofan Engines AGENCY: Federal Aviation Administration (FAA), DOT... all Engine Alliance GP7270 and GP7277 turbofan engines. This AD requires initial and repetitive...) Applicability This AD applies to all Engine Alliance GP7270 and GP7277 turbofan engines with a high-pressure...

  2. Firm Performance and Alliance Capability: The mediating role of culture

    NARCIS (Netherlands)

    de Man, A.P.; Luvison, D.

    2015-01-01

    Purpose – Extant literature has looked at the effect of alliance capability and organizational culture on alliance portfolio performance, but the relationship between the two has not been explored. The purpose of this paper is to explore the hypothesis that an alliance supportive culture is not only

  3. An Overview of Strategic Alliances between Universities and Corporations

    Science.gov (United States)

    Elmuti, Dean; Abebe, Michael; Nicolosi, Marco

    2005-01-01

    Purpose: Strategic alliances generally represent inter-firm cooperative agreements aimed at achieving competitive advantage for the partners. In recent years, there has been a dramatic increase in strategic alliances by multinational firms. This paper aims to explore the essence of these alliances and why they have become such a growing area of…

  4. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  5. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

  6. Bioinformatics on the Cloud Computing Platform Azure

    Science.gov (United States)

    Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  7. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  8. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  9. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  10. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  11. Alliance group formation: enabling and constraining effects of embeddedness and social capital in strategic technology alliance networks

    NARCIS (Netherlands)

    Duysters, G.M.; Lemmens, C.E.A.V.

    2003-01-01

    The role of embeddedness and social capital in the process of alliance group formation in strategic technology alliance networks is examined. In particular, the social mechanisms that enable and enforce alliance group formation is studies. It is argued that the enabling effect of embeddedness during

  12. Therapeutic alliance in a randomized clinical trial for bulimia nervosa.

    Science.gov (United States)

    Accurso, Erin C; Fitzsimmons-Craft, Ellen E; Ciao, Anna; Cao, Li; Crosby, Ross D; Smith, Tracey L; Klein, Marjorie H; Mitchell, James E; Crow, Scott J; Wonderlich, Stephen A; Peterson, Carol B

    2015-06-01

    This study examined the temporal relation between therapeutic alliance and outcome in two treatments for bulimia nervosa (BN). Eighty adults with BN symptoms were randomized to 21 sessions of integrative cognitive-affective therapy (ICAT) or enhanced cognitive-behavioral therapy (CBT-E). Bulimic symptoms (i.e., frequency of binge eating and purging) were assessed at each session and posttreatment. Therapeutic alliance (Working Alliance Inventory) was assessed at Sessions 2, 8, 14, and posttreatment. Repeated-measures analyses using linear mixed models with random intercepts were conducted to determine differences in alliance growth by treatment and patient characteristics. Mixed-effects models examined the relation between alliance and symptom improvement. Overall, patients in both treatments reported strong therapeutic alliances. Regardless of treatment, greater therapeutic alliance between (but not within) subjects predicted greater reductions in bulimic behavior; reductions in bulimic behavior also predicted improved alliance. Patients with higher depression, anxiety, or emotion dysregulation had a stronger therapeutic alliance in CBT-E than ICAT, while those with more intimacy problems had greater improvement in therapeutic alliance in ICAT compared to CBT-E. Therapeutic alliance has a unique impact on outcome, independent of the impact of symptom improvement on alliance. Within- and between-subjects effects revealed that changes in alliance over time did not predict symptom improvement, but rather that individuals who had a stronger alliance overall had better bulimic symptom outcomes. These findings indicate that therapeutic alliance is an important predictor of outcome in the treatment of BN. (c) 2015 APA, all rights reserved).

  13. A FRAMEWORK FOR SUBCONTRACTOR INTEGRATION IN ALLIANCE CONTRACTS

    Directory of Open Access Journals (Sweden)

    Vilasini, Nimesha

    2012-04-01

    Full Text Available Project alliancing involves the active collaboration of construction project owners and non-owner participants (designer, contractors, and suppliers to deliver projects in an atmosphere of shared responsibilities and liabilities. Alliancing connotes integration but in real practice, it fails to create a true alliance environment since only part of the value chain (owner, designer, main contractor is considered for integration. Consequently subcontractors are very often left out of the key alliance. Therefore this study identifies improvement areas to current alliance practice and suggests changes that will permit critical sub-contracting processes to be integrated into a project’s main alliance. To achieve this objective the research follows a comparative study approach. Information obtained from relevant literature is used to identify current subcontractor management practices and best practices for subcontractor integration in alliances. A case study of an alliance project is used to identify improvement areas in subcontractor management practices in an alliance environment. From these findings, the study proposes a revised alliance framework that integrates subcontractors from the early stages in alliance contracts, thus enabling the realisation of benefits accruable to projects through early contractor involvement.

  14. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  15. Alliance - a paradigm shift in energy transportation

    International Nuclear Information System (INIS)

    Cornelson, D.W.

    1997-01-01

    Key components of the Alliance Pipeline Project were outlined. This joint Canada - U.S. venture consists of a $Can 3.7 billion, producer-driven, high-pressure, rich-gas pipeline from producing fields in western Canada to an interconnection with the North American pipeline grid near Chicago. The initial volume for the system is 1.3 Bcfd, with provision for expansion to 2 Bcfd at minimal cost. The project also includes a $Can 200 million, non-regulated, natural gas liquids extraction plant and delivery system originating near Chicago. Alberta ethane supply and demand for 1995 and supply projections for 2010, (for delivery through the Alliance pipeline?), were also highlighted. 11 figs

  16. 'Mechanical restraint-confounders, risk, alliance score'

    DEFF Research Database (Denmark)

    Deichmann Nielsen, Lea; Bech, Per; Hounsgaard, Lise

    2017-01-01

    . AIM: To clinically validate a new, structured short-term risk assessment instrument called the Mechanical Restraint-Confounders, Risk, Alliance Score (MR-CRAS), with the intended purpose of supporting the clinicians' observation and assessment of the patient's readiness to be released from mechanical...... restraint. METHODS: The content and layout of MR-CRAS and its user manual were evaluated using face validation by forensic mental health clinicians, content validation by an expert panel, and pilot testing within two, closed forensic mental health inpatient units. RESULTS: The three sub-scales (Confounders......, Risk, and a parameter of Alliance) showed excellent content validity. The clinical validations also showed that MR-CRAS was perceived and experienced as a comprehensible, relevant, comprehensive, and useable risk assessment instrument. CONCLUSIONS: MR-CRAS contains 18 clinically valid items...

  17. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  18. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  19. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  20. Investigation of miRNA Biology by Bioinformatic Tools and Impact of miRNAs in Colorectal Cancer: Regulatory Relationship of c-Myc and p53 with miRNAs

    Directory of Open Access Journals (Sweden)

    Yaguang Xi

    2007-01-01

    Full Text Available MicroRNAs (miRNAs are a class of small non-coding RNAs that mediate gene expression at the posttranscriptional and translational levels and have been demonstrated to be involved in diverse biological functions. Mounting evidence in recent years has shown that miRNAs play key roles in tumorigenesis due to abnormal expression of and mutations in miRNAs. High throughput miRNA expression profiling of several major tumor types has identified miRNAs associated with clinical diagnosis and prognosis of cancer treatment. Previously our group has discovered a novel regulatory relationship between tumor suppressor gene p53 with miRNAs expression and a number of miRNA promoters contain putative p53 binding sites. In addition, others have reported that c-myc can mediate a large number of miRNAs expression. In this review, we will emphasize algorithms to identify mRNA targets of miRNAs and the roles of miRNAs in colorectal cancer. In particular, we will discuss a novel regulatory relationship of miRNAs with tumor suppressor p53 and c-myc. miRNAs are becoming promising novel targets and biomarkers for future cancer therapeutic development and clinical molecular diagnosis.

  1. Cluster as a Form of Strategic Alliance

    Directory of Open Access Journals (Sweden)

    Marzena Godlewska

    2007-07-01

    Full Text Available The article presents the theory of clusters that are treated as natural elements of European model of economic development. There are highlighted Polish Forum of Lisbon Strategy point of view that indicated clusters as one of fundamental ideas recommended for Polish economy. In based on literature and observation of articles authors the concept, examples of Polish clusters and their role in strategic alliance are presented.

  2. Strategic Alliances: the Potential for Russian Nanoindustry

    OpenAIRE

    Inshakova Elena Ivanovna

    2015-01-01

    Strategic alliances as a form of interfirm cooperation (including international cooperation) increase the potential of solving large-scale problems of national nanoindustry development, providing synergy of participants resources united by the principle of complementarity and substitution in the process of joint implementation of complex R&D programs, mobilization and input of significant financial, material, technical and intellectual resources of the participants in nanotechnology projects....

  3. Trusting Relationships in the NATO Alliance

    DEFF Research Database (Denmark)

    Keating, Vincent Charles

    – particularly given the historical (and even current) animosities between some of the member states. How is it that so many states can work together given the structural bias towards distrust in the international system? Given the goal of the papers on this panel to investigate how NATO might in fact facilitate......, in order to reveal the points of intersection that might help us to understand how and why trusting relationships can be formed within the NATO alliance....

  4. The clinical partnership as strategic alliance.

    Science.gov (United States)

    Novotny, Jeanne M; Donahue, Moreen; Bhalla, Bharat B

    2004-01-01

    The purpose of this article is to describe a renewed partnership between a collegiate school of nursing and a community hospital. Universities and hospitals are searching for creative solutions to increase the number of registered nurses available to meet the demand for nursing care. An affiliation agreement had been in existence for many years, but health care system imperatives made it necessary to redesign the partnership between nursing education and nursing service. The model used to develop this new partnership is based on the work done in the field of management and is in the form of a strategic alliance. The success of a strategic alliance depends on two key factors: the relationship between partners and partnership performance. Identified outcomes show that this partnership is helping to meet the increasing demand for nursing care by building student capacity, satisfying mutual needs of faculty and clinical staff, and removing economic barriers. This article describes the development of the strategic alliance, its current status, and strategies for the future.

  5. The Alliance Negotiation Scale: A psychometric investigation.

    Science.gov (United States)

    Doran, Jennifer M; Safran, Jeremy D; Muran, J Christopher

    2016-08-01

    This study investigates the utility and psychometric properties of a new measure of psychotherapy process, the Alliance Negotiation Scale (ANS; Doran, Safran, Waizmann, Bolger, & Muran, 2012). The ANS was designed to operationalize the theoretical construct of negotiation (Safran & Muran, 2000), and to extend our current understanding of the working alliance concept (Bordin, 1979). The ANS was also intended to improve upon existing measures such as the Working Alliance Inventory (WAI; Horvath & Greenberg, 1986, 1989) and its short form (WAI-S; Tracey & Kokotovic, 1989) by expanding the emphasis on negative therapy process. The present study investigates the psychometric validity of the ANS test scores and interpretation-including confirming its original factor structure and evaluating its internal consistency and construct validity. Construct validity was examined through the ANS' convergence and divergence with several existing scales that measure theoretically related constructs. The results bolster and extend previous findings about the psychometric integrity of the ANS, and begin to illuminate the relationship between negotiation and other important variables in psychotherapy research. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  6. Predicting Ecosystem Alliances Using Landscape Theory

    Directory of Open Access Journals (Sweden)

    Shruti Satsangi

    2012-08-01

    Full Text Available Previous articles in the TIM Review have covered various aspects of the concept of business ecosystems, from the types of ecosystems to keystone strategy, to different member roles and value co-creation. While there is no dearth of suggested best practices that organizations should follow as ecosystem members, it can be difficult to apply these insights into actionable steps for them to take. This is especially true when the ecosystem members already have a prior history of cooperation or competition with each other, as opposed to where a new ecosystem is created. Landscape theory, a political science approach to predicting coalition formation and strategic alliances, can be a useful complement to ecosystems studies by providing a tool to evaluate the best possible alliance options for an organization, given information about itself and the other companies in the system. As shown in the case study of mobile device manufacturers choosing platform providers in the mobile ecosystem, this tool is highly flexible and customizable, with more data providing a more accurate view of the alliances in the ecosystem. At the same time, with even basic parameters, companies can glean significant information about which coalitions will best serve their interest and overall standing within the ecosystem. This article shows the synergies between landscape theory and an ecosystems approach and offers a practical, actionable way in which to analyze individual member benefits.

  7. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  8. The Healthy ALLiances (HALL) framework: prerequisites for success.

    Science.gov (United States)

    Koelen, Maria A; Vaandrager, Lenneke; Wagemakers, Annemarie

    2012-04-01

    Chronic conditions are on the rise worldwide, and there is increasingly a call for the primary care and public health sectors to join forces in alliances. GPs have an important role to play in such alliances. However, successful cooperation is not as obvious as it may seem, and the sectors are not used to working together. The objective is to identify conditions and prerequisites for successful alliances. Identification of conditions and prerequisites is mainly based on stepwise analysis and iterative developments in research on collaboration processes in the area of health promotion and public health. The process as a whole resulted in the framework presented in this paper. This so-called HALL framework identifies three clusters of factors that either hinder or facilitate the success of alliances: (i) institutional factors, (ii) personal factors of participants in the alliance and (iii) factors relating to the organization of the alliance. The institutional and personal factors 'stick' to the stakeholders and are brought into the alliance. The third group refers to the lessons learned from dealing with the first two characteristics to make the alliance successful. Partners in alliances bring in personal attributes and institutional characteristics that can form obstacles to successful alliances, but, when they are addressed in a flexible and positive way, obstacles can be turned in contributory factors, leading to many potential benefits, such as collaborative learning and innovation.

  9. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  10. 5-year follow-up of a randomized controlled trial of immediate versus delayed zoledronic acid for the prevention of bone loss in postmenopausal women with breast cancer starting letrozole after tamoxifen: N03CC (Alliance) trial.

    Science.gov (United States)

    Wagner-Johnston, Nina D; Sloan, Jeff A; Liu, Heshan; Kearns, Ann E; Hines, Stephanie L; Puttabasavaiah, Suneetha; Dakhil, Shaker R; Lafky, Jacqueline M; Perez, Edith A; Loprinzi, Charles L

    2015-08-01

    Postmenopausal women with breast cancer receiving aromatase inhibitors are at an increased risk of bone loss. The current study was undertaken to determine whether upfront versus delayed treatment with zoledronic acid (ZA) impacted bone loss. This report described the 5-year follow-up results. A total of 551 postmenopausal women with breast cancer who completed tamoxifen treatment and were undergoing daily letrozole treatment were randomized to either upfront (274 patients) or delayed (277 patients) ZA at a dose of 4 mg intravenously every 6 months. In the patients on the delayed treatment arm, ZA was initiated for a postbaseline bone mineral density T-score of prevented bone loss compared with delayed treatment in postmenopausal women receiving letrozole and these differences were maintained at 5 years. The incidence of osteoporosis or fractures was not found to be significantly different between treatment arms. © 2015 American Cancer Society.

  11. Strategic alliances for improved performance in underground mining

    International Nuclear Information System (INIS)

    Bessinger, S.L.; Langley, S.B.

    1999-01-01

    As the competitive climate of the modern coal industry continues, it seems clear that only by the intervention of small, highly focused workgroups will new efficiency and economy result in the continuous improvement required to survive and prosper. Strategic Alliances, drawing from known and proven principles, can contribute to efficiency and economy. However, individual attitudes and corporate-cultures often must change to foster the growth of functional Strategic Alliances. Motivating personal change in individuals within prospective Strategic Alliance partners is perhaps the most difficult element about establishing a new Strategic Alliance or maintaining an existing Alliance. Ultimately, Strategic Alliances are not fundamentally about corporations, or executives as leaders, but about individuals throughout the endeavors of both partner-organizations and a shared-vision to achieve a common goal

  12. AN INVESTIGATION INTO FACTORS INFLUENCING INTERNATIONAL STRATEGIC ALLIANCE PROCESS

    OpenAIRE

    Sari Wahyuni; Theo J.B.M. Postma

    2003-01-01

    Empirical research indicates that strategic alliances, like other organizational forms, emerge as an adaptive mechanism to market uncertainty, and their developments over time reflect the co-evolution of distinctive firm capabilities and of industry and market activities. Interestingly, most strategic alliances go through similar revolutionary cycles in terms of their motives and capabilities toward the cooperative relationship. Studies in this areas how that alliance failure is an outcome of...

  13. Coal mine enterprise integration based on strategic alliance

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Q.; Sun, J.; Xu, S. [Tsinghua University, Beijing (China). Dept. of Computer Science and Technology

    2003-07-01

    The relationship between coal mine and related enterprise was analysed. Aiming at the competitive world market as well as the dynamic requirement, a coal mine enterprise integration strategy and a enterprise strategic alliance were proposed for the product providing service business pattern. The modelling method of the enterprise strategic alliance was proposed, including the relationship view model, information view model and business process view model. The idea of enterprise strategic alliance is useful for enterprise integration. 6 refs., 2 figs.

  14. Product development alliances: factors influencing formation and success

    DEFF Research Database (Denmark)

    Olsen, Johanne Rønnow; Harmsen, Hanne; Friis, Alan

    2008-01-01

    , results indicate that success factors are rather universal across industries and types of alliances. Research limitations/implications - Further research should explore the findings further, both within the food industry context, as well as more broadly in terms of geography and industry. Practical...... implications - Managers obtain a tool for planning and refining their innovation strategy and actions regarding product development alliances. Originality/value - This research contributes to the presently limited literature on product development alliances, specifically in the food industry context....

  15. Persistence of and interrelation between horizontal and vertical technology alliances

    OpenAIRE

    Belderbos, R.A.; Gilsing, V.; Lokshin, B.

    2009-01-01

    We examine how and to what extent the propensity to be engaged in alliances with different partner types (suppliers, customers and competitors) depends on prior alliance engagement with partner firms of the same type (persistence) and prior engagement in alliances with the other partner types (interrelation). We derive hypotheses from a combined competence and governance view of collaboration, and test these on an extensive panel dataset of innovation-active Dutch firms during 1996-2004. We f...

  16. IMPORTANCE OF STRATEGIC ALLIANCES IN COMPANY’S ACTIVITY

    OpenAIRE

    Elena BARANOV

    2013-01-01

    Strategic alliance is an agreement between two or more organizations to cooperate in a specific business activity, so that each benefits from the strengths of the other, and gains competitive advantage. The formation of strategic alliances has been seen as a response to globalization and increasing uncertainty and complexity in the business environment. Strategic alliances involve the sharing of knowledge and expertise between partners as well as the reduction of risk and costs in areas such ...

  17. G-DOC Plus - an integrative bioinformatics platform for precision medicine.

    Science.gov (United States)

    Bhuvaneshwar, Krithika; Belouali, Anas; Singh, Varun; Johnson, Robert M; Song, Lei; Alaoui, Adil; Harris, Michael A; Clarke, Robert; Weiner, Louis M; Gusev, Yuriy; Madhavan, Subha

    2016-04-30

    G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available

  18. Possibility of Strategic Alliance from Competition:A Game Analysis

    Institute of Scientific and Technical Information of China (English)

    张树义; 陈彦茹

    2004-01-01

    The possibility for two competitive firms to form a strategic alliance was quantitatively analyzed with the game theory. The strategic alliance could be formed in an infinitely repeated game with complete information or a finitely repeated game with incomplete information. In the former situation, the discount ratio is important. If the discount ratio is large enough, alliance would be a possible solution. In the latter situation, the bigger the possibility of the rationality is, the more possible is for both firms to make strategic alliance.

  19. Therapeutic working alliance: From a psychoanalitical to a pantheoretical conception

    Directory of Open Access Journals (Sweden)

    Peter Praper

    2004-05-01

    Full Text Available Although the concept of therapeutic working alliance was rooted in psychoanalysis, today it is more prominent in psychoanalytic psychotherapies than psychoanalysis. It is rather surprising that we cannot find the concept in the Laplanche and Pontalis Dictionary. During the last two decades a growing body of empirical research material on therapeutic working alliance was published, confirming the idea of the alliance as a separate dimension of therapeutic relationship with few recognisable components. The dimension of the therapeutic working alliance was examined in several approaches and proved as one of the most important therapeutic factors, regardless of the approach, and it has finally been accepted as a pantheoretical concept.

  20. The Alliance Capability of Technology-Based Born Globals

    DEFF Research Database (Denmark)

    Oxtorp, Liliya Altshuler; Elg, Ulf

    2015-01-01

    A detailed investigation of the aspects comprising the alliance capability of technology-based born globals. Alliance capability is regarded as a set of organizational skills necessary from the decision to search for a partner for a technology collaboration, which may also involve a marketing...... and risks of collaborating with MNEs.Methodology: A longitudinal process study of a Danish technology born global with three embedded cases of its R&D and marketing alliances with Asian MNEs.Findings: The organisational skills comprising the alliance capability are defined to be internal and external...

  1. IMPORTANCE OF STRATEGIC ALLIANCES IN COMPANY’S ACTIVITY

    Directory of Open Access Journals (Sweden)

    Elena BARANOV

    2013-01-01

    Full Text Available Strategic alliance is an agreement between two or more organizations to cooperate in a specific business activity, so that each benefits from the strengths of the other, and gains competitive advantage. The formation of strategic alliances has been seen as a response to globalization and increasing uncertainty and complexity in the business environment. Strategic alliances involve the sharing of knowledge and expertise between partners as well as the reduction of risk and costs in areas such as relationships with suppliers and the development of new products and technologies. A strategic alliance is sometimes equated with a joint venture, but an alliance may involve competitors, and generally has a shorter life span. Strategic partnership is a closely related concept. This article analyzes definition of strategic alliance, its benefits, types, process of formation, and provides a few cases studies of strategic alliances. This paper tries to synthesize the scope and role of marketing functions in the determination of effectiveness of strategic alliances. Several propositions from a marketing viewpoint concerning the analysis of alliance process are formulated. On the basis of the propositions, a framework is developed for future research.

  2. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  3. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  4. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  5. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  6. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  7. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  8. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  9. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  10. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  11. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  12. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  13. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  14. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  15. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  16. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  17. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  18. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  19. The development and application of bioinformatics core competencies to improve bioinformatics training and education.

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

  20. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  1. The Impacts of Control Mechanism in Strategic Alliance on Alliance Performance: From the Perspective of Boundary Dilemma

    Institute of Scientific and Technical Information of China (English)

    SHEN Hao; XIE En; WANG Dong

    2016-01-01

    In order to solve the problem of boundary dilemma in the strategic alliance,this paper firstly examines the impact of the control mechanism in the strategic alliance on the coordinative efficiency and opportunistic risks of the alliance,and then it tests the different impacts of coordinative efficiency and opportunistic risks on the performances of the alliance members.The empirical results indicate that the formal contract control can efficiently resolve the problem of opportunistic risks in the boundary dilemma,so as to improve the performance of the alliance members;whereas the informal social control including relation control and information technology control can efficiently solve the problem of coordinative efficiency in the boundary dilemma,so as to improve the performance of the alliance members.These findings can enrich and extend existing literature in strategic alliance management and provide significant empirical evidences and theoretical supports for the strategic alliance members to resolve boundary dilemma and further enhance alliance cooperative performance.

  2. Alliance building and narcissistic personality disorder.

    Science.gov (United States)

    Ronningstam, Elsa

    2012-08-01

    Building a therapeutic alliance with a patient with pathological narcissism or narcissistic personality disorder is a challenging process. A combined alliance building and diagnostic strategy is outlined that promotes patients' motivation and active engagement in identifying their own problems. The main focus is on identifying grandiosity, self-regulatory patterns, and behavioral fluctuations in their social and interpersonal contexts while engaging the patient in meaningful clarifications and collaborative inquiry. A definition of grandiosity as a diagnostic characterological trait is suggested, one that captures self-criticism, inferiority, and fragility in addition to superiority, assertiveness, perfectionism, high ideals, and self-enhancing and self-serving interpersonal behavior. These reformulations serve to expand the spectrum of grandiosity-promoting strivings and activities, capture their fluctuations, and help clinicians attend to narcissistic individuals' internal experiences and motivation as well as to their external presentation and interpersonal self-enhancing, self-serving, controlling, and aggressive behavior. A case example illustrates this process. © 2012 Wiley Periodicals, Inc.

  3. Learning about Breast Cancer

    Science.gov (United States)

    Skip to main content Learning About Breast Cancer Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  4. Impact of Race, Ethnicity and BMI on Achievement of Pathologic Complete Response Following Neoadjuvant Chemotherapy for Breast Cancer: A Pooled Analysis of Four Prospective Alliance Clinical Trials (A151426)

    Science.gov (United States)

    Warner, Erica T.; Ballman, Karla V.; Strand, Carrie; Boughey, Judy; Buzdar, Aman U.; Carey, Lisa A.; Sikov, William M.; Partridge, H.

    2016-01-01

    Purpose Previous studies demonstrated poor response to neoadjuvant systemic therapy (NST) for breast cancer among black women and women who are overweight or obese but this may be due to chemotherapy under dosing. We assessed associations of race, ethnicity and body mass index (BMI) with pathologic complete response (pCR) in clinical trial populations. Methods 1797 women enrolled in four NST trials (CALGB 40601, 40603; ACOSOG Z1041, Z1071) were included. Tumor subtypes were defined by estrogen receptor (ER) and HER2 status. Logistic regression generated odds ratios (OR) and 95% confidence intervals (CI) for the associations of race, ethnicity, and BMI with pCR adjusting for subtype, study arm, lymph node status, tumor size, and tumor grade. Results 253 (14.1%) were black, 199 (11.1%) Hispanic, 520 (28.9%) overweight, and 743 (41.4%) obese. Compared to whites, Blacks and Hispanics were more likely to be obese and Blacks were more likely to have triple-negative cancer. pCR rates differed significantly by tumor subtype. In multivariate analyses, neither race (black vs. white: OR: 1.18, 95% CI: 0.85–1.62) nor ethnicity (Hispanic vs. non-Hispanic: OR: 1.30, 95% CI: 0.67–2.53) were significant predictors of pCR overall or by subtype. Overweight and obese women had lower pCR rates in ER+/HER2+, but higher pCR rates in ER−/HER2+ cancers. Conclusions There was no difference in breast pCR according to race or ethnicity. Overall, there was no major difference in pCR rates by BMI. These findings suggest that pCR with optimally dosed NST is a function of tumor, rather than patient, biology. PMID:27449492

  5. Bioinformatics: Cheap and robust method to explore biomaterial from Indonesia biodiversity

    Science.gov (United States)

    Widodo

    2015-02-01

    Indonesia has a huge amount of biodiversity, which may contain many biomaterials for pharmaceutical application. These resources potency should be explored to discover new drugs for human wealth. However, the bioactive screening using conventional methods is very expensive and time-consuming. Therefore, we developed a methodology for screening the potential of natural resources based on bioinformatics. The method is developed based on the fact that organisms in the same taxon will have similar genes, metabolism and secondary metabolites product. Then we employ bioinformatics to explore the potency of biomaterial from Indonesia biodiversity by comparing species with the well-known taxon containing the active compound through published paper or chemical database. Then we analyze drug-likeness, bioactivity and the target proteins of the active compound based on their molecular structure. The target protein was examined their interaction with other proteins in the cell to determine action mechanism of the active compounds in the cellular level, as well as to predict its side effects and toxicity. By using this method, we succeeded to screen anti-cancer, immunomodulators and anti-inflammation from Indonesia biodiversity. For example, we found anticancer from marine invertebrate by employing the method. The anti-cancer was explore based on the isolated compounds of marine invertebrate from published article and database, and then identified the protein target, followed by molecular pathway analysis. The data suggested that the active compound of the invertebrate able to kill cancer cell. Further, we collect and extract the active compound from the invertebrate, and then examined the activity on cancer cell (MCF7). The MTT result showed that the methanol extract of marine invertebrate was highly potent in killing MCF7 cells. Therefore, we concluded that bioinformatics is cheap and robust way to explore bioactive from Indonesia biodiversity for source of drug and another

  6. High p95HER2/HER2 Ratio Associated With Poor Outcome in Trastuzumab-Treated HER2-Positive Metastatic Breast Cancer NCCTG N0337 and NCCTG 98-32-52 (Alliance).

    Science.gov (United States)

    Chumsri, Saranya; Sperinde, Jeff; Liu, Heshan; Gligorov, Joseph; Spano, Jean-Philippe; Antoine, Martine; Moreno Aspitia, Alvaro; Tan, Winston; Winslow, John; Petropoulos, Christos J; Chenna, Ahmed; Bates, Michael; Weidler, Jodi Marie; Huang, Weidong; Dueck, Amylou; Perez, Edith A

    2018-03-12

    Purpose: p95HER2 is a truncated form of HER2 that confers resistance to trastuzumab in vitro , but clinical results have been conflicting to date. Given that p95HER2 levels correlate with total HER2 expression levels, which confer better outcomes, we sought to evaluate the p95HER2/HER2 ratio in the North Central Cancer Treatment Group N0337 and N98-32-52 trials. Experimental Design: The HERmark assay and VeraTag technology (Monogram Biosciences) were used to measure total HER2 and p95HER2 expression levels in 91 patient samples. Results: In the multivariate model, increasing total HER2 level was significantly associated with longer (OS; HR, 0.33; P = 0.002) and decreasing p95HER2 level was significantly associated with longer OS (HR, 4.2; P = 0.01). Total HER2 expression level was significantly associated with longer progression-free survival (PFS) (HR, 0.57; P = 0.04), whereas p95HER2 level was not (HR, 1.7; P = 0.25). However, there was a positive association between p95HER2 and total HER2 expression levels ( R 2 = 0.48; P < 0.001). Consistent with our hypothesis, the ratio of p95HER2/HER2 was significantly associated with worsening PFS (HR, 1.7; P = 0.04) and OS (HR, 2.8; P = 0.002). Patients with the highest tertile of p95HER2/HER2 values had significantly less favorable PFS (HR, 1.8; P = 0.06) and OS (HR, 2.3; P = 0.02). Conclusions: A high p95HER2/HER2 ratio identified patients with metastatic breast cancer with poor outcomes on trastuzumab-based therapies. Further investigation of the p95HER2/HER2 ratio as a potential prognostic or predictive biomarker for HER2-targeted therapy is warranted. Clin Cancer Res; 1-6. ©2018 AACR. ©2018 American Association for Cancer Research.

  7. The allianced enterprise : global strategies for corporate collaboration

    NARCIS (Netherlands)

    Duysters, G.M.; Man, de A.P.; Vasudevan, A.

    2001-01-01

    Firms all over the world are entering into strategic alliances. Successful alliance management, however, requires corporations to adapt their management models to the demands of this new mode of organization. New tools, techniques and ideas need to be introduced in order to fully benefit from the

  8. Exploration of a Contextual Management Framework for Strategic Learning Alliances

    Science.gov (United States)

    Dealtry, Richard

    2008-01-01

    Purpose: This article aims to take a further step forward in examining those important business factors that will shape the future of best practice in the quality management of internal and external strategic alliances. Design/methodology/approach: The article presents a speculative scenario on the future of strategic alliances in education,…

  9. Persistence of, and interrelation between, horizontal and vertical technology alliances

    NARCIS (Netherlands)

    Belderbos, R.; Gilsing, V.A.; Lokshin, B.

    2012-01-01

    The authors explore to what extent there is persistence in, and interrelation between, alliance strategies with different partner types (customers, suppliers, competitors). In a panel data set of innovation-active firms in the Netherlands from 1996 to 2004, the authors find persistence in alliance

  10. Beyond contracts : Governing structures in non-equity alliances

    NARCIS (Netherlands)

    Reuer, Jeffrey; Devarakonda, S.V.

    Non-equity alliances are often portrayed in the literature as purely contractual collaborative agreements. This paper questions the notion that contractual safeguards and incentives alone provide the formal governance mechanisms that undergird non-equity alliances. We argue and show that partners

  11. Representations of Parent-Child Alliances in Children's Family Drawings

    Science.gov (United States)

    Leon, Kim; Wallace, Tamar; Rudy, Duane

    2007-01-01

    The purpose of this study was to investigate relationships between children's representations of parent-child alliances (PCA) and their peer relationship quality, using a new scale that was developed to rate representations of PCA in children's family drawings. The parent-child alliance pattern is characterized by a relationship between parent and…

  12. Strategic Alliances in Education: The Knowledge Engineering Web

    Science.gov (United States)

    Westera, Wim; van den Herik, Jaap; van de Vrie, Evert

    2004-01-01

    The field of higher education shows a jumble of alliances between fellow institutes. The alliances are strategic in kind and serve an economy-of-scales concept. A large scale is a prerequisite for allocating the budgets for new educational methods and technologies in order to keep the educational services up-to-date. All too often, however,…

  13. Validity of the Working Alliance Inventory within Child Protection Services

    Science.gov (United States)

    Killian, Michael; Forrester, Donald; Westlake, David; Antonopoulou, Paraskevi

    2017-01-01

    The Working Alliance Inventory remains a widely studied measure of quality of therapeutic relationships between the practitioner and client. No prior study has examined the psychometrics and validity of the Working Alliance Inventory-Short (WAI-S) in a sample of families, social workers, and trained observers within child protection services.…

  14. The Integrative Psychotherapy Alliance: Family, Couple and Individual Therapy Scales.

    Science.gov (United States)

    Pinsof, William M.; Catherall, Donald R.

    1986-01-01

    Presents an integrative definition of the therapeutic alliance that conceptualizes individual, couple and family therapy as occurring within the same systemic framework. The implications of this concept for therapy reserach are examined. Three new systematically oriented scales to measure the alliance are presented along with some preliminary data…

  15. The dynamics of alliances. A game theoretical approach

    NARCIS (Netherlands)

    Ridder, A. de

    2007-01-01

    In this dissertation, Annelies de Ridder presents a game theoretical approach to strategic alliances. More specifically, the dynamics of and within alliances have been studied. To do so, four new models have been developed in the game theoretical tradition. Both coalition theory and strategic game

  16. The interplay of structural and relational governance in innovation alliances

    NARCIS (Netherlands)

    Garbade, P.J.P.; Omta, S.W.F.; Fortuin, F.T.J.M.

    2016-01-01

    The present paper aims to extend the discussion in the governance literature about whether structural and relational governance mechanisms complement or substitute each other in innovation alliances. Where structural governance mechanisms refer to the division of tasks within the alliance and to

  17. A perfect match : an empirical investigation into partner selection as an alliance capability

    OpenAIRE

    Duisters, Danielle

    2013-01-01

    Strategic alliances have become a cornerstone of business development. Not only the number of alliances but also the percentage of revenues coming from alliances has increased. Individual companies form alliances to enter new markets, to gain knowledge, or to share risk and resources to bring value to their consumers. So alliances are more and more integrated into company strategy. In this study, alliances are defined as voluntary, evolving, open-ended, and flexible organizational forms betwe...

  18. Managing Adaptation in Multi-Partner Collaboration: Role of Alliance Board

    OpenAIRE

    Barbic, Frano; Hidalgo Nuchera, Antonio

    2015-01-01

    Adaptation to changing circumstances is crucial for success of alliances. Using a longitudinal case study of the R&D non-equity multi-partner alliance between four partners, we examine how the alliance board can complement incomplete contracts for coordinated adaptation. We trace the interactions between the partners in order to explore the functioning of the alliance board in multi-partner alliances for coordinated adaptation. We found that alliance board can complement incomplete contract, ...

  19. Ki67 Proliferation Index as a Tool for Chemotherapy Decisions During and After Neoadjuvant Aromatase Inhibitor Treatment of Breast Cancer: Results From the American College of Surgeons Oncology Group Z1031 Trial (Alliance)

    Science.gov (United States)

    Ellis, Matthew J.; Suman, Vera J.; Hoog, Jeremy; Goncalves, Rodrigo; Sanati, Souzan; Creighton, Chad J.; DeSchryver, Katherine; Crouch, Erika; Brink, Amy; Watson, Mark; Luo, Jingqin; Tao, Yu; Barnes, Michael; Dowsett, Mitchell; Budd, G. Thomas; Winer, Eric; Silverman, Paula; Esserman, Laura; Carey, Lisa; Ma, Cynthia X.; Unzeitig, Gary; Pluard, Timothy; Whitworth, Pat; Babiera, Gildy; Guenther, J. Michael; Dayao, Zoneddy; Ota, David; Leitch, Marilyn; Olson, John A.; Allred, D. Craig; Hunt, Kelly

    2017-01-01

    Purpose To determine the pathologic complete response (pCR) rate in estrogen receptor (ER) –positive primary breast cancer triaged to chemotherapy when the protein encoded by the MKI67 gene (Ki67) level was > 10% after 2 to 4 weeks of neoadjuvant aromatase inhibitor (AI) therapy. A second objective was to examine risk of relapse using the Ki67-based Preoperative Endocrine Prognostic Index (PEPI). Methods The American College of Surgeons Oncology Group (ACOSOG) Z1031A trial enrolled postmenopausal women with stage II or III ER-positive (Allred score, 6 to 8) breast cancer whose treatment was randomly assigned to neoadjuvant AI therapy with anastrozole, exemestane, or letrozole. For the trial ACOSOG Z1031B, the protocol was amended to include a tumor Ki67 determination after 2 to 4 weeks of AI. If the Ki67 was > 10%, patients were switched to neoadjuvant chemotherapy. A pCR rate of > 20% was the predefined efficacy threshold. In patients who completed neoadjuvant AI, stratified Cox modeling was used to assess whether time to recurrence differed by PEPI = 0 score (T1 or T2, N0, Ki67 2) versus PEPI > 0 disease. Results Only two of the 35 patients in ACOSOG Z1031B who were switched to neoadjuvant chemotherapy experienced a pCR (5.7%; 95% CI, 0.7% to 19.1%). After 5.5 years of median follow-up, four (3.7%) of the 109 patients with a PEPI = 0 score relapsed versus 49 (14.4%) of 341 of patients with PEPI > 0 (recurrence hazard ratio [PEPI = 0 v PEPI > 0], 0.27; P = .014; 95% CI, 0.092 to 0.764). Conclusion Chemotherapy efficacy was lower than expected in ER-positive tumors exhibiting AI-resistant proliferation. The optimal therapy for these patients should be further investigated. For patients with PEPI = 0 disease, the relapse risk over 5 years was only 3.6% without chemotherapy, supporting the study of adjuvant endocrine monotherapy in this group. These Ki67 and PEPI triage approaches are being definitively studied in the ALTERNATE trial (Alternate Approaches for

  20. Library Services Alliance of New Mexico. 1994 Annual report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    The Library Services Alliance is a unique multi-type library consortium committed to resource sharing. As a voluntary association of university and governmental laboratory libraries supporting scientific research, the Alliance has become a leader in New Mexico in using cooperative ventures to cost-effectively expand resources supporting their scientific and technical communities. During 1994, the alliance continued to expand on their strategic planning foundation to enhance access to research information for the scientific and technical communities. Significant progress was made in facilitating easy access to the on-line catalogs of member libraries via connections through the Internet. Access to Alliance resources is now available via the World Wide Web and Gopher, as well as links to other databases and electronic information. This report highlights the accomplishments of the Alliance during calendar year 1994.

  1. Group Innovation Ability of Agricultural Technological Innovation Strategic Alliance

    Institute of Scientific and Technical Information of China (English)

    Chishun; MA; Jintian; YU

    2013-01-01

    Agricultural technological innovation strategic alliance, as an important form of strategic alliance, has steadily strengthened the collaborative management among organizations and raised competitive power with the backing of improved group innovation ability. This article studies innovation ability from individual innovation ability to the group innovation ability. Firstly, basic connotation of group innovation ability is to be concluded through the comparison of individual and group innovation ability. Secondly, evaluation index system is to be established based on the influencing factors of the group innovation ability of agricultural technological innovation strategic alliance and evaluation is based on three dimensions, namely organization technological innovation ability, alliance collaborative innovation ability as well as innovation environment. Furthermore, basic methods for promoting the group innovation ability of alliance are to be proposed.

  2. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  3. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  4. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  5. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  6. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  7. Further Validation of the Learning Alliance Inventory: The Roles of Working Alliance, Rapport, and Immediacy in Student Learning

    Science.gov (United States)

    Rogers, Daniel T.

    2015-01-01

    This study further examined the reliability and validity of the Learning Alliance Inventory (LAI), a self-report measure designed to assess the working alliance between a student and a teacher. The LAI was found to have good internal consistency and test--retest reliability, and it demonstrated the predicted convergence with measures of immediacy…

  8. Tissue Banking, Bioinformatics, and Electronic Medical Records: The Front-End Requirements for Personalized Medicine

    Science.gov (United States)

    Suh, K. Stephen; Sarojini, Sreeja; Youssif, Maher; Nalley, Kip; Milinovikj, Natasha; Elloumi, Fathi; Russell, Steven; Pecora, Andrew; Schecter, Elyssa; Goy, Andre

    2013-01-01

    Personalized medicine promises patient-tailored treatments that enhance patient care and decrease overall treatment costs by focusing on genetics and “-omics” data obtained from patient biospecimens and records to guide therapy choices that generate good clinical outcomes. The approach relies on diagnostic and prognostic use of novel biomarkers discovered through combinations of tissue banking, bioinformatics, and electronic medical records (EMRs). The analytical power of bioinformatic platforms combined with patient clinical data from EMRs can reveal potential biomarkers and clinical phenotypes that allow researchers to develop experimental strategies using selected patient biospecimens stored in tissue banks. For cancer, high-quality biospecimens collected at diagnosis, first relapse, and various treatment stages provide crucial resources for study designs. To enlarge biospecimen collections, patient education regarding the value of specimen donation is vital. One approach for increasing consent is to offer publically available illustrations and game-like engagements demonstrating how wider sample availability facilitates development of novel therapies. The critical value of tissue bank samples, bioinformatics, and EMR in the early stages of the biomarker discovery process for personalized medicine is often overlooked. The data obtained also require cross-disciplinary collaborations to translate experimental results into clinical practice and diagnostic and prognostic use in personalized medicine. PMID:23818899

  9. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  10. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

  11. Strategic hospital alliances: impact on financial performance.

    Science.gov (United States)

    Clement, J P; McCue, M J; Luke, R D; Bramble, J D; Rossiter, L F; Ozcan, Y A; Pai, C W

    1997-01-01

    Acute care hospitals have increasingly been forming local strategic hospital alliances (SHAs), which consume considerable resources in forming and may affect the competitiveness of provider markets. This research shows that SHAs and market factors, which have been perceived to be threats to hospitals, are related to hospitals' financial performance. Among the findings are that SHA members have higher net revenues but that they are not more effective at cost control. Nor do the higher net revenues result in higher cash flow. However, increasing SHA penetration in a market is related to lower net revenues per case. In addition, the penetration of private health maintenance organizations in markets is associated with lower revenues and expenses.

  12. The coming alliance revolution in health care.

    Science.gov (United States)

    Lynch, R P

    1993-01-01

    Like it or not, the health care profession is being "shifted" into a revolutionary new world. The question is not will it change but rather how will it change? Who will determine its fate? What form will these changes take? What are the best alternatives for physicians, institutions, health care workers, insurers, employers, and, most importantly, patients? Some of the changes will come from government mandate, others from market forces. To understand what the future might bring, we should look at both the driving forces behind the changes and how other industries have responded to similar forces. An important consideration for health care professionals will be how, if at all, the concepts of collaboration and cooperation that are inherent in networking and alliances will guide their planning.

  13. Alliance Coordination, Dysfunctions, and the Protection of Idiosyncratic Knowledge in Strategic Learning Alliances

    OpenAIRE

    Müller, Dirk

    2010-01-01

    In high technology industries firms use strategic learning alliances to create value that can’t be created alone. While they open their interorganizational membrane to gain new skills and competences, generate new products and services, accelerate development speed, and enter into new markets their idiosyncratic knowledge base may be impaired when knowledge related dysfunctions like the unintended knowledge transfer, asymmetric learning speed or premature closing occur. Within a value approac...

  14. Reactive transport models and simulation with ALLIANCES

    International Nuclear Information System (INIS)

    Leterrier, N.; Deville, E.; Bary, B.; Trotignon, L.; Hedde, T.; Cochepin, B.; Stora, E.

    2009-01-01

    Many chemical processes influence the evolution of nuclear waste storage. As a result, simulations based only upon transport and hydraulic processes fail to describe adequately some industrial scenarios. We need to take into account complex chemical models (mass action laws, kinetics...) which are highly non-linear. In order to simulate the coupling of these chemical reactions with transport, we use a classical Sequential Iterative Approach (SIA), with a fixed point algorithm, within the mainframe of the ALLIANCES platform. This approach allows us to use the various transport and chemical modules available in ALLIANCES, via an operator-splitting method based upon the structure of the chemical system. We present five different applications of reactive transport simulations in the context of nuclear waste storage: 1. A 2D simulation of the lixiviation by rain water of an underground polluted zone high in uranium oxide; 2. The degradation of the steel envelope of a package in contact with clay. Corrosion of the steel creates corrosion products and the altered package becomes a porous medium. We follow the degradation front through kinetic reactions and the coupling with transport; 3. The degradation of a cement-based material by the injection of an aqueous solution of zinc and sulphate ions. In addition to the reactive transport coupling, we take into account in this case the hydraulic retroaction of the porosity variation on the Darcy velocity; 4. The decalcification of a concrete beam in an underground storage structure. In this case, in addition to the reactive transport simulation, we take into account the interaction between chemical degradation and the mechanical forces (cracks...), and the retroactive influence on the structure changes on transport; 5. The degradation of the steel envelope of a package in contact with a clay material under a temperature gradient. In this case the reactive transport simulation is entirely directed by the temperature changes and

  15. Disentangling the change-alliance relationship: Observational assessment of the therapeutic alliance during change and stuck episodes.

    Science.gov (United States)

    Mellado, Augusto; Suárez, Nicolás; Altimir, Carolina; Martínez, Claudio; Pérez, Janet; Krause, Mariane; Horvath, Adam

    2017-09-01

    The therapeutic alliance is considered the most robust process variable associated with positive therapeutic outcome in a variety of psychotherapeutic models [Alexander, L. B., & Luborsky, L. (1986). The Penn Helping Alliance Scales. In L. S. Greenberg & W. M. Pinsoff (Eds.), The psychotherapeutic process: A research handbook (pp. 325-356). New York: Guilford Press; Horvath, A. O., Gaston, L., & Luborsky, L. (1993). The alliance as predictor of benefits of counseling and therapy. In N. Miller, L. Luborsky, J. Barber, & J. P. Docherty (Eds.), Psychodynamic treatment research: A handbook for clinical practice (pp. 247-274). New York, NY: Basic Books; Horvath, A. O., Del Re, A. C., Flückiger, C., & Symonds, D. (2011). Alliance in individual psychotherapy. Psychotherapy, 48, 9-16; Orlinky, D., Grawe, K., & Parks, B. (1994). Process and outcome in psychotherapy: Noch einmal. In A. Bergin & J. S. Garfield (Eds.), Handbook of psychotherapy and behaviour change (4th ed., pp. 270-378). New York, NY: Wiley and Sons]. The relationship between alliance and outcome has traditionally been studied based on measures that assess these therapy factors at a global level. However, the specific variations of the alliance process and their association with therapy segments that are relevant for change have not yet been fully examined. The present study examines the variations in the therapeutic alliance in 73 significant in-session events: 35 change and 38 stuck episodes identified through the observation of 14 short-term therapies of different theoretical orientations. Variations in the alliance were assessed using the VTAS-SF [Shelef, K., & Diamond, G. (2008). Short form of the revised Vanderbilt Therapeutic Alliance Scale: Development, reliability, and validity. Psychotherapy Research, 18, 433-443]. Nested analyses (HLM) indicate a statistically significant better quality of the alliance during change episodes.

  16. International Childhood Cancer Cohort Consortium

    Science.gov (United States)

    An alliance of several large-scale prospective cohort studies of children to pool data and biospecimens from individual cohorts to study various modifiable and genetic factors in relation to cancer risk

  17. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

  18. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  19. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we

  20. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  1. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  2. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  3. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource

  4. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  5. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  6. Pumping services alliance: A new strategy for the 90's

    International Nuclear Information System (INIS)

    Milligan, M.R.; Smith, T.; Crombie, D.

    1993-01-01

    Shell Canada has forged a pumping services alliance with Nowsco Well Service Ltd. for an initial two year period. The alliance will cover pumping related services such as well cementation, well stimulation, coiled tubing work and, in the future could include other services such as pressure testing, corrosion inhibition treatments, flowline pigging, and pumping pipeline inspection tools. The alliance represents a major challenge in operating philosophy away from a competitive bidding strategy to a new strategy of forging business alliances that afford both parties benefits in a more cooperative mode. The alliance incorporates the service company more into the business of Shell Canada and comprises engineering and operations capability. The perceived benefits such an alliance would bring to the business are identified and the key issues that guided selection are documented. Detailed submissions from four major service companies were received and reviwed in a prequalification stage; final selection was made by a multi-disciplinary team. A joint mission statement was prepared that represented Nowsco's and Shell's vision of the alliance and helped guide the negotiations leading to a contract being struck complete with key result areas and performance measurement criteria. 5 refs

  7. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  8. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  9. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  10. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  11. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  12. Stereotactic Radiosurgery With or Without Whole-Brain Radiation Therapy for Limited Brain Metastases: A Secondary Analysis of the North Central Cancer Treatment Group N0574 (Alliance) Randomized Controlled Trial.

    Science.gov (United States)

    Churilla, Thomas M; Ballman, Karla V; Brown, Paul D; Twohy, Erin L; Jaeckle, Kurt; Farace, Elana; Cerhan, Jane H; Anderson, S Keith; Carrero, Xiomara W; Garces, Yolanda I; Barker, Fred G; Deming, Richard; Dixon, Jesse G; Burri, Stuart H; Chung, Caroline; Ménard, Cynthia; Stieber, Volker W; Pollock, Bruce E; Galanis, Evanthia; Buckner, Jan C; Asher, Anthony L

    2017-12-01

    To determine whether whole-brain radiation therapy (WBRT) is associated with improved overall survival among non-small cell lung cancer (NSCLC) patients with favorable prognoses at diagnosis. In the N0574 trial, patients with 1 to 3 brain metastases were randomized to receive stereotactic radiosurgery (SRS) or SRS plus WBRT (SRS + WBRT), with a primary endpoint of cognitive deterioration. We calculated diagnosis-specific graded prognostic assessment (DS-GPA) scores for NSCLC patients and evaluated overall survival according to receipt of WBRT and DS-GPA score using 2 separate cut-points (≥2.0 vs <2.0 and ≥2.5 vs <2.5). A total of 126 NSCLC patients were included for analysis, with median follow-up of 14.2 months. Data for DS-GPA calculation were available for 86.3% of all enrolled NSCLC patients. Overall, 50.0% of patients had DS-GPA score ≥2.0, and 23.0% of patients had DS-GPA scores ≥2.5. The SRS and SRS + WBRT groups were well balanced with regard to prognostic factors. The median survival according to receipt of WBRT was 11.3 months (+WBRT) and 17.9 months (-WBRT) for patients with DS-GPA ≥2.0 (favorable prognoses, P=.63; hazard ratio 0.86; 95% confidence interval 0.47-1.59). Median survival was 3.7 months (+WBRT) and 6.6 months (-WBRT) for patients with DS-GPA <2.0 patients (unfavorable prognoses, P=.85; hazard ratio 0.95; 95% confidence interval 0.56-1.62). Outcomes according to the receipt of WBRT and DS-GPA remained similar utilizing DS-GPA ≥2.5 as a cutoff for favorable prognoses. There was no interaction between the continuum of the DS-GPA groups and WBRT on overall survival (P=.53). We observed no significant differences in survival according to receipt of WBRT in favorable-prognosis NSCLC patients. This study further supports the approach of SRS alone in the majority of patients with limited brain metastases. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Research on Efficiency of Knowledge Transfer in Technical Innovation Alliances

    Science.gov (United States)

    Zhang-sheng, Jiang

    The knowledge transfer efficiency (KTE) is closely relative to the success or failure of technology innovation in strategic alliances. This paper takes the KTE as the essential variable to establish the benefit function model of technology innovations to explore the KTE's influences on partners' innovative decisions under two different modes: independent innovations and alliance innovations. It is found that the higher the KTE, the greater the reducing extent of production costs is. The results could provide some theoretical supports for selections of the optimal competitive-ooperative relationship and managerial flexibility in technical innovation alliances.

  14. A Realist Study of the North Korea-China Alliance

    OpenAIRE

    Hedengran, Rasmus Duus; Kondrup, Alexander Schmidt

    2017-01-01

    The aim of this project was to investigate the nature of the China-North Korea alliance in light of recent developments on the Korean Peninsula. The project found this issue relevant to examine, as this relationship is often identified as being a key factor in shaping the current conflict. The research was centered around the foundations of the alliance and how it has changed to this day. This framework was made possible through the use of Stephen Walt’s balance of threat and alliance formati...

  15. Science and Engineering Alliance: A new resource for the nation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-04-01

    The Lawrence Livermore National Laboratory and four major Historically Black Colleges and Universities with strong research and development capabilities in science, engineering and computer technology have formed the Science and Engineering Alliance. Located in California, Alabama, Mississippi, Louisiana and Texas, each brings to the Alliance a tradition of research and development and educational excellence. This unique consortium is now available to perform research development and training to meet the needs of the public and private sectors. The Alliance was formed to help assure an adequate supply of top-quality minority scientists in the next century, while simultaneously meeting the research and development needs of the public and private sectors.

  16. Ties that tear apart : the social embeddedness of strategic alliance termination

    NARCIS (Netherlands)

    Rooks, G.; Snijders, C.C.P.; Duysters, G.M.

    2013-01-01

    Strategic alliances between firms are inherently unstable, and many alliances fail before the planned termination date. Most studies of the instability of strategic alliances focus on internal factors, such as tensions between alliance partners. In the present study social networks, in particular

  17. Ties that tear apart. The social embeddedness of strategic alliance termination

    NARCIS (Netherlands)

    Rook, G.; Snijders, C.; Duijsters, G.M.

    2013-01-01

    Strategic alliances between firms are inherently unstable, and many alliances fail before the planned termination date. Most studies of the instability of strategic alliances focus on internal factors, such as tensions between alliance partners. In the present study social networks, in particular

  18. The Effects of Trust in Virtual Strategic-Alliance Performance Outcomes

    Science.gov (United States)

    Preston-Ortiz, Dina

    2010-01-01

    Outsourcing increases supported by technology have led to the formation of virtual strategic partnerships. Historically, 70% to 75% of alliance partnerships fail because members are often competitors outside the alliance network. To address alliance failure, a Delphi Study was conducted to identify the role of trust and alliance performance…

  19. A perfect match : an empirical investigation into partner selection as an alliance capability

    NARCIS (Netherlands)

    Duisters, Danielle

    2013-01-01

    Strategic alliances have become a cornerstone of business development. Not only the number of alliances but also the percentage of revenues coming from alliances has increased. Individual companies form alliances to enter new markets, to gain knowledge, or to share risk and resources to bring value

  20. 78 FR 63559 - Order of Suspension of Trading; In The Matter of Crown Alliance Capital Limited

    Science.gov (United States)

    2013-10-24

    ... Alliance Capital Limited (``Crown Alliance''), quoted under the ticker symbol CACL, because of questions regarding the accuracy of assertions in Crown Alliance's public filings concerning the company's assets and... of Crown Alliance Capital Limited October 22, 2013. It appears to the Securities and Exchange...

  1. Competition between alliance blocks : the case of the RISC microprocessor technology

    NARCIS (Netherlands)

    Vanhaverbeke, W.P.M.; Noorderhaven, N.G.

    2001-01-01

    Competition between alliance blocks is a new form of rivalry: groups of firms link together for a common purpose by means of strategic alliances, and competition between alliance blocks is superimposed on competition between individual firms. This paper focuses on alliance blocks in the RISC

  2. FROM ME TO US: THE CONSTRUCTION OF FAMILY ALLIANCE.

    Science.gov (United States)

    Galdiolo, Sarah; Roskam, Isabelle

    2016-01-01

    This longitudinal prospective and multi-informant study based on a three-wave research program (pregnancy, 12 months' postpartum, and 16 months' postpartum) aimed to determine the process of construction of family alliance, as assessed by the Lausanne Trilogue Play (Fivaz-Depeursinge & Corboz-Warnery, 1999). A model using parents' individual characteristics (i.e., personality traits and attachment orientations) as distal variables, coparenting as a mediator, child's temperament as a moderator, and family alliance as outcome was tested using structural equation modeling on 62 nonreferred families. Results showed that both parents' conscientiousness was positively and mothers' avoidant attachment and fathers' anxious attachment were negatively and indirectly (via coparenting) associated with the family alliance. The discussion underlines mothers' and fathers' different roles and the importance of coparenting as a core mechanism in the development of family alliance. © 2015 Michigan Association for Infant Mental Health.

  3. UbuntuNet Alliance : Consolidating Research and Education ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    UbuntuNet Alliance : Consolidating Research and Education Networking - Phase II ... North of Sahara, South of Sahara, United States ... social science, population and public health, and health systems research relevant to the emerging crisis.

  4. The U.S.-Japan Alliance: Sustaining the Transformation

    National Research Council Canada - National Science Library

    Wright, bruce A; Hague, Mark O

    2007-01-01

    .... Most significantly, it outlines the strategic foundations for the alliance and provides operational-level guidance to further the partnership in support of the National Security Strategy and the four...

  5. Networks of military alliances, wars, and international trade.

    Science.gov (United States)

    Jackson, Matthew O; Nei, Stephen

    2015-12-15

    We investigate the role of networks of alliances in preventing (multilateral) interstate wars. We first show that, in the absence of international trade, no network of alliances is peaceful and stable. We then show that international trade induces peaceful and stable networks: Trade increases the density of alliances so that countries are less vulnerable to attack and also reduces countries' incentives to attack an ally. We present historical data on wars and trade showing that the dramatic drop in interstate wars since 1950 is paralleled by a densification and stabilization of trading relationships and alliances. Based on the model we also examine some specific relationships, finding that countries with high levels of trade with their allies are less likely to be involved in wars with any other countries (including allies and nonallies), and that an increase in trade between two countries correlates with a lower chance that they will go to war with each other.

  6. The Physician-Patient Working Alliance in Hemodialysis Treatment.

    Science.gov (United States)

    Fuertes, Jairo N; Rubinstein, Sofia; Reyes, Mariela; Iampornpipopchai, Pichet; Mujeeb, Shanza; Smith, Carroll R; Toporovsky, Arielle

    2017-01-01

    Over the past 20 years, the role of psychological and social factors, including the physician-patient working alliance, have emerged as integral components of medical care for patients with a myriad of health conditions. The current study examines a model comprised of psychological-interpersonal factors and the extent to which it explains patient satisfaction with and adherence to hemodialysis treatment. One hundred and seven adults with end-stage renal disease who were receiving regular outpatient hemodialysis participated in the study. Path analyses show that the physician-patient working alliance indirectly predicts patient adherence through patient satisfaction and patients' outcome expectations. The working alliance directly predicts patients' quality of life. It is concluded that consistent with previous research, the physician-patient working alliance is a significant factor in predicting key patient behaviors in medical care.

  7. Cooperation in International Strategic Alliances and Impact on Host Economies

    DEFF Research Database (Denmark)

    Christoffersen, Jeppe

    2013-01-01

    Researchers have suggested that linkages between multinational enterprises entering developing countries and local firms can promote knowledge upgrading in local firms. Alliances are a particularly intense type of linkage, and this study investigates how the construct of cooperation, which...

  8. Revolution in Business Affairs: Strategic Business Alliances in Army Transformation

    National Research Council Canada - National Science Library

    Bliss, Gary

    2002-01-01

    .... What commercial business practices could assist the Army in its Transformation? Can Strategic Business Alliances between the government and contractors help forge a winning team to aid in the Transformation effort?

  9. Commodity Alliance Model – An Option for Advancing Private and ...

    African Journals Online (AJOL)

    Commodity Alliance Model – An Option for Advancing Private and Commercial ... that ensure adequate value addition and ultimate remunerative price for farmers' ... and integrating them in terms of fair price determination, information flow and ...

  10. Formalized classification of European fen vegetation at the alliance level

    DEFF Research Database (Denmark)

    Peterka, Tomáš; Hájek, Michal; Jiroušek, Martin

    2017-01-01

    Aims Phytosociological classification of fen vegetation (Scheuchzerio palustris-Caricetea fuscae class) differs among European countries. Here we propose a unified vegetation classification of European fens at the alliance level, provide unequivocal assignment rules for individual vegetation plot...

  11. Wind Alliance for the Sustainable Development

    Energy Technology Data Exchange (ETDEWEB)

    Camacho, Damarys Gonzalez [Puerto Rico Energy Affairs Administration, San Juan (Puerto Rico). Executive Office of the Commonwealth of Puerto Rico

    2012-09-30

    The Puerto Rico Energy Affairs Administration (PREAA) is actively engaged in the implementation of existing public policy for the conservation of energy and promotion of renewable energy to reduce consumer’s costs and reduce environmental impact. Puerto Rico is an island in where no own reserves of gas, oil or coal exists. This severe dependence in on foreign oil is reflected in the higher cost of electricity in Puerto Rico, which is significantly higher than most of the United States. Therefore, public energy policy of Puerto Rico places emphasis on diversification of energy sources and the use of renewable energy technologies. The Wind energy Alliance for the Sustainable Development project focused on the formation of a wind energy working group to educate and promote wind energy technologies; at the same time the evaluating the viability of wind energy in Puerto Rico. The educational outreach was performed through a series of wind energy workshops where interested parties such as, installers, sellers, engineers, general public even opposing groups participate from the activities.

  12. Alliance for Sequestration Training, Outreach, Research & Education

    Energy Technology Data Exchange (ETDEWEB)

    Olson, Hilary [Univ. of Texas, Austin, TX (United States). Inst. for Geophysics Jackson School of Geosciences

    2013-12-31

    The Sequestration Training, Outreach, Research and Education (STORE) Alliance at The University of Texas at Austin completed its activity under Department of Energy Funding (DE-FE0002254) on September 1, 2013. The program began as a partnership between the Institute for Geophysics, the Bureau of Economic Geology and the Petroleum and Geosystems Engineering Department at UT. The initial vision of the program was to promote better understanding of CO2 utilization and storage science and engineering technology through programs and opportunities centered on training, outreach, research and technology transfer, and education. With over 8,000 hrs of formal training and education (and almost 4,500 of those hours awarded as continuing education credits) to almost 1,100 people, STORE programs and activities have provided benefits to the Carbon Storage Program of the Department of Energy by helping to build a skilled workforce for the future CCS and larger energy industry, and fostering scientific public literacy needed to continue the U.S. leadership position in climate change mitigation and energy technologies and application. Now in sustaining mode, the program is housed at the Center for Petroleum and Geosystems Engineering, and benefits from partnerships with the Gulf Coast Carbon Center, TOPCORP and other programs at the university receiving industry funding.

  13. Required Steps of Managing International Equity Placement Strategic Alliance

    OpenAIRE

    Wandebori, Harimukti; de Bruijn, Erik Joost; Steenhuis, Harm-Jan

    2011-01-01

    The purpose of the research is to unravel the steps of managing international equity placement strategic alliance (IEPSA). The steps of managing an IEPSA are obtained by conducting theoretical review. The theoretical reviews consist of theory of strategic alliance; definition, classification, and finding definition of an IEPSA, political and analytical considerations and the necessary steps. These steps of managing IEPSA can be classified into analyzing of macro consideration, micro considera...

  14. Combining service marketing and strategic alliances in health care.

    Science.gov (United States)

    Lazarus, I R

    1993-11-01

    With or without federal health care reform to impact the delivery of health care services in the U.S., hospitals must commit to service marketing and strategic alliances as a fundamental business strategy. Service marketing not only differentiates the provider, but with the proper programs in place, it may actually facilitate the formation of strategic alliances. The combination of these strategies will be particularly effective in preparing for any health care policy change.

  15. International Alliance of Green Hotels to Reach Sustainable Competitive Advantages

    OpenAIRE

    Hufei Ge; Silu Chen; Yujie Chen

    2018-01-01

    Under increasing environmental pressure, hotel firms need to improve their ability to access international alliances while maintaining good performance for sustainable development. This paper uses survey data from 784 hotels running at different levels of service in China to test the hypothesis in an integrated analytical model, and the findings show that the impact of international alliances varies with different levels of green hotels. Despite operating in the same sector, hotels running at...

  16. A transaction cost approach to strategic alliances in telecommunications

    OpenAIRE

    Camino Blasco, David; Trecu, Juan Ramón

    1996-01-01

    An emerging form of international business organization is the strategic alliance, a species of joint-venture in which an innovator of technology contracts with another firm for the joint exploitation of technology and other assets across a number of national territories. This work will examine international alliances, applying insights from both the transaction cost and foreign investment theories to the telecommunications service industry and asking whether these cooperation agreements are ...

  17. Advantages and pitfalls of South Africa-Angola strategic alliances

    Directory of Open Access Journals (Sweden)

    A. J. Vogel

    2010-12-01

    Full Text Available Purpose: Owing to a shortage of South African research focusing on international strategic alliances, this study aimed to determine whether the advantages and pitfalls of international strategic alliances referred to in international business publications are also applicable to South African international strategic alliances. Design/Methodology/Approach: This was a formal, empirical study that targeted the 163 South African enterprises which were members of the South African-Angolan Chamber of Commerce in 2005 and 2006. Findings: The results identified joint ventures as the most prominent mode of entry when expanding into developing countries and, with few exceptions, the findings support the advantages and pitfalls of international strategic alliances identified in other international publications. Value of the research: A great deal of international management research over the years has been focused on the importance of strategic alliances as a mode of entry, as well as on the pitfalls experienced by alliance partners, particularly in developed countries. However, the lack of such research in Africa in general and South Africa in particular means that South African enterprises must base their entry mode selection on non-South African research findings, and although this sample size was small, the lack of other Africa-specific research makes this research significant. Implications: With South Africa being the largest source of FDI into the rest of Africa, the findings of this paper show that South African enterprises can attain the advantages associated with international strategic alliances when using this mode of entry into Africa. In terms of pitfalls, the findings highlight the need for multinational enterprises to pay specific attention to the role of governments when forming strategic alliances.

  18. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  19. History and structure of Japan-US nuclear alliance

    International Nuclear Information System (INIS)

    Yoshioka, Hitoshi

    2011-01-01

    'Japan-US nuclear alliance' for civil use of nuclear energy was used here as technical term for the state Japanese commercial power plants were all water-cooled reactors under the US nuclear engineering umbrella and US admitted Japanese development of all 'SNT: sensitive nuclear technology' in the area of nuclear fuel cycle. 'Japan-US alliance' was used for various areas closely related with national security while 'Japan-US nuclear weapon alliance' was for military use of nuclear energy such as nuclear weapon (transport methods included) and counter weapon system. Military and civil use of nuclear energy relied fundamentally on common technical bases and especially nuclear fuel cycle related technologies were directly connected to both uses and called 'SNT'. Japanese nuclear policy sticking to SNT might come from the axiom: nuclear engineering for national security, that meant Japan refrained from nuclear arms but maintained technical and industrial potential of nuclear arms. This could be called 'nuclear arms standby strategy' and derived from compromise of both countries to play role of stabilizer of 'Japan-US alliance'. History of Japanese nuclear power development could be well understood as formation process of 'Japan-US nuclear alliance'. If Fukushima Daiichi accident forced nuclear power to phase out, nuclear fuel cycle would be obliged to terminate. This meant failure of the axiom and dissolution of 'Japan-US nuclear alliance'. (T. Tanaka)

  20. AN INVESTIGATION INTO FACTORS INFLUENCING INTERNATIONAL STRATEGIC ALLIANCE PROCESS

    Directory of Open Access Journals (Sweden)

    Sari Wahyuni

    2003-02-01

    Full Text Available Empirical research indicates that strategic alliances, like other organizational forms, emerge as an adaptive mechanism to market uncertainty, and their developments over time reflect the co-evolution of distinctive firm capabilities and of industry and market activities. Interestingly, most strategic alliances go through similar revolutionary cycles in terms of their motives and capabilities toward the cooperative relationship. Studies in this areas how that alliance failure is an outcome of the co-evolutionary adjustment to changes in the market, the competitive dynamics between partners, and assessment of efficiency of the alliance as an alternative governance structure. It is thus critical to adopt a dynamics perspective and historical observations of cooperative process. This paper attempts to distil, derive and integrate theories across different perspectives into a unified framework that offers a better understanding of alliance process development. Our analysis shows that we can divide strategic alliance development into three phases of development: formation, operation and evaluation. We further endeavor to seek the important factors that should be taken into account in each stage of their life.

  1. Caracterization of the process of forming strategic alliances

    Directory of Open Access Journals (Sweden)

    Luciano Mattana

    2009-03-01

    Full Text Available The union between companies has represented an increase in their competitive capabilities. The strategic alliances have been shown as alternatives for the adequacy of the conduct and organizational framework of the companies toward the market and the world economic juncture. Nevertheless, researches demonstrate that a good number of enterprises of this nature fail. In this sense, this study aimed at characterizing the formation and sustentation of a strategic alliance which has already been formed for 26 years and, thus, verifying the main foundations which are responsible for the maintenance of the union health. The unity of analysis was the alliance between companies as FEMSA and CVI Indústria de Refrigerantes Ltda. Through the method of case study, using the qualitative technique with the aim of describing the case in study, four managers and one collaborator, all of them linked to the alliance, were interviewed. The research allowed establishing that the main foundations of sustaining the alliance in study are in the individual abilities of the partnerships, in the synergy among individual strategies and in the feeling of mutual confidence which exists. Moreover, it was found out that, in the moments of crisis, the major factor responsible for the maintenance of the business is the determination of the upper management on keeping a climate of enthusiasm between the participants of the strategic alliance.

  2. Challenges Fostering Unwillingness to Form Strategic Alliances among Medium-Sized Manufacturing Firms in Tanzania

    OpenAIRE

    Kafigi Jeje

    2014-01-01

    For many years, strategic alliances have attracted the attention of researchers. The most researched area is the challenges facing the development and maintenance of strategic alliances. Most studies on alliance challenges have concentrated on strategic alliances among large firms in developed economies. Little research has been done on the link between these challenges and firms¡¯ unwillingness to form strategic alliances. We therefore want to find whether the unwillingness to form strategic...

  3. China-Russia Alliance - a common choice of the two countries

    Directory of Open Access Journals (Sweden)

    Ma Hang

    2015-01-01

    Full Text Available Compared with Sino-Soviet Alliance and NATO countries alliance, China -Russia Alliance should have its own characteristics. China-Russia Alliance can further enhance strategic mutual trust betweeneach other, enhance cooperation quality and space, to promote the mutualprogress and prosperity, achieve national revival of China and Russia as soon as possible, which is the ultimate goal of theChina-Russia Alliance.

  4. A Measure of the Parent-Team Alliance in Youth Residential Psychiatry: The Revised Short Working Alliance Inventory

    NARCIS (Netherlands)

    Lamers, A.; Delsing, M.J.M.H.; Van Widenfelt, B.M.; Vermeiren, R.R.J.M.

    2015-01-01

    Background: The therapeutic alliance between multidisciplinary teams and parents within youth (semi) residential psychiatry is essential for the treatment process and forms a promising process variable for Routine Outcome Monitoring (ROM). No short evaluative instrument, however, is currently

  5. Item response theory analysis of Working Alliance Inventory, revised response format, and new Brief Alliance Inventory.

    Science.gov (United States)

    Mallinckrodt, Brent; Tekie, Yacob T

    2016-11-01

    The Working Alliance Inventory (WAI) has made great contributions to psychotherapy research. However, studies suggest the 7-point response format and 3-factor structure of the client version may have psychometric problems. This study used Rasch item response theory (IRT) to (a) improve WAI response format, (b) compare two brief 12-item versions (WAI-sr; WAI-s), and (c) develop a new 16-item Brief Alliance Inventory (BAI). Archival data from 1786 counseling center and community clients were analyzed. IRT findings suggested problems with crossed category thresholds. A rescoring scheme that combines neighboring responses to create 5- and 4-point scales sharply reduced these problems. Although subscale variance was reduced by 11-26%, rescoring yielded improved reliability and generally higher correlations with therapy process (session depth and smoothness) and outcome measures (residual gain symptom improvement). The 16-item BAI was designed to maximize "bandwidth" of item difficulty and preserve a broader range of WAI sensitivity than WAI-s or WAI-sr. Comparisons suggest the BAI performed better in several respects than the WAI-s or WAI-sr and equivalent to the full WAI on several performance indicators.

  6. A Measure of the Parent-Team Alliance in Youth Residential Psychiatry: The Revised Short Working Alliance Inventory.

    Science.gov (United States)

    Lamers, Audri; Delsing, Marc J M H; van Widenfelt, Brigit M; Vermeiren, Robert R J M

    The therapeutic alliance between multidisciplinary teams and parents within youth (semi) residential psychiatry is essential for the treatment process and forms a promising process variable for Routine Outcome Monitoring (ROM). No short evaluative instrument, however, is currently available to assess parent-team alliance. In this study, the Working Alliance Inventory-Short Version (WAV-12), a widely used alliance questionnaire, was adjusted to assess parent-team alliance from both a parent and team perspective within a youth residential setting. Psychometric properties, including factor structure and validity of the subscales, were explored. A sample of youth with mainly complex developmental disorders admitted to 11 inpatient and day patient units of a child and adolescent psychiatric institute participated in this study. The case manager involved with the youth and the primary caregiver of 87 youth completed the revised WAV-12 (WAV-12R). The team version of the WAV-12R showed a good fit to the original conceptualized model, and distinguished Bond, Task and Goal scales. For the parents' version an adjusted model with Insight, Bond and combined Task/Goal scales had the best fit. The reliability and validity of the scales were shown to be good. This paper presents preliminary evidence that the parent and treatment team versions of the WAV-12R are psychometrically sound for assessing parent-team alliance within youth (semi) residential psychiatry in the Netherlands. The team and parents' versions of the WAV-12R are recommended instruments to complement outcome measures in ROM.

  7. The International Planetary Data Alliance (IPDA)

    Science.gov (United States)

    Stein, Thomas; Gopala Krishna, Barla; Crichton, Daniel J.

    2016-07-01

    The International Planetary Data Alliance (IPDA) is a close association of partners with the aim of improving the quality of planetary science data and services to the end users of space based instrumentation. The specific mission of the IPDA is to facilitate global access to, and exchange of, high quality scientific data products managed across international boundaries. Ensuring proper capture, accessibility and availability of the data is the task of the individual member space agencies. The IPDA is focused on developing an international standard that allows discovery, query, access, and usage of such data across international planetary data archive systems. While trends in other areas of space science are concentrating on the sharing of science data from diverse standards and collection methods, the IPDA concentrates on promoting governing data standards that drive common methods for collecting and describing planetary science data across the international community. This approach better supports the long term goal of easing data sharing across system and agency boundaries. An initial starting point for developing such a standard will be internationalization of NASA's Planetary Data System's (PDS) PDS4 standard. The IPDA was formed in 2006 with the purpose of adopting standards and developing collaborations across agencies to ensure data is captured in common formats. It has grown to a dozen member agencies represented by a number of different groups through the IPDA Steering Committee. Member agencies include: Armenian Astronomical Society, China National Space Agency (CNSA), European Space Agency (ESA), German Aerospace Center (DLR), Indian Space Research Organization (ISRO), Italian Space Agency (ASI), Japanese Aerospace Exploration Agency (JAXA), National Air and Space Administration (NASA), National Centre for Space Studies (CNES), Space Research Institute (IKI), UAE Space Agency, and UK Space Agency. The IPDA Steering Committee oversees the execution of

  8. What Do Chinese and Foreign Universities Value about Their Strategic Alliances? Exploring a Dimension of Higher Education Alliances in a Cross Cultural Context

    Science.gov (United States)

    Willis, Mike

    2003-01-01

    There are now over 5,000 alliances between Chinese and foreign universities but there is little research on how managers from the two sides value the various aspects of their educational alliances. This research finds that both sides valued a range of alliance levels, types, activities, sizes and structures but there were significant differences.…

  9. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  10. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  11. Required Steps of Managing International Equity Placement Strategic Alliance

    Directory of Open Access Journals (Sweden)

    Harimukti Wandebori

    2012-01-01

    Full Text Available The purpose of the research is to unravel the steps of managing international equity placement strategic alliance (IEPSA. The steps of managing an IEPSA are obtained by conducting theoretical review. The theoretical reviews consist of theory of strategic alliance; definition, classification, and finding definition of an IEPSA, political and analytical considerations and the necessary steps. These steps of managing IEPSA can be classified into analyzing of macro consideration, micro consideration, domestic company’s stakeholder support, cultural understanding, strategic planning, internal support, human resource management, organizational arrangement, management control system, evolved cultural understanding, and evaluating results. In this research, the domestic partners who formed the IEPSAs are limited to State-Owned Enterprises (SOEs. The IEPSA was one of the means of privatization. The research will be beneficial for both foreign and domestic partners who form an IEPSA in the previous SOEs. By knowing the steps of managing the IEPSA both partners will be able to secure a successful implementation of IEPSA. By identifying the steps of managing the IEPSA, the stakeholder will not see IEPSA as threat rather as an opportunity to improve performance, to create synergy, and generate benefits for both partners and stakeholder. By knowing the necessary steps of managing the IEPSA, the stakeholder including society and politician will envisage the IEPSA as a means of effectively improving the SOEs’ performances.The research was espected to provide contributions for the research on strategic alliances. Apparently, there exist no literatures discussing about IEPSA in the domain of strategic alliances. Keywords: strategic alliance, equity placement, international equity placement strategic alliance, privatization, steps of international equity placement strategic alliance, state-owned enterprises

  12. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  13. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  14. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik

    2013-01-01

    their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes...... to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse...

  15. How Partner Characteristics Can Affect Performance of Alliances with Different Time Frames?

    Directory of Open Access Journals (Sweden)

    Seyed Hossein JALALI

    2017-11-01

    Full Text Available Firms increasingly adopt cooperative strategies and form strategic alliances with foreign partners to be prosperous in entering to international market. Most of scholars have typically focused on generic, conceptual models for alliances partner selection, addressing only limited dimensions of the partner characteristics. This paper presents a new empirical framework that considering the effect of partner characteristics on export performance of alliances, in the case of short/mediumterm alliances and long-term ones. The study explores the effective partner characteristics for each type of alliances based on a sample of 540 alliances which rooted in East European region and also, have at least one Iranian partner. The findings stress the differences between varied partner characteristics in short/medium-term and long-term alliances. More specifically, results introduce a framework that addresses certain and specific partner characteristics to improve the export performance of alliances, due to the time frame of strategic alliances.

  16. Strategic Classification and Examination of the Development of Current Airline Alliance Activities

    Science.gov (United States)

    Wang, Zhi H.; Evans, Michael

    2002-01-01

    Previous research argues that despite the fact that strategic alliances have become an important feature of the world airline industry, little rigorous analysis has been done on the effects of these alliances. This is partially because there is a lack of precise definitions to specify different types of airline alliances in the literature. This research identifies several categories of airline alliances through a strategic classification of the current alliance activities involving the major airlines for the period 1989 to 1999. The classification enables this research to examine how strategic alliance activities are evolving, particularly to compare how airlines in North America, the European Union and the Asia Pacific region have committed to different alliances. Findings show that there is a significant difference between the number and scope of alliances adopted in the three aviation markets. These findings facilitate research to further analyse the impact of market liberalization on various formations of strategic airline alliances.

  17. Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial

    Directory of Open Access Journals (Sweden)

    Nicolas eServant

    2014-05-01

    Full Text Available Precision medicine (PM requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i warranting the integration and the traceability of data, ii ensuring the correct processing and analyses of genomic data and iii applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.

  18. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  19. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  20. The Factor Structure of The Working Alliance Inventory in Cognitive-Behavioral Therapy

    Science.gov (United States)

    Andrusyna, Tomasz P.; Tang, Tony Z.; DeRubeis, Robert J.; Luborsky, Lester

    2001-01-01

    Studies of the therapeutic alliance in cognitive-behavioral therapy (CBT) have varied in their results, necessitating a deeper understanding of this construct. Through an exploratory factor analysis of the alliance in CBT, as measured by the Working Alliance Inventory (shortened, observer-rated version), the authors found a two-factor structure of alliance that challenges the commonly accepted one general factor of alliance. The results suggest that the relationship between therapist and client (Relationship) may be largely independent of the client's agreement with and confidence in the therapist and CBT (Agreement/ Confidence), necessitating independent measures of these two factors, not one measure of a general alliance factor. PMID:11402080

  1. Study on the partner selecting method of strategic alliance in high and new technology enterprises

    Institute of Scientific and Technical Information of China (English)

    王宏起; 唐宇; 迟运领

    2004-01-01

    A successful and effective strategic alliance involves many factors, of which selecting a proper partner is the most important factor to achieve the success of the alliance. In view of the characteristics of strategic alliance in high and new technology enterprises and according to the analysis on the standards of partner selecting and the factors of the success of alliance, this paper does some deeper research on the partner selecting and the alliance evaluation process from the perspective of different strategic levels by using a fuzzy comprehensive evaluating method, thus providing a method to select the alliance partner for high and new technology enterprises in China.

  2. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  3. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  4. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  5. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  6. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  7. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  8. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  9. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  10. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  11. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  13. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  14. Bioinformatic survey of ABC transporters in dermatophytes.

    Science.gov (United States)

    Gadzalski, Marek; Ciesielska, Anita; Stączek, Paweł

    2016-01-15

    ATP binding cassette (ABC) transporters constitute a very large and ubiquitous superfamily of membrane proteins. They are responsible for ATP hydrolysis driven translocation of countless substrates. Being a very old and diverse group of proteins present in all organisms they share a common feature, which is the presence of an evolutionary conservative nucleotide binding domain (NBD)--the engine that drives the transport. Another common domain is a transmembrane domain (TMD) which consists of several membrane-spanning helices. This part of protein is substrate-specific, thus it is much more variable. ABC transporters are known for driving drug efflux in many pathogens and cancer cells, therefore they are the subject of extensive studies. There are many examples of conferring a drug resistance phenotype in fungal pathogens by ABC transporters, however, little is known about these proteins in dermatophytes--a group of fungi causing superficial mycoses. So far only a single ABC transporter has been extensively studied in this group of pathogens. We analyzed available genomic sequences of seven dermatophyte species in order to provide an insight into dermatophyte ABC protein inventory. Phylogenetic studies of ABC transporter genes and their products were conducted and included ABC transporters of other fungi. Our results show that each dermatophyte genome studied possesses a great variety of ABC transporter genes. Detailed analysis of selected genes and their products indicates that relatively recent duplication of ABC transporter genes could lead to novel substrate specificity. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Presentation of political Alliances in the Romanian audiovisual media

    Directory of Open Access Journals (Sweden)

    Flaviu Calin RUS

    2011-01-01

    Full Text Available This material wishes to highlight the way in which the main political alliances have been formed in Romania in the last 20 years, as well as the way they have been reflected in the media. Moreover, we have tried to analyze the involvement of journalists and political analysts in explaining these political events. The study will focus on four political alliances, namely: CDR (the Romanian Democratic Convention, D.A. (Y.E.S. - Justice and Truth between PNL – the National Liberal Party and PD - the Democratic Party, ACD (the Centre-Right Alliance between PNL and PC – the Conservative Party and USL (the Social-Liberal Union between PSD – the Social Democrat Party, PNL and PC.

  16. A Socio-technical Approach for Transient SME Alliances

    Science.gov (United States)

    Rezgui, Yacine

    The paper discusses technical requirements to promote the adoption of alliance modes of operation by SMEs in the construction sector. These requirements have provided a basis for specifying a set of functionality to support the collaboration and cooperation needs of SMEs. While service-oriented architectures and semantic web services provide the middleware technology to implement the identified functionality, a number of key technical limitations have been identified, including lack of support for the dynamic and non-functional characteristics of SME alliances distributed business processes, lack of execution monitoring functionality to manage running business processes, and lack of support for semantic reasoning to enable SME business process service composition. The paper examines these issues and provides key directions for supporting SME alliances effectively.

  17. International Alliance of Green Hotels to Reach Sustainable Competitive Advantages

    Directory of Open Access Journals (Sweden)

    Hufei Ge

    2018-02-01

    Full Text Available Under increasing environmental pressure, hotel firms need to improve their ability to access international alliances while maintaining good performance for sustainable development. This paper uses survey data from 784 hotels running at different levels of service in China to test the hypothesis in an integrated analytical model, and the findings show that the impact of international alliances varies with different levels of green hotels. Despite operating in the same sector, hotels running at different levels of service vary their respective tactics to gain sustainable competitive advantage and achieve significantly different results. This study intends to inform hotel managers in obtaining specific performance goals by developing absorptive capacity, and by choosing the most suitable alliance for their level of operation.

  18. Best intentions: Lessons learned on international partnering and alliance contracts

    International Nuclear Information System (INIS)

    Farrell, S.; McDermott, J.R.; Ramsay, A.; Watzke, J.

    1996-01-01

    Although the energy industry is still in the early stages of partnering and alliancing, there is enough accumulated experience to be worth sharing information on what has worked and what has not. This paper explores the lessons learned in six agreements in the UK, the US, and the Middle East. It concludes that not all projects are potential candidates for partnering or alliances. Those likely to be successful will contain common characteristics of complexity, uncertainty, technology and duration. Management structure is moving towards integrated teams, although projects currently fall along a broad spectrum before becoming truly integrated. The risk/reward structure is becoming more complex over time, although it is unclear that tinkering with percentage sharing schemes will actually change the behavior of project participants and result in additional cost savings. The use of team building techniques and facilitators may well enhance the alliance implementation, but the choice of both company and individual members is fundamental to success. The overriding success factor, however, is the setting of fair and achievable targets. All of the managers surveyed stated that their projects benefited from the use of a partnering or alliance structure. Three of the projects were far enough along to cite significant cost savings. Although some in the industry are still doubtful that alliances can make a true difference to a project's outcome, those who have participated are convinced they have achieved results which would have been unattainable in a traditional structure. They would add, however, that partnering and alliancing is not easy, and not for all projects. The industry must share practical information if significant learning is to occur

  19. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  20. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  1. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  2. International Education Alliance for education in Radioactive Waste Management

    International Nuclear Information System (INIS)

    King, G.P.

    1993-01-01

    Sharing information among countries about technologies being used or planned for spent nuclear fuel and high-level radioactive waste management, storage, and disposal is important toward building national confidence and trust within nations for proceeding with implementation of long-term solutions to waste management. To facilitate the effective sharing, specific mechanisms or vehicles are required. To this end, in 1992, the International Education Alliance for Education in Radioactive Waste Management was established. This paper discusses the purpose, objectives, plans, activities, and benefits of this newly-formed first-of-a-kind international education alliance in this field

  3. Understanding the working alliance with clients diagnosed with anorexia nervosa.

    Science.gov (United States)

    Oyer, Laura; O'Halloran, Mary Sean; Christoe-Frazier, Liesel

    2016-01-01

    The therapeutic working alliance is a vital ingredient of psychotherapy, specifically for clients diagnosed with anorexia nervosa, as progress is often slow and treatment difficult. This qualitative phenomenological study investigated the experiences of eight clients with anorexia nervosa and seven therapists who work with this population, regarding which therapist factors aided in and challenged the working alliance formation in individual psychotherapy. Data was gathered through semi-structured interviews. Some helpful therapist factors included collaboration, appropriate self-disclosure, providing a warm and safe environment, and willingness to be contacted outside of a session. Unhelpful factors included lack of attunement and objectivity and failure to individualize treatment.

  4. Analysis on stability of strategic alliance: A game theory perspective

    Institute of Scientific and Technical Information of China (English)

    CHEN Fei-qiong; FAN Liang-cong

    2006-01-01

    Strategic alliance has suffered much instabilities since its first implementation. Scholars have carried out many embedded, precise and comprehensive researches from both theory and empiricism. Here we try to find certain stable solutions by employing game theory, in an attempt to construct theoretical bases for strategic alliance, which people called "one of the most important organizational innovation in the end of the 20th century" (Shi, 2001), to exploit its advantages in the process of globalization. Finally, this article puts forward some advices for its success.

  5. Partner Selection for Strategic Alliance in Networked Manufacturing

    Institute of Scientific and Technical Information of China (English)

    CHENYou-ping; YINYong; ZHOUZu-de

    2004-01-01

    Networked Manufacturing is the trend evolution for manufacture enterprise to gain core competence in the networked economy environment. In this paper, the definition of the strategic alliance is introduced and its life cycle is described. As the selection of suitable partners is of vital importance to the success for strategic alliance in Networked Manufacturing environment, also in this paper, the definition, criteria and process for partner selection are introduced. Then the fuzzy-AHP (Analytic Hierarchy Process) method, as a fuzzy extension of analytic hierarchical approach for partner selection, is given. In the end, a case study is provided.

  6. Information Technology and Telecommunications: Impacts on Strategic Alliance

    Institute of Scientific and Technical Information of China (English)

    张延峰; 刘益; 李垣

    2002-01-01

    Strategic alliance (SA) is an important way with which the enterprise can grow up. However, the development of information technology and telecommunications (IT&Ts) has vital impacts on the theory and practice of SA management. This paper analyzes these impacts from four respects: the management thinking, forming, inter-organizational interaction, information exchange and knowledge transferring of SA. We point out the new characteristics of SA management in the information age and then put forward corresponding countermeasures on the basic of analyzing current alliance management theory and issue. Finally we discuss some issues that would be researched further in the future.

  7. The Authorized Economic Operator in the Pacific Alliance

    OpenAIRE

    Vega Cancino, Jorge

    2017-01-01

    This paper portrays an up-to-date status of the Authorized Economic Operator (AEO) Programs in the Pacific Alliance (PA), shining a light on the different obstacles these programs have encountered and what their probable outcomes will be in the coming years. The main goal with this investigation is to answer two questions: (1) What is the current situation of the AEO programs within the Pacific Alliance? (2) What impact will the PA’s AEO programs have in the medium term? Can these programs be...

  8. The HISH-alliance and the Arab spring

    DEFF Research Database (Denmark)

    Dandan, Salem Ben Souhail

    , in terms of relative strength, as being essential in understanding the alliance. It then goes on to look at what the Arab-spring has so far meant for the different actors and how this has impacted the alliance. It is argued that the ability of the non-state armed entities, Hezbollah and Hamas...... within the global community, due to the current systemic situation and the Arab-spring. In short, the paper aims to establish a correlation between the international and regional changes, the newly found autonomy of the non-state entities and the decreasing capabilities of the states, in order...

  9. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  10. Predicting the performance of a strategic alliance: an analysis of the Community Clinical Oncology Program.

    Science.gov (United States)

    Kaluzny, A D; Lacey, L M; Warnecke, R; Hynes, D M; Morrissey, J; Ford, L; Sondik, E

    1993-06-01

    This study is designed to examine the effects of environment and structure of the Community Clinical Oncology Program (CCOP) on performance as measured by patient accrual to National Cancer Institute (NCI)-approved treatment protocols. Data and analysis are part of a larger evaluation of the NCI Community Clinical Oncology Program during its second funding cycle, June 1987-May 1990. Data, taken from primary and secondary sources, included a survey of selected informants in CCOPs and research bases, CCOP grant applications, CCOP annual progress reports, and site visits to a subsample of CCOPs (N = 20) and research bases (N = 5). Accrual data were obtained from NCI records. Analysis involved three complementary sets of factors: the local health care resources environment available to the CCOP, the larger policy environment as reflected by the relationship of the CCOP to selected research bases and the NCI, and the operational structure of the CCOP itself. A hierarchical model examined the separate and cumulative effects of local and policy environment and structure on performance. Other things equal, the primary predictors of treatment accrual were: (1) the larger policy environment, as measured by the attendance of nurses at research base meetings; and (2) operational structure, as measured by the number and character of components within participating CCOPs and the number of hours per week worked by data managers. These factors explained 73 percent of the total variance in accrual performance. Findings suggest criteria for selecting the types of organizations to participate in the alliance, as well as for establishing guidelines for managing such alliances. A future challenge is to determine the extent to which factors predicting accrual to cancer treatment clinical trials are equally important as predictors of accrual to cancer prevention and control trials.

  11. The Comparative Effects of Transaction Cost Economics and Resource Based View: A Technological Alliance Motivational Perspective

    Directory of Open Access Journals (Sweden)

    Hwan Jin Kim

    2016-06-01

    Full Text Available This paper examines the impact of two main alliance motivation theories, transaction cost economics (TCE and resource based view (RBV, on alliance processes among Korean manufacturing high-tech ventures. Results show that TCE and RBV are complimentarily explaining the formation of inter-firm alliances. TCE variables are more related with alliance partner characteristics while RBV is more linked with partner capabilities. Both show positive effects on performance. No significant effect is found on determining an alliance governance structure. While selecting appropriate technological alliance partners show positive effects on performance, no significant effect is found between alliance governance structure and performance. Factors of both theories impacting each alliance stage and analytical explanations of such impacts are discussed.

  12. Lessons Learned: A Strategic Alliance to Improve Elementary Physical Education in an Urban School District.

    Science.gov (United States)

    Thompson, Hannah R; Haguewood, Robin; Tantoco, Nicole; Madsen, Kristine A

    2015-01-01

    Physical education (PE) can help to achieve important public health goals, but is often under-prioritized and lacking in schools. To detail the actions, impact, and successes of a strategic alliance formed by three collaborating organizations to improve PE in a large California school district. Semistructured interviews with alliance members, principals, and teachers in 20 elementary schools, 3 years after the alliance formation. Interviewees reported district-level increases in priority and funding for PE and attributed improvements to the alliance's collection and dissemination of local data on the status of PE. Common goals, trust, and open communication within the alliance were seen as critical to the alliance's success. However, changes in district- or school-level accountability measures for PE were not reported. This strategic alliance succeeded in promoting district-level priority and funding for PE. Ongoing alliance work will focus on increasing accountability measures for PE, which may take longer to implement.

  13. Maternal Depression Mediates the Link Between Therapeutic Alliance and Improvements in Adolescent Externalizing Behavior

    NARCIS (Netherlands)

    Granic, I.; Otten, R.; Blokland, K.; Solomon, T.; Engels, R.C.M.E.; Ferguson, B.

    2012-01-01

    The current study: (1) examined the relation between therapeutic alliance and changes in adolescent externalizing behavior in Multisystemic Therapy; (2) tested whether maternal depression mediates this relation; and (3) determined whether mothers' and clinicians' perceptions of the alliance

  14. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  15. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  16. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  17. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  18. Motives behind Strategic Alliance Formation among Medium-Sized Manufacturing Firms in Tanzania

    OpenAIRE

    Kafigi Jeje

    2014-01-01

    Research on strategic alliance motives has attracted a great attention as firms strive to become market leaders. One critical area is to assess the contribution of these motives to strategic alliance formation. Most studies on alliance motives concentrate on international strategic alliances that involve large or multinational corporations from developed economies. Little research has been done on Small and Medium Enterprises (SMEs), particularly Medium-Sized Enterprises (MEs) from the manufa...

  19. Game Theory Study on Distributors' Alliance to Gain Competitive Advantage in Marketing Channel

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shi-ying; CHEN Jie; WANG Fang-hua

    2005-01-01

    Using the Cournot Game Model, this paper has analyzed the motivation of the distributors' alliance to gain competitive advantage in marketing channel. At first, this paper separately analyzed the advantage of alliance in the situation of oneshort game and infinitely repeated game, then, based on the analysis of distributors' betrayal of the alliance under infinitely repeated game, the conditions to maintain the distributors alliance are put forward and discussed.

  20. Relational Governance,Alliance Type and Alliance Performance in Chinese Strategic Alliances%战略联盟中关系控制与联盟类型对联盟绩效的影响研究

    Institute of Scientific and Technical Information of China (English)

    乐琦; 李建媛; 蒋峦

    2016-01-01

    基于中国境内141个企业战略联盟样本,首先验证了在中国情境下战略联盟中关系控制对联盟绩效的积极作用,在此基础上检验了联盟类型对关系控制与联盟绩效关系的调节作用。结果表明:与产权联盟相比,非产权联盟中关系控制对联盟绩效的积极作用更大;与横向联盟和非相关联盟相比,纵向联盟中关系控制对联盟绩效的积极作用更大;与本地联盟相比,跨区联盟中关系控制对联盟绩效的积极作用更大;与短期联盟相比,长期联盟中关系控制对联盟绩效的积极作用更大。%Based on a sample of 141 alliances,this paper testifies the positive effect of relational governance on alliance per-formance. Moreover,it is focus on the moderating role of alliance type on the relationship between relational governance and alliance performance. The empirical results show that,compared with equity-based alliance,relational governance has more positive effect on alliance performance in non equity-based alliance;compared to horizontal alliance and irrelevant alliance, relational governance has more positive effect on alliance performance in vertical alliance;compared with local alliance,re-lational governance has more positive effect on alliance performance in cross-region alliance;compared with short-time alli-ance,relational governance has more positive effect on alliance performance in long-time alliance.

  1. Crisis in the transition of Telecom Alliance Unisource

    NARCIS (Netherlands)

    van Marrewijk, A.H.

    2004-01-01

    The telecom sector has changed dramatically during the last decade. In order to meet new regulations, fierce competition and a growing demand for cheap and high quality telecom services by multinationals, European public telecom operators have created pan-European strategic alliances. This paper

  2. National Alliance of Business Sales Techniques and Results (STAR).

    Science.gov (United States)

    Golightly, Steven J.

    This paper presents an overview of the Sales Techniques and Results (STAR) training program developed by the National Alliance of Business in conjunction with IBM. The STAR training program can be used to help vocational directors, teachers, and counselors to be better salespersons for cooperative education or job placement programs. The paper…

  3. Management of strategic coopetition among partners within international airline alliances

    Directory of Open Access Journals (Sweden)

    Frank Himpel

    2012-03-01

    Full Text Available Background: International network-carriers span the globe by linking airports on all five continents. At the core of those networks are hub-airports that serve as the centers for (inter-national in- and outbound traffic flows. From a business model point of view, the major international carriers are so-called network-carriers, for their core concept is based on transfer-oriented hub-and-spoke-systems. In order to maximize revenue streams of network-carriers, changes in strategic slot allocation and strategic net planning are becoming increasingly relevant. The aim of this work was to analyze the impact of various elements of the management of strategic coopetition among partners within international airline alliances on the revenues obtained by individual partners. Methods: the problems related to the optimization of strategic slot allocation and strategic net planning from the point of view of the individual profit shared and added net contribution margins were discussed. Results and conclusions: Two extreme scenarios may be projected. The first one is that partners within a given alliance system may start to increase merger and acquisition activities. Thereby scale effects may be utilized. The other one is, when rivalry becomes too dominant over time, some partners may (have to exit alliance systems. Thereby "atomic" subsystems may be on the rebound. Strategic coopetition management is aimed to keep leading international network carriers "on track" in the field of alliance management of that nature.

  4. Institutional Distance and Partner Selection in International Technological Alliances

    NARCIS (Netherlands)

    Krammer, Marius

    2013-01-01

    This study posits that institutional distance has a negative influence on partner selection in international technological alliances. Empirical results based on a dataset of firms in the global tire industry confirm that firms prefer technological partners from closer cognitive, normative and

  5. Clinical Perspective The parent-child-therapist alliance: A case ...

    African Journals Online (AJOL)

    Journal of Child and Adolescent Mental Health ... The parent-child-therapist alliance: A case study using a strategic approach. Thirusha Naidu, Sheethal Behari. Abstract. In this paper we present a single case study of a clinical approach that ...

  6. Alliance Formation Motives in SMEs An Explorative Conjoint Analysis Study

    NARCIS (Netherlands)

    Van Gils, Anita; Zwart, Peter S.

    Cooperative agreements are important tools to improve the competitive position of small and medium-sized firms.This explorative conjoint analysis study simultaneously examines the importance of firm, environmental and partner motives on the formation of two types of SME-alliances. In addition, we

  7. Required Steps of Managing International Equity Placement Strategic Alliance

    Directory of Open Access Journals (Sweden)

    Harimukti Wandebori

    2011-12-01

    Full Text Available The purpose of the research is to unravel the steps of managing international equity placement strategic alliance (IEPSA. The steps of managing an IEPSA are obtained by conducting theoretical review. The theoretical reviews consist of theory of strategic alliance; definition, classification, and finding definition of an IEPSA, political and analytical considerations and the necessary steps. These steps of managing IEPSA can be classified into analyzing of macro consideration, micro consideration, domestic company’s stakeholder support, cultural understanding, strategic planning, internal support, human resource management, organizational arrangement, management control system, evolved cultural understanding, and evaluating results. In this research, the domestic partners who formed the IEPSAs are limited to State-Owned Enterprises (SOEs. The IEPSA was one of the means of privatization. The research will be beneficial for both foreign and domestic partners who form an IEPSA in the previous SOEs. By knowing the steps of managing the IEPSA both partners will be able to secure a successful implementation of IEPSA. By identifying the steps of managing the IEPSA, the stakeholder will not see IEPSA as threat rather as an opportunity to improve performance, to create synergy, and generate benefits for both partners and stakeholder. By knowing the necessary steps of managing the IEPSA, the stakeholder including society and politician will envisage the IEPSA as a means of effectively improving the SOEs’ performances.The research was espected to provide contributions for the research on strategic alliances. Apparently, there exist no literatures discussing about IEPSA in the domain of strategic alliances.

  8. Strategic Alliances: the prospect for business growth | Obo | Global ...

    African Journals Online (AJOL)

    To this end, the business firms are classified as runners up firm and weak business firm. An alternative concept, the strategic alliances, is hereby proposed as the only way forward to help resolve these differences and to provide a better framework for managing business firms that would enhance growth and profitability.

  9. Corporate Developments and Strategic Alliances in E-Learning.

    Science.gov (United States)

    Clarke, Thomas; Hermens, Antoine

    2001-01-01

    Describes the emergence of corporate universities and strategic alliances among universities, electronic learning companies, and technology companies that are providing online delivery of interactive education and training. Outlines characteristics of comprehensive electronic learning and cautions against the use of new technologies to deliver…

  10. Advisory Working Alliance, Perceived English Proficiency, and Acculturative Stress

    Science.gov (United States)

    Wei, Meifen; Tsai, Pei-Chun; Chao, Ruth Chu-Lien; Du, Yi; Lin, Shu-Ping

    2012-01-01

    The aim of this study was to examine the moderators of (a) general or cross-cultural advisory working alliances and (b) perceived English proficiency on the association between acculturative stress and psychological distress. A total of 143 East Asian international students completed an online survey. Results from a hierarchical regression…

  11. Alliances in the Dutch BeweegKuur lifestyle intervention

    NARCIS (Netherlands)

    Hartog-van den Esker, den F.G.; Wagemakers, A.; Vaandrager, L.; Dijk, van M.; Koelen, M.A.

    2014-01-01

    Objective: BeweegKuur (Exercise Therapy) is a Dutch lifestyle programme in which participants are referred by a general practitioner (GP) to a lifestyle advisor. To support participants, regional and local alliances are established. The present study explored the successes and challenges associated

  12. 76 FR 65696 - Battelle Energy Alliance, et al.;

    Science.gov (United States)

    2011-10-24

    ... DEPARTMENT OF COMMERCE International Trade Administration Battelle Energy Alliance, et al.; Notice of Consolidated Decision on Applications for Duty-Free Entry of Electron Microscope This is a decision consolidated pursuant to Section 6(c) of the Educational, Scientific, and Cultural Materials...

  13. Abstracts of 3. congress of global anti-nuclear alliance

    International Nuclear Information System (INIS)

    2000-01-01

    The 3 congress of global anti-nuclear alliance was held on 18-20 May, 2000 in Astana. There were 55 reports on different aspects of nuclear disarmament; nuclear safeguards; safe operation of nuclear power plants; rehabilitation of population and lands, damaged from many-years tests in Semipalatinsk site; radiobiological monitoring of ecosystems and others presented at the congress

  14. IDRC Pre-ICN Forum on Competition and Development Alliance ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    dzavalamora

    2011-05-17

    May 17, 2011 ... Alliance Building for A Culture of Compliance. Session 1: The general case for ... Big business: cost benefit equation may be negative. • Small business and farmers ... constitutions (e.g. US, Australia ) and treaties. (e.g. TFEU).

  15. UbuntuNet Alliance : Consolidating Research and Education ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    13 août 2009 ... UbuntuNet Alliance was established in 2005 to address these issues and foster the development of national research and education networking (NREN) in ... politique (IREEP) est un organisme indépendant à but non lucratif établi en 2004 afin de contribuer à la formation de la prochaine génération d&.

  16. Chinese firms entering Europe : internationalization through acquistitions and strategic alliances

    NARCIS (Netherlands)

    Zhang, Y.; Duysters, G.M.; Filloppv, S.

    2012-01-01

    Purpose – The purpose of this study is to examine specific use of strategic alliances and acquisitions for Chinese firms to catch-up technologically and to enhance their internationalization competence. Design/methodology/approach – The paper offers a conceptual analysis of internationalization

  17. Chinese firms entering Europe : Internationalization through acquisitions and strategic alliances

    NARCIS (Netherlands)

    Duijsters, G.M.; Zhang, Y.; Filippov, S.

    2012-01-01

    Purpose – The purpose of this study is to examine specific use of strategic alliances and acquisitions for Chinese firms to catch‐up technologically and to enhance their internationalization competence. Design/methodology/approach – The paper offers a conceptual analysis of internationalization

  18. A Review of Antecedents of International Strategic Alliance Performance

    DEFF Research Database (Denmark)

    Christoffersen, Jeppe

    2013-01-01

    This paper provides a systematic review of 165 empirical studies on the antecedents of performance in international strategic alliances. It provides the most detailed display of definitions, rationales, measures and findings currently available. Hence, this state-of-the art literature review...

  19. Alliance Pipeline : the new kid on the block

    International Nuclear Information System (INIS)

    Cornelson, D.

    1998-01-01

    An update on progress of Alliance Pipelines, comments on issues facing gas transporters from western Canada, some discussion of gas supply in general, and the prospects for future expansion of the natural gas industry are provided. According to industry insiders, North American gas demand is expected to increase by 1.5 per cent per year. In order for Canadian gas to participate in this growth additional pipeline capacity is needed. The Alliance Pipeline capacity represents about 20 per cent of this demand growth over the next 5 years. The Alliance Pipeline development will create an opportunity to deliver western Canadian gas to Chicago, a point where North American market competition exists and the market volume and liquidity is large. This presentation also provides an update on the current regulatory status and construction timing. Currently, Alliance has over C$8 billion in firm shipping commitments and up to C$5 billion in financing in place. Pipeline construction will begin in the spring of 1999; it is expected to be operational by the fall of 2000. tabs., figs

  20. Alliance between tobacco and alcohol industries to shape public policy

    Science.gov (United States)

    Jiang, Nan

    2013-01-01

    Aims The tobacco and alcohol industries share common policy goals when facing regulation, opposing policies such as tax increases and advertising restrictions. The collaboration between these two industries in the tobacco policy arena is unknown. This study explored if tobacco and alcohol companies built alliances to influence tobacco legislation, and if so, how those alliances worked. Methods Analysis of previously secret tobacco industry documents. Findings In the early 1980s, tobacco companies started efforts to build coalitions with alcohol and other industries to oppose cigarette excise taxes, clean indoor air policies, and tobacco advertising and promotion constraints. Alcohol companies were often identified as a key partner and source of financial support for the coalitions. These coalitions had variable success interfering with tobacco control policymaking. Conclusions The combined resources of tobacco and alcohol companies may have affected tobacco control legislation. These alliances helped to create the perception that there is a broader base of opposition to tobacco control. Advocates should be aware of the covert alliances between tobacco, alcohol, and other industries and expose them to correct this misperception. PMID:23587076

  1. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  2. An Exploration of the Working Alliance in Mental Health Case Management

    Science.gov (United States)

    Kondrat, David C.; Early, Theresa J.

    2010-01-01

    The working alliance between clients and helpers has been identified as a common factor of treatment effectiveness, yet very little research has explored variables associated with working alliance between mental health case managers and their consumers. This study explored the potential covariates of working alliance within community mental health…

  3. Creating Value from Alliance Portfolios : Connecting Internal Structures and External Knowledge Recombination

    NARCIS (Netherlands)

    Bos, Brenda

    2016-01-01

    Nowadays many firms are simultaneously engaged in multiple alliances with different partners. Alliance scholars have therefore started to develop a portfolio perspective, which analyzes the performance implications of the total collection of firms’ alliances. In this dissertation, we point to an

  4. 75 FR 70363 - Alliance Bancorp, Inc. of Pennsylvania, Broomall, PA; Approval of Conversion Application

    Science.gov (United States)

    2010-11-17

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision [AC-54: OTS No. H-4752] Alliance Bancorp... November 10, 2010, the Office of Thrift Supervision approved the application of Alliance Mutual Holding Company and Greater Delaware Valley Savings Bank, dba Alliance Bank, Broomall, Pennsylvania, to convert to...

  5. Early Therapeutic Alliance and Treatment Outcome in Individual and Family Therapy for Adolescent Behavior Problems

    Science.gov (United States)

    Hogue, Aaron; Dauber, Sarah; Stambaugh, Leyla Faw; Cecero, John J.; Liddle, Howard A.

    2006-01-01

    The impact of early therapeutic alliance was examined in 100 clients receiving either individual cognitive-behavioral therapy (CBT) or family therapy for adolescent substance abuse. Observational ratings of adolescent alliance in CBT and adolescent and parent alliance in family therapy were used to predict treatment retention (in CBT only) and…

  6. A study into the role of a partner selection process in alliance capability building

    NARCIS (Netherlands)

    Duisters, D.; Duysters, G.M.; Man, de A.P.

    2008-01-01

    This study of partner selection supports prior scientific research and explanations of alliance capabilities, a critical success factor for alliances. Although prior research was focused on the importance of these capabilities for the success of alliances, it was less on the role of specific

  7. Sense-making’s role in creating alliance supportive organizational cultures

    NARCIS (Netherlands)

    de Man, A.P.; Luvison, D.

    2014-01-01

    Purpose: The aim of this paper is to analyze the way in which organizational culture affects alliance performance. The literature has begun to focus on intra-firm antecedents of alliance success, but so far has mainly focused on structural aspects like the presence of an alliance department. This

  8. Movement to Create 'Academic Alliances' of Teachers of Same Subjects at All Education Levels Is Growing.

    Science.gov (United States)

    Watkins, Beverly T.

    1988-01-01

    The movement to create "academic alliances" of high-school and college teachers is discussed. The alliances owe much of their strength to the increased sense of self-esteem and the pleasure that members find in the company of disciplinary colleagues. A directory of some alliances is included. (MLW)

  9. Dynamics of alliance formation and the egalitarian revolution.

    Directory of Open Access Journals (Sweden)

    Sergey Gavrilets

    Full Text Available BACKGROUND: Arguably the most influential force in human history is the formation of social coalitions and alliances (i.e., long-lasting coalitions and their impact on individual power. Understanding the dynamics of alliance formation and its consequences for biological, social, and cultural evolution is a formidable theoretical challenge. In most great ape species, coalitions occur at individual and group levels and among both kin and non-kin. Nonetheless, ape societies remain essentially hierarchical, and coalitions rarely weaken social inequality. In contrast, human hunter-gatherers show a remarkable tendency to egalitarianism, and human coalitions and alliances occur not only among individuals and groups, but also among groups of groups. These observations suggest that the evolutionary dynamics of human coalitions can only be understood in the context of social networks and cognitive evolution. METHODOLOGY/PRINCIPAL FINDINGS: Here, we develop a stochastic model describing the emergence of networks of allies resulting from within-group competition for status or mates between individuals utilizing dyadic information. The model shows that alliances often emerge in a phase transition-like fashion if the group size, awareness, aggressiveness, and persuasiveness of individuals are large and the decay rate of individual affinities is small. With cultural inheritance of social networks, a single leveling alliance including all group members can emerge in several generations. CONCLUSIONS/SIGNIFICANCE: We propose a simple and flexible theoretical approach for studying the dynamics of alliance emergence applicable where game-theoretic methods are not practical. Our approach is both scalable and expandable. It is scalable in that it can be generalized to larger groups, or groups of groups. It is expandable in that it allows for inclusion of additional factors such as behavioral, genetic, social, and cultural features. Our results suggest that a rapid

  10. Identification of the intestinal type gastric adenocarcinoma transcriptomic markers using bioinformatic and gene expression analysis

    Directory of Open Access Journals (Sweden)

    V. V. Volkomorov

    2017-01-01

    Full Text Available Introduction. Searching for specific and sensitive molecular tumor markers is one of the important tasks of modern oncology. These markers can be used for early tumor diagnosis and prognosis as well as for prediction of therapeutic response, estimation of tumor volume or to assess disease recurrence through monitoring. Gene expression data base mining followed by experimental validation of results obtained is one of the promising approaches for searching of that kind.Objective: to identify several membrane proteins which can be used for serum diagnosis of intestinal type of gastric adenocarcinoma.Materials and methods. We used bioinformatic-driven search using Gene Ontology and The Cancer Genome Atlas (TCGA data to identify mRNA up-regulated in gastric cancer (GC. Then, the expression levels of the mRNAs in 55 pare clinical specimens were investigated using reverse transcription polymerase chain reaction.Results. Comparative analysis of the mRNA levels in normal and tumor tissues using a new bioinformatics algorithm allowed to identify 3 high-copy transcripts (SULF1, PMEPA1 and SPARC, intracellular content of which markedly increased in GC. Expression analysis of these genes in clinical specimens showed significantly higher mRNA levels of PMEPA1 and SPARC in tumor as compared to normal gastric tissue. Interestingly more than twofold increase in expression level of these genes was observed in 75 % of intestinal-type GC. The same results were found only in 25 and 38 % of diffuse-type GC respectively.Conclusions. As a result of original bioinforamtic analysis using TCGA data base two genes (PMEPA1 and SPARC were shown to be significantly upregulated in intestinal-type gastric adenocarcinoma. The findings show the importance of further investigation to clarify the clinical value of their expression level in stomach tumors as well as their role in carcinogenesis.

  11. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  12. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  13. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

  14. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  15. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  16. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  17. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  18. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  19. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  20. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023