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8. Power logit regression for modeling bounded data

Author

Queiroz, Francisco Felipe and Ferrari, Silvia Lopes Paula

Subjects
Statistics - Methodology
Abstract

The main purpose of this paper is to introduce a new class of regression models for bounded continuous data, commonly encountered in applied research. The models, named the power logit regression models, assume that the response variable follows a distribution in a wide, flexible class of distributions with three parameters, namely the median, a dispersion parameter and a skewness parameter. The paper offers a comprehensive set of tools for likelihood inference and diagnostic analysis, and introduces the new R package PLreg. Applications with real and simulated data show the merits of the proposed models, the statistical tools, and the computational package.

Published
2022

13. Survival Analysis of Organizational Network – An Exploratory Study

Author

Lopes, Paula, Campos, Pedro, Meira-Machado, Luís, Soutinho, Gustavo, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Gervasi, Osvaldo, editor, Murgante, Beniamino, editor, Rocha, Ana Maria A. C., editor, Garau, Chiara, editor, Scorza, Francesco, editor, Karaca, Yeliz, editor, and Torre, Carmelo M., editor

Published
2023
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16. Survival Analysis of Organizational Networks -- An Exploratory Study

Author

Lopes, Paula, Campos, Pedro, and Meira-Machado, Luis

Subjects
Statistics - Applications, 62N02
Abstract

Organizations interact with the environment and with other organizations, and these interactions constitute an important way of learning and evolution. To overcome the problems that they face during their existence, organizations must certainly adopt survival strategies, both individually and in group. The aim of this study is to evaluate the effect of a set of prognostic factors (organizational, size, collaborate strategies, etc.) in the survival of organizational networks. Statistical methods for time to event data were used to analyze the data. We have used the Kaplan-Meier product-limit method to compute and plot estimates of survival, while hypothesis tests were used to compare survival times across several groups. Regression models were used to study the effect of continuous predictors as well as to test multiple predictors at once. Since violations of the proportional hazards were found for several predictors, accelerated failure time models were used to study the effect of explanatory variables on network survival., Comment: 13 pages, 5 figures, 7 tables

Published
2020

19. Conclusion

Author

Freire, Maria Raquel, Lopes, Paula Duarte, Nascimento, Daniela, Simão, Licínia, Freire, Maria Raquel, editor, Lopes, Paula Duarte, editor, Nascimento, Daniela, editor, and Simão, Licínia, editor

Published
2022
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21. Colorectal carcinomas with microsatellite instability display a different pattern of target gene mutations according to large bowel site of origin

Author

Santos Lúcio, Fragoso Maria, Sousa Olga, Afonso Luís, Costa Vera, Pinto Carla, Veiga Isabel, Lind Guro E, Danielsen Stine A, Ahlquist Terje, Pinheiro Manuela, Henrique Rui, Lopes Paula, Lopes Carlos, Lothe Ragnhild A, and Teixeira Manuel R

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Only a few studies have addressed the molecular pathways specifically involved in carcinogenesis of the distal colon and rectum. We aimed to identify potential differences among genetic alterations in distal colon and rectal carcinomas as compared to cancers arising elsewhere in the large bowel. Methods Constitutional and tumor DNA from a test series of 37 patients with rectal and 25 patients with sigmoid carcinomas, previously analyzed for microsatellite instability (MSI), was studied for BAX, IGF2R, TGFBR2, MSH3, and MSH6 microsatellite sequence alterations, BRAF and KRAS mutations, and MLH1 promoter methylation. The findings were then compared with those of an independent validation series consisting of 36 MSI-H carcinomas with origin from each of the large bowel regions. Immunohistochemical and germline mutation analyses of the mismatch repair system were performed when appropriate. Results In the test series, IGFR2 and BAX mutations were present in one and two out of the six distal MSI-H carcinomas, respectively, and no mutations were detected in TGFBR2, MSH3, and MSH6. We confirmed these findings in the validation series, with TGFBR2 and MSH3 microsatellite mutations occurring less frequently in MSI-H rectal and sigmoid carcinomas than in MSI-H colon carcinomas elsewhere (P = 0.00005 and P = 0.0000005, respectively, when considering all MSI-carcinomas of both series). No MLH1 promoter methylation was observed in the MSI-H rectal and sigmoid carcinomas of both series, as compared to 53% found in MSI-H carcinomas from other locations (P = 0.004). KRAS and BRAF mutational frequencies were 19% and 43% in proximal carcinomas and 25% and 17% in rectal/sigmoid carcinomas, respectively. Conclusion The mechanism and the pattern of genetic changes driving MSI-H carcinogenesis in distal colon and rectum appears to differ from that occurring elsewhere in the colon and further investigation is warranted both in patients with sporadic or hereditary disease.

Published
2010
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22. Chromosome copy number changes carry prognostic information independent of KIT/PDGFRA point mutations in gastrointestinal stromal tumors

Author

Lopes Paula, Santos Lúcio, Dinis José, Soares Marta, Santos Catarina, Mesquita Bárbara, Pinheiro Manuela, Pinto Carla, Vieira Joana, Ribeiro Franclim R, Veiga Isabel, Silva Mara, Afonso Mariana, Lopes Carlos, and Teixeira Manuel R

Subjects
Medicine
Abstract

Abstract Background Oncogenic point mutations in KIT or PDGFRA are recognized as the primary events responsible for the pathogenesis of most gastrointestinal stromal tumors (GIST), but additional genomic alterations are frequent and presumably required for tumor progression. The relative contribution of such alterations for the biology and clinical behavior of GIST, however, remains elusive. Methods In the present study, somatic mutations in KIT and PDGFRA were evaluated by direct sequencing analysis in a consecutive series of 80 GIST patients. For a subset of 29 tumors, comparative genomic hybridization was additionally used to screen for chromosome copy number aberrations. Genotype and genomic findings were cross-tabulated and compared with available clinical and follow-up data. Results We report an overall mutation frequency of 87.5%, with 76.25% of the tumors showing alterations in KIT and 11.25% in PDGFRA. Secondary KIT mutations were additionally found in two of four samples obtained after imatinib treatment. Chromosomal imbalances were detected in 25 out of 29 tumors (86%), namely losses at 14q (88% of abnormal cases), 22q (44%), 1p (44%), and 15q (36%), and gains at 1q (16%) and 12q (20%). In addition to clinico-pathological high-risk groups, patients with KIT mutations, genomic complexity, genomic gains and deletions at either 1p or 22q showed a significantly shorter disease-free survival. Furthermore, genomic complexity was the best predictor of disease progression in multivariate analysis. Conclusions In addition to KIT/PDGFRA mutational status, our findings indicate that secondary chromosomal changes contribute significantly to tumor development and progression of GIST and that genomic complexity carries independent prognostic value that complements clinico-pathological and genotype information.

Published
2010
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24. Brazilian Society of Otology task force – Vestibular Schwannoma ‒ evaluation and treatment

Author

Silva, Vagner Antonio Rodrigues, Lavinsky, Joel, Pauna, Henrique Furlan, Vianna, Melissa Ferreira, Santos, Vanessa Mazanek, Ikino, Cláudio Márcio Yudi, Sampaio, André Luiz Lopes, Tardim Lopes, Paula, Lamounier, Pauliana, Maranhão, André Souza de Albuquerque, Soares, Vitor Yamashiro Rocha, Polanski, José Fernando, Denaro, Mariana Moreira de Castro, Chone, Carlos Takahiro, Bento, Ricardo Ferreira, and Castilho, Arthur Menino

Published
2023
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30. High resolution melting analysis of microsatellite markers applied to grapevine varietal fingerprinting throughout the wine production chain

Author

Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Barrias, Sara [0000-0003-2536-2107], Ibáñez Marcos, Javier [0000-0002-6286-5638], Martins-Lopes, Paula [0000-0001-8229-0117], Barrias, Sara, Ibáñez Marcos, Javier, Martins-Lopes, Paula, Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Barrias, Sara [0000-0003-2536-2107], Ibáñez Marcos, Javier [0000-0002-6286-5638], Martins-Lopes, Paula [0000-0001-8229-0117], Barrias, Sara, Ibáñez Marcos, Javier, and Martins-Lopes, Paula

Abstract

The accurate varietal identification is an essential requirement for every process involved in the exploitation of grapevine resources and derived products. The advancements achieved during the last years allowed the simultaneous analysis of multiple molecular markers capable of identifying grapevine varieties. Despite the establishment of a recommended set of nine microsatellite (SSR) markers for this purpose, their effective application with DNA extracted from must and wine samples remains a challenging task. This work aimed to develop High Resolution Melting (HRM) assays based on SSR markers applicable for grapevine varietal identification using leaf, must and wine samples. The grapevine varieties used were Cabernet Sauvignon, Touriga Franca, Touriga Nacional and Rufete. A total of 12 SSR markers were used to screen the varieties: nine markers recommended by the OIV (VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VVS2, VrZAG62 and VrZAG79) and three markers selected based on their repeat motif and length (VvIv35, VChr5c and VChr9a). The results from multiplex PCR amplification of DNA from wine samples revealed that these three markers performed better than the nine established SSR markers. HRM assays were developed targeting markers VvIv35, VChr5c and VChr9a, successfully discriminating the varietal composition in must DNA samples. Promising results were obtained using wine DNA, where assay HRM-VChr9a proved to have the highest discriminant power. The HRM-SSR assays need to be applied in a larger number of varieties, to explore its suitability for grapevine fingerprinting applications throughout the wine chain. Overall, the proposed small SSR makers can be more suitable for wine DNA analysis. The HRM-SSR approach presented here provides fast results, allowing the complete discrimination of varietal composition in must DNA. It also shows to be a promising tool to discriminate the varieties using wine DNA, a task usually hampered by the inherent complexity of wine s

Published
2024

31. Human Right to Water and Water Rights

Author

Lopes, Paula Duarte, Ofori, Alesia Dedaa, Section editor, Leal Filho, Walter, Series Editor, Azul, Anabela Marisa, editor, Brandli, Luciana, editor, Lange Salvia, Amanda, editor, and Wall, Tony, editor

Published
2022
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36. Water Footprint and Virtual Water

Author

Schnepper, Roxane, Lopes, Paula Duarte, Fatta – Kassinos, Despo, Section editor, Leal Filho, Walter, Series Editor, Azul, Anabela Marisa, editor, Brandli, Luciana, editor, Lange Salvia, Amanda, editor, and Wall, Tony, editor

Published
2022
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38. Water Conflicts: An Obstacle to SDG6

Author

Sosa-Rodriguez, Fabiola S., Violeta Yoalli, Alvarado Arriaga, Lopes, Paula, Section editor, Leal Filho, Walter, Series Editor, Azul, Anabela Marisa, editor, Brandli, Luciana, editor, Lange Salvia, Amanda, editor, and Wall, Tony, editor

Published
2022
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40. Water and Gender Issues

Author

Houart, Carlota, Lopes, Paula, Section editor, Leal Filho, Walter, Series Editor, Azul, Anabela Marisa, editor, Brandli, Luciana, editor, Lange Salvia, Amanda, editor, and Wall, Tony, editor

Published
2022
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42. Legal Approaches to the Achievement of SDG 6

Author

Phillips, Freedom-Kai, Harrington, Alexandra, Lopes, Paula, Section editor, Ofori, Alesia Dedaa, Section editor, Filho, Walter Leal, Section editor, Leal Filho, Walter, Series Editor, Azul, Anabela Marisa, editor, Brandli, Luciana, editor, Lange Salvia, Amanda, editor, and Wall, Tony, editor

Published
2022
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45. Situational factors shape moral judgements in the trolley dilemma in Eastern, Southern and Western countries in a culturally diverse sample

Author

Bago, Bence, Kovacs, Marton, Protzko, John, Nagy, Tamas, Kekecs, Zoltan, Palfi, Bence, Adamkovic, Matus, Adamus, Sylwia, Albalooshi, Sumaya, Albayrak-Aydemir, Nihan, Alfian, Ilham N., Alper, Sinan, Alvarez-Solas, Sara, Alves, Sara G., Amaya, Santiago, Andresen, Pia K., Anjum, Gulnaz, Ansari, Daniel, Arriaga, Patrícia, Aruta, John Jamir Benzon R., Arvanitis, Alexios, Babincak, Peter, Barzykowski, Krystian, Bashour, Bana, Baskin, Ernest, Batalha, Luisa, Batres, Carlota, Bavolar, Jozef, Bayrak, Fatih, Becker, Benjamin, Becker, Maja, Belaus, Anabel, Białek, Michał, Bilancini, Ennio, Boller, Daniel, Boncinelli, Leonardo, Boudesseul, Jordane, Brown, Benjamin T., Buchanan, Erin M., Butt, Muhammad M., Calvillo, Dustin P., Carnes, Nate C., Celniker, Jared B., Chartier, Christopher R., Chopik, William J., Chotikavan, Poom, Chuan-Peng, Hu, Clancy, Rockwell F., Çoker, Ogeday, Correia, Rita C., Adoric, Vera Cubela, Cubillas, Carmelo P., Czoschke, Stefan, Daryani, Yalda, de Grefte, Job A. M., de Vries, Wieteke C., Burak, Elif G. Demirag, Dias, Carina, Dixson, Barnaby J. W., Du, Xinkai, Dumančić, Francesca, Dumbravă, Andrei, Dutra, Natalia B., Enachescu, Janina, Esteban-Serna, Celia, Eudave, Luis, Evans, Thomas R., Feldman, Gilad, Felisberti, Fatima M., Fiedler, Susann, Findor, Andrej, Fleischmann, Alexandra, Foroni, Francesco, Francová, Radka, Frank, Darius-Aurel, Fu, Cynthia H. Y., Gao, Shan, Ghasemi, Omid, Ghazi-Noori, Ali-Reza, Ghossainy, Maliki E., Giammusso, Isabella, Gill, Tripat, Gjoneska, Biljana, Gollwitzer, Mario, Graton, Aurélien, Grinberg, Maurice, Groyecka-Bernard, Agata, Harris, Elizabeth A., Hartanto, Andree, Hassan, Widad A. N. M., Hatami, Javad, Heimark, Katrina R., Hidding, Jasper J. J., Hristova, Evgeniya, Hruška, Matej, Hudson, Charlotte A., Huskey, Richard, Ikeda, Ayumi, Inbar, Yoel, Ingram, Gordon P. D., Isler, Ozan, Isloi, Chris, Iyer, Aishwarya, Jaeger, Bastian, Janssen, Steve M. J., Jiménez-Leal, William, Jokić, Biljana, Kačmár, Pavol, Kadreva, Veselina, Kaminski, Gwenaël, Karimi-Malekabadi, Farzan, Kasper, Arno T. A., Kendrick, Keith M., Kennedy, Bradley J., Kocalar, Halil E., Kodapanakkal, Rabia I., Kowal, Marta, Kruse, Elliott, Kučerová, Lenka, Kühberger, Anton, Kuzminska, Anna O., Lalot, Fanny, Lamm, Claus, Lammers, Joris, Lange, Elke B., Lantian, Anthony, Lau, Ivy Y.-M., Lazarevic, Ljiljana B., Leliveld, Marijke C., Lenz, Jennifer N., Levitan, Carmel A., Lewis, Savannah C., Li, Manyu, Li, Yansong, Li, Haozheng, Lima, Tiago J. S., Lins, Samuel, Liuzza, Marco Tullio, Lopes, Paula, Lu, Jackson G., Lynds, Trent, Máčel, Martin, Mackinnon, Sean P., Maganti, Madhavilatha, Magraw-Mickelson, Zoe, Magson, Leon F., Manley, Harry, Marcu, Gabriela M., Seršić, Darja Masli, Matibag, Celine-Justine, Mattiassi, Alan D. A., Mazidi, Mahdi, McFall, Joseph P., McLatchie, Neil, Mensink, Michael C., Miketta, Lena, Milfont, Taciano L., Mirisola, Alberto, Misiak, Michal, Mitkidis, Panagiotis, Moeini-Jazani, Mehrad, Monajem, Arash, Moreau, David, Musser, Erica D., Narhetali, Erita, Ochoa, Danielle P., Olsen, Jerome, Owsley, Nicholas C., Özdoğru, Asil A., Panning, Miriam, Papadatou-Pastou, Marietta, Parashar, Neha, Pärnamets, Philip, Paruzel-Czachura, Mariola, Parzuchowski, Michal, Paterlini, Julia V., Pavlacic, Jeffrey M., Peker, Mehmet, Peters, Kim, Piatnitckaia, Liudmila, Pinto, Isabel, Policarpio, Monica Renee, Pop-Jordanova, Nada, Pratama, Annas J., Primbs, Maximilian A., Pronizius, Ekaterina, Purić, Danka, Puvia, Elisa, Qamari, Vahid, Qian, Kun, Quiamzade, Alain, Ráczová, Beáta, Reinero, Diego A., Reips, Ulf-Dietrich, Reyna, Cecilia, Reynolds, Kimberly, Ribeiro, Matheus F. F., Röer, Jan P., Ross, Robert M., Roussos, Petros, Ruiz-Dodobara, Fernando, Ruiz-Fernandez, Susana, Rutjens, Bastiaan T., Rybus, Katarzyna, Samekin, Adil, Santos, Anabela C., Say, Nicolas, Schild, Christoph, Schmidt, Kathleen, Ścigała, Karolina A., Sharifian, MohammadHasan, Shi, Jiaxin, Shi, Yaoxi, Sievers, Erin, Sirota, Miroslav, Slipenkyj, Michael, Solak, Çağlar, Sorokowska, Agnieszka, Sorokowski, Piotr, Söylemez, Sinem, Steffens, Niklas K., Stephen, Ian D., Sternisko, Anni, Stevens-Wilson, Laura, Stewart, Suzanne L. K., Stieger, Stefan, Storage, Daniel, Strube, Justine, Susa, Kyle J., Szekely-Copîndean, Raluca D., Szostak, Natalia M., Takwin, Bagus, Tatachari, Srinivasan, Thomas, Andrew G., Tiede, Kevin E., Tiong, Lucas E., Tonković, Mirjana, Trémolière, Bastien, Tunstead, Lauren V., Türkan, Belgüzar N., Twardawski, Mathias, Vadillo, Miguel A., Vally, Zahir, Vaughn, Leigh Ann, Verschuere, Bruno, Vlašiček, Denis, Voracek, Martin, Vranka, Marek A., Wang, Shuzhen, West, Skye-Loren, Whyte, Stephen, Wilton, Leigh S., Wlodarczyk, Anna, Wu, Xue, Xin, Fei, Yadanar, Su, Yama, Hiroshi, Yamada, Yuki, Yilmaz, Onurcan, Yoon, Sangsuk, Young, Danielle M., Zakharov, Ilya, Zein, Rizqy A., Zettler, Ingo, Žeželj, Iris L., Zhang, Don C., Zhang, Jin, Zheng, Xiaoxiao, Hoekstra, Rink, and Aczel, Balazs

Published
2022
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