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5. PFP Compressed Suffix Trees

Author

Boucher, C., Cvacho, O., Gagie, T., Holub, J., Manzini, G., Navarro, G., and Rossi, M.

Subjects
Data_CODINGANDINFORMATIONTHEORY, Article
Abstract

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string S, it produces a dictionary D and a parse P of overlapping phrases such that BWT(S) can be computed from D and P in time and workspace bounded in terms of their combined size |PFP(S)|. In practice D and P are significantly smaller than S and computing BWT(S) from them is more efficient than computing it from S directly, at least when S is the concatenation of many genomes. In this paper, we consider PFP(S) as a data structure and show how it can be augmented to support full suffix tree functionality, still built and fitting within O(|PFP(S)|) space. This entails the efficient computation of various primitives to simulate the suffix tree: computing a longest common extension (LCE) of two positions in S; reading any cell of its suffix array (SA), of its inverse (ISA), of its BWT, and of its longest common prefix array (LCP); and computing minima over ranges and next/previous smaller value queries over the LCP. Our experimental results show that the PFP suffix tree can be efficiently constructed for very large repetitive datasets and that its operations perform competitively with other compressed suffix trees that can only handle much smaller datasets.

Published
2021

17. Face-Fusion of Icosahedral Boron Hydride Increases Affinity to γ-Cyclodextrin: closo,closo-[B21H18]− as an Anion with Very Low Free Energy of Dehydration

Author

Assaf, K. I., Holub, J., Bernhardt, E., Oliva, José M., Fernández Pérez, M. I., Canle, M., Santaballa, J. A., Fanfrlík, J., Hnyk, D., Nau, W. M., German Research Foundation, Czech Science Foundation, Xunta de Galicia, and Ministerio de Ciencia, Innovación y Universidades (España)

Subjects
Anion binding, Intermolecular interactions, Boron clusters, Desolvation, Host-guest chemistry
Abstract

6 pags., 5 figs., 1 tab., The supramolecular recognition of closo,closo-[BH] by cyclodextrins (CDs) has been studied in aqueous solution by isothermal titration calorimetry and nuclear magnetic resonance spectroscopy. These solution studies follow up on previous mass-spectrometric measurements and computations, which indicated the formation and stability of CD ⋅ BH complexes in the gas phase. The thermodynamic signature of solution-phase binding is exceptional, the association constant for the γ-CD complex with BH reaches 1.8×10 M, which is on the same order of magnitude as the so far highest observed value for the complex between γ-CD and a metallacarborane. The nature of the intermolecular interaction is also examined by quantum-mechanical computational protocols. These suggest that the desolvation penalty, which is particularly low for the BH anion, is the decisive factor for its high binding strength. The results further suggest that the elliptical macropolyhedral boron hydride is another example of a CD binder, whose extraordinary binding affinity is driven by the chaotropic effect, which describes the intrinsic affinity of large polarizable and weakly solvated chaotropic anions to hydrophobic cavities and surfaces in aqueous solution., K.I.A. and W.M.N. are grateful to the DFG for grant NA-686/8within the priority program SPP 1807 “Control of London Dispersion Interactions in Molecular Chemistry”. J.H., J.F., and D.H.thank the Czech Science Foundation (grant number 17-08045S) and M.I.F.P., M.C.L, and J.A.S.L. thank the regional government Xunta de Galicia for financial support (Project Grupo Potencial Crecemento -GPC- ED431B 2017/59). J.M.O.-E. acknowledgesfinancial support from the Spanish MICINN through project CTQ2018-094644-B-C22

Published
2020

20. Session 02 Hormone metabolism and action

Author

Boyd, A. J., Wahrlich, S. M., Poole, P. R., Brabcová, P., Čapková, V., LuŠtinec, J., Březinová, A., Motyka, V., Auer, C., Holík, J., Kamínek, M., Burdach, Z., Karcz, W., Chauvaux, N., Poduje, L., Child, R., Van Onckelen, H., Cherepneva, G. N., Dieleman, J. A., Kuiper, D., Dimova-Terziivanova, S. D., Tsonev, T. D., Terziivanov, D. N., Gudumak, F. A., Derendovskaya, A. I., Hammerton, R. D., Nicander, B., Tillberg, E., Holub, J., Ievinsh, G., Kreicbergs, O., Iturriagatoitia-Bueno, T., John, P., Kovač, M., Ravnikar, M., Kurtyka, R., Stolarek, J., Kuznetsov, V. V., Oelmuller, R., Herrmann, R. G., Kulaeva, O. N., Lehmann, J., Atzorn, R., Leopold, J., Wasternack, C., Parthier, B., Lutova, L. A., Buzovkina, I. S., Shishkova, S. O., Tikhodeev, O. N., Makoveychuk, A. Yu., Malkowski, E., Martinez, R., Parra, M., Valero, D., Gomes, A. I. M., Moya-Leon, M. A., Musatenko, L. I., Padun, A. A., Mustafina, A. R., Kudoyarova, G. R., Nazarenko, L. V., Semenenko, V. E., Ördög, V., Molnár, Z., Padun, A. A., Pastor, A., Alegre, L., Pelkonen, V. -P., Kauppi, A., Junttila, O., Reski, R., Kruse, S., Kasten, B., Reutter, K., Wehe, M., Faust, M., Gorr, G., Abel, W. O., Rukasz, I., Schmúlling, T., Faiss, M., Strnad, M., Gatz, C., Schneider, Gernot, Serdyuk, O. P., Smolygna, L. D., Laurinavichene, T. V., Tsyganskov, A. A., Shakirova, F. M., Bezrukova, M. V., Smolygina, L. D., Serdyuk, O. P., Laurinavichene, T. V., Tsyganskov, A. A., Stikic, R., Pekic, S., Davies, W. J., Quarrie, S. A., Tomljanovic, L., Jovanovic, Z., Strnad, M., Redig, P., Hanus, J., Van Dongen, V., Van Onckelen, H., Szabó, M., Köves, S. E., Stefanov, I., Molnár, J., Titika, M. D., Vasjuk, V. A., Andrianova, T. V., Vuylsteker, C., Palms, B., Leleu, O., Rambour, S., Wang, Y. Z., Cramer, M. D., Schierholt, A., Lips, S. H., Zažímalová, E., Zhong, W., Hartung, W., Schobert, C., and Komor, E.

Published
1994
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21. Parent tricarbollides [nido-7,8,9-C3B8H11]-, nido-7,8,9-C3B8H12, [nido-7,8,10-C3B8H11]- , and their derivatives

Author

Holub, J., Stibr, B., Hnyk, D., Fusek, J., Cisarova, I., Teixidor, F., Vinas, C., Plzak, Z., and Schleyer, P.v.R.

Subjects
Organic compounds -- Synthesis, Organoboron compounds -- Analysis, Chemistry
Abstract

A novel method for the synthesis of nido-7,8,9-C3B8H12 and [nido-7,8,10-C3B8H11]- was developed based on the deamination of the Me3N derivative of 7-(Me3N)-nido-7,8,9-C3B8H10 with sodium metal in THF. The resulting isomeric series of parent tricarbollide compounds were produced by the addition of CsOH which induced the isolation of Cs+[nido-7,8,9-C3B8H11]- and (Cs+)[7,8,9-C3B8H11]-. The new parent tricarbaboranes also facilitated the formation of unsubstituted 10-vertex tricarbaboranes via boron elimination reactions.

Published
1997

27. Many-MADFAct: concurrently constructing MADFAs

Author

Runge, T., Schaefer, I., Cleophas, L.G.W.A., Watson, B.W., Holub, J., and Zdarek, J.

Abstract

Minimal acyclic deterministic finite automata (MADFAs) are used to represent dictionaries, i.e., finite sets of finite words, in, e.g., spell checkers and network security applications. Given the size of such dictionaries, which may contain millions of words, their efficient construction is a critical issue. Watson (2010) published a classification of such algorithms in an algorithm taxonomy with correctness arguments. We report on a new algorithm which constructs MADFAs in parallel---each for a keyword set from a partition of the original keyword set---and afterwards merges and minimizes the resulting automata into a single MADFA; on our experience implementing the algorithms in a Java-based toolkit; and on empirical performance results obtained.

Published
2017

30. The advantage of women in cancer survival: An analysis of EUROCARE-4 data

Author

Micheli, A., Ciampichini, R., Oberaigner, W., Ciccolallo, L., de Vries, E., Izarzugaza, I., Zambon, P., Gatta, G., De Angelis, R., Hackl, M., Van Eycken, E., Verstreken, Martine, Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hedelin, G., Velten, M., Tron, I., Le Gall, E., Launoy, G., Guizard, A. V., Faivre, J., Bouvier, A. M., Carli, P. M., Maynadie, M., Danzon, A., Buemi, A., Tretarre, B., Lacour, B., Desandes, E., Colonna, M., Molinie, F., Bara, S., Schvartz, C., Ganry, O., Grosclaude, P., Brenner, H., Kaatsch, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Sant, M., Sowe, S., Zigon, G., Tagliabue, G., Contiero, P., Bellu`, F., Giacomin, A., Ferretti, S., Serraino, D., Dal Maso, L., De Dottori, M., D. e. Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Pannelli, F., Federico, M., Rashid, I., Cirilli, C., Fusco, M., Traina, A., De Lisi, V., Bozzani, F., Magnani, C., Pastore, G., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Patriarca, S., Zanetti, R., Rosso, S., Piffer, S., Franchini, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gozdz, S., Siudowska, U., Mezyk, R., Bielska-Lasota, M., Zwierko, M., Pinheiro, P. S., Primic-Zakelj, M., Mateos, A., Torrella-Ramos, A., Zurriaga, Oscar, Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Martinez-Garcia, C., Sanchez, M. J., Navarro, C., Chirlaque, M. D., Peris-Bonet, R., Ardanaz, E., Moreno, C., Galceran, J., Klint, A., Talback, M., Jundt, G., Usel, M., Frick, H., Ess, S. M., Bordoni, A., Luthi, J. C., Konzelmann, I., Probst, N., Lutz, J. M., Pury, P., Visser, O., Otter, R., Schaapveld, M., Coebergh, J. W. W., Janssen-Heijnen, M. L., Louis van der Heijden, Null, Greenberg, D. C., Coleman, M. P., Woods, Laura, Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Stiller, C., Gavin, A., Black, R. J., Brewster, D. H., Steward, J. A., Basque Country Cancer Registry, Vitoria-Gasteiz, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), and Public Health

Subjects
Oncology, Male, Pathology, Cancer Research, cancer survival - women, MESH : Age Distribution, MESH : Aged, MESH: Risk Assessment, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 0302 clinical medicine, MESH: Aged, 80 and over, Residence Characteristics, Neoplasms, 80 and over, Gender differences, Sex hormones, MESH: Neoplasms, MESH : Female, MESH: Residence Characteristics, Young adult, Age of Onset, MESH : Risk Assessment, MESH : Sex Distribution, MESH: Diagnosis-Related Groups, MESH: Aged, Aged, 80 and over, 0303 health sciences, education.field_of_study, MESH: Middle Aged, Relative survival, Thyroid, MESH: Sex Distribution, Middle Aged, MESH : Adult, 3. Good health, MESH : Age of Onset, Europe, MESH : Diagnosis-Related Groups, medicine.anatomical_structure, MESH: Young Adult, 030220 oncology & carcinogenesis, MESH: Survival Analysis, MESH : Residence Characteristics, Female, EUROCARE, Adult, medicine.medical_specialty, Adolescent, MESH: Age of Onset, MESH : Male, MESH : Sex Factors, Population, MESH : Europe, MESH : Young Adult, Rectum, Socio-culturale, [SDV.CAN]Life Sciences [q-bio]/Cancer, Risk Assessment, 03 medical and health sciences, Young Adult, Age Distribution, Sex Factors, MESH: Sex Factors, SDG 3 - Good Health and Well-being, Internal medicine, MESH : Adolescent, medicine, Humans, MESH : Middle Aged, Sex Distribution, education, MESH : Aged, 80 and over, MESH: Age Distribution, Survival analysis, Diagnosis-Related Groups, 030304 developmental biology, Aged, MESH: Adolescent, MESH: Humans, business.industry, MESH : Humans, Cancer, Cancer survival, Survival Analysis, MESH: Adult, medicine.disease, MESH : Neoplasms, MESH: Male, MESH: Europe, Age of onset, MESH : Survival Analysis, business, MESH: Female
Abstract

We analysed 1.6 million population-based EUROCARE-4 cancer cases (26 cancer sites, excluding sex-specific sites, and breast) from 23 countries to investigate the role of sex in cancer survival according to age at diagnosis, site, and European region. For 15 sites (salivary glands, head and neck, oesophagus, stomach, colon and rectum, pancreas, lung, pleura, bone, melanoma of skin, kidney, brain, thyroid, Hodgkin disease and non-Hodgkin's lymphoma) age- and region-adjusted relative survival was significantly higher in women than men. By multivariable analysis, women had significantly lower relative excess risk (RER) of death for the sites listed above plus multiple myeloma. Women significantly had higher RER of death for biliary tract, bladder and leukaemia. For all cancers combined women had a significant 5% lower RER of death. Age at diagnosis was the main determinant of the women's advantage, which, however, decreased with increasing age, becoming negligible in the elderly, suggesting that sex hormone patterns may have a role in women's superior ability to cope with cancer. (C) 2008 Elsevier Ltd. All rights reserved.

Published
2009

33. Quantum leap pattern matching

Author

Watson, B.W., Kourie, D.G., Cleophas, L., Holub, J., and Žďárek, J.

Abstract

Quantum leap matching is introduced as a generic pattern matching strategy for the single keyword exact pattern matching problem, that can be used on top of existing Boyer-Moore-style string matching algorithms. The cost of the technique is minimal: an additional shift table (of one dimension, for shifts in the opposite direction to the parent algorithm’s shifts), and the replacement of a simple table lookup assignment statement in the original algorithm with a similar conditional assignment. Together with each of the conventional shift table lookups, the additional shift table is typically also indexed on the text character that is at a distance of z away from the current sliding window. Under conditions that are identified, the returned values from the two shift tables allow a “quantum leap” of distance more than the length of the keyword for the next matching attempt. If the conditions are not met, then there is a fall back is to the traditional shift. Quick Search (by Sunday) is used as a case study to illustrate the technique. The performance of the derived “Quantum Leap Quick Search” algorithm is compared against Quick Search. When searching for shorter patterns over natural language and genomic texts, the technique improves on Quick Search’s time for most values of z. Improvements are also sometimes seen for various values of z on larger patterns. Most interestingly, under best case conditions it performs, on average, at about three times faster than Quick Search.

Published
2015

36. Predictions of survival up to 10 years after diagnosis for european women with breast cancer in 2000-2002

Author

Allemani, Claudia, Minicozzi, Pamela, Berrino, Franco, Bastiaannet, Esther, Gavin, Anna, Galceran, Jaume, Ameijide, Alberto, Siesling, Sabine, Mangone, Lucia, Ardanaz, Eva, Hã©delin, Guy, Mateos, Antonio, Micheli, Andrea, Sant, Milena, Holub, J., Jurickova, L., Hakulinen, T., Tryggvadottir, L., Berrino, F., Allemani, C., Baili, P., Ciampichini, R., Ciccolallo, L., Gatta, G., Micheli, A., Margutti, C., Minicozzi, P., Sant, M., Sowe, S., Tereanu, C., Zigon, G., Ferretti, S., Federico, M., Rashid, I., Cirilli, C., De Lisi, V., Bozzani, F., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Falcini, F., Foca, F., Giorgetti, S., Paci, E., Crocetti, E., Caldora, M., Capocaccia, R., Carrani, E., De Angelis, R., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gã³åºdåº, S., Siudowska, U., Mä™å¼yk, R., Bielska-Lasota, M., Zwierko, M., Safaei Diba, C., Primič-Žakelj, M., Klint, Ã. …., Talbã¤ck, M., Usel, M., Ess, S. M., Lutz, J. M., Pury, P., Visser, O., Greenberg, D. C., Coleman, M. P., Woods, L., Forman, D., Cooper, N., Roche, M., Lawrence, G., Black, R. J., Brewster, D. H., and Steward, J. A.

Subjects
Adult, medicine.medical_specialty, Cancer Research, Adolescent, Population, breast cancer, cancer survival, Socio-culturale, Breast Neoplasms, Disease, Breast cancer, Age Distribution, medicine, 80 and over, Humans, Registries, Stage (cooking), education, Survival rate, Survival analysis, EUROCARE, long-term survival, stage, Aged, Aged, 80 and over, Europe, Female, Middle Aged, Prognosis, Survival Analysis, Survival Rate, Oncology, Gynecology, education.field_of_study, Relative survival, business.industry, Cancer, medicine.disease, business, Demography
Abstract

Few studies have addressed longer-term survival for breast cancer in European women. We have made predictions of 10-year survival for European women diagnosed with breast cancer in 2000-2002. Data for 114,312 adult women (15-99 years) diagnosed with a first primary malignant cancer of the breast during 2000-2002 were collected in the EUROCARE-4 study from 24 population-based cancer registries in 14 European countries. We estimated relative survival at 1, 5, and 10 years after diagnosis for women who were alive at some point during 2000-2002, using the period approach. We also estimated 10-year survival conditional on survival to 1 and 5 years after diagnosis. Ten-year survival exceeded 70% in most regions, but was only 54% in Eastern Europe, with the highest value in Northern Europe (about 75%). Ten-year survival conditional on survival for 1 year was 2-6% higher than 10-year survival in all European regions, and geographic differences were smaller. Ten-year survival for women who survived at least 5 years was 88% overall, with the lowest figure in Eastern Europe (79%) and the highest in the UK (91%). Women aged 50-69 years had higher overall survival than older and younger women (79%). Six cancer registries had adequate information on stage at diagnosis; in these jurisdictions, 10-year survival was 89% for local, 62% for regional and 10% for metastatic disease. Data on stage are not collected routinely or consistently, yet these data are essential for meaningful comparison of population-based survival, which provides vital information for improving breast cancer control. What's new? Policy-makers and health-care planners need accurate data on long-term survival to improve cancer control. This Europe-wide study of 10-year survival identified low survival in Eastern Europe for women with breast cancer in 2000-2002, and wide variation by age at diagnosis. Data on stage at diagnosis are crucial for meaningful comparison of population-based survival, and fundamental for improving breast cancer control, but our analyses confirmed that stage data are not collected routinely or consistently

Published
2013

42. Failure deterministic finite automata

Author

Kourie, D.G., Watson, B.W., Cleophas, L.G.W.A., Venter, F., Holub, J., and Zdarek, J.

Subjects
TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES, TheoryofComputation_COMPUTATIONBYABSTRACTDEVICES, Computer Science::Formal Languages and Automata Theory
Abstract

Inspired by failure functions found in classical pattern matching algorithms, a failure deterministic finite automaton (FDFA) is defined as a formalism to recognise a regular language. An algorithm, based on formal concept analysis, is proposed for deriving from a given deterministic finite automaton (DFA) a language-equivalent FDFA. The FDFA’s transition diagram has fewer arcs than that of the DFA. A small modification to the classical DFA’s algorithm for recognising language elements yields a corresponding algorithm for an FDFA.

Published
2012

43. Oesophageal cancer survival in Europe: A EUROCARE-4 study

Author

Gavin, A. T., Francisci, S., Foschi, R., Donnelly, D. W., Lemmens, V., Brenner, H., Anderson, L. A., Oberaigner, W., Hackl, M., Van Eycken, E., Henau, K., Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hã©delin, G., Velten, M., Tron, I., Le Gall, E., Launoy, G., Guizard, A. V., Faivre, J., Bouvier, A. M., Carli, P. M., Maynadiã©, M., Danzon, A., Buemi, A., Tretarre, B., Lacour, B., Desandes, E., Colonna, M., Moliniã©, F., Bara, S., Schvartz, C., Ganry, O., Grosclaude, P., Kaatsch, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Casella, I., Margutti, C., Ciccolallo, L., Gatta, G., Micheli, A., Minicozzi, P., Sant, M., Sowe, S., Tereanu, C., Zigon, G., Tagliabue, G., Contiero, P., Bellu`, F., Giacomin, A., Ferretti, S., Serraino, D., Dal Maso, L., De Dottori, M., De Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Vitarelli, S., Federico, M., Rashid, I., Cirilli, C., Fusco, M., Traina, A., De Lisi, V., Bozzani, F., Magnani, C., Pastore, G., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Zanetti, R., Patriarca, S., Rosso, S., Piffer, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Zambon, P., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., De Angelis, R., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., England, K., Micallef, R., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Go´ z´dz´, S., Siudowska, U., Me?z? yk, R., Bielska-Lasota, M., Sklodowska, M., Zwierko, M., Miranda, A., Diba, C. S., Plesko, I., Primic-Z?akelj, M., Mateos, A., Izarzugaza, I., Torrella-Ramos, A., Zurriaga, O., Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Martinez-Garcia, C., Saâ´nchez, M. J., Navarro, C., Chirlaque, M. D., Peris-Bonet, R., Ardanaz, E., Moreno, C., Galceran, J., Klint, A., Talbaâck, M., Khan, S., Jundt, G., Usel, M., Frick, H., Ess, S. M., Bordoni, A., Konzelmann, I., Dehler, S., Lutz, J. M., Pury, P., Siesling, S., Visser, O., Otter, R., Coebergh, J. W. W., Janssen-Heijnen, M. L., Louis van der Heijden, Null, Greenberg, D. C., Coleman, M. P., Woods, L., Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Stiller, C., Black, R. J., Brewster, D. H., Steward, J. A., Bouchardy Magnin, Christine, and Usel, Massimo

Subjects
Stage, Adult, Male, Cancer Research, Survival, Adolescent, Esophageal Neoplasms, Epidemiology, Socio-culturale, Subtype, Disease, Europe/epidemiology, Young Adult, Cancer, Europe, Oesophagus, Trends, Aged, Aged, 80 and over, Female, Humans, Middle Aged, Neoplasm Staging, Prognosis, Registries, Survival Rate, Oncology, medicine, 80 and over, Young adult, Stage (cooking), cancer survival, Survival rate, ddc:613, Relative survival, business.industry, Oesophageal cancer, Cancer survival, medicine.disease, Esophageal Neoplasms/mortality/pathology, business, Demography, Cohort study
Abstract

Oesophageal cancer survival is poor with variation across Europe. No pan-European studies of survival differences by oesophageal cancer subtype exist. This study investigates rates and trends in oesophageal cancer survival across Europe. Data for primary malignant oesophageal cancer diagnosed in 1995-1999 and followed up to the end of 2003 was obtained from 66 cancer registries in 24 European countries. Relative survival was calculated using the Hakulinen approach. Staging data were available from 19 registries. Survival by region, gender, age, morphology and stage was investigated. Cohort analysis and the period approach were applied to investigate survival trends from 1988 to 2002 for 31 registries in 17 countries. In total 51,499 cases of oesophageal cancer diagnosed 1995-1999 were analysed. Overall, European 1- and 5-year survival rates were 33.4% (95% CI 32.9-33.9%) and 9.8% (95% CI 9.4-10.1%), respectively. Males, older patients and patients with late stage disease had poorer 1- and 5-year relative survival. Patients with squamous cell carcinoma had poorer 1-year relative survival. Regional variation in survival was observed with Central Europe above and Eastern Europe below the European pool. Survival for distant stage disease was similar across Europe while survival rates for localised disease were below the European pool in Eastern and Southern Europe. Improvement in European 1-year relative survival was reported (p=0.016). Oesophageal cancer survival was poor across Europe. Persistent regional variations in 1-year survival point to a need for a high resolution study of diagnostic and treatment practices of oesophageal cancer.

Published
2012

44. Survival of European patients with central nervous system tumors

Author

Sant, Milena, Minicozzi, Pamela, Lagorio, Susanna, Børge Johannesen, Tom, Marcos-Gragera, Rafael, Francisci, Silvia, Oberaigner, W., Hackl, M., Van Eycken, E., Verstreken, Martine, Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hã©delin, G., Velten, M., Guizard, A. V., Danzon, A., Buemi, A., Tretarre, B., Colonna, M., Bara, S., Ganry, O., Grosclaude, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Ciampichini, R., Ciccolallo, L., Gatta, G., Margutti, C., Micheli, A., Minicozzi, P., Sant, M., Sowe, S., Tereanu, C., Zigon, G., Tagliabue, G., Contiero, P., Bellã¹, F., Giacomin, A., Ferretti, S., Serraino, D., Dal Maso, L., De Dottori, M., De Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Pannelli, F., Federico, M., Rashid, I., Cirilli, C., Fusco, M., De Lisi, V., Bozzani, F., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Zanetti, R., Patriarca, S., Rosso, S., Piffer, S., Franchini, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Zambon, P., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., De Angelis, R., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gã³åºdåº, S., Siudowska, U., Mezyk, R., Bielska-Lasota, M., Zwierko, M., Miranda, A., Safaei Diba, Chakameh, Primic-Źakelj, M., Izarzugaza, I., Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Navarro, C., Chirlaque, M. D., Ardanaz, E., Moreno, C., Galceran, J., Klint, Ã. …., Talbã¤ck, M., Jundt, G., Usel, M., Ess, S. M., Bordoni, A., Luthi, J. C., Konzelmann, I., Lutz, J. M., Pury, P., Visser, O., Otter, R., Siesling, S., van der Zwan, J. M., Schaapveld, M., Coebergh, J. W. W., Janssen-Heijnen, M. L., van der Heijden, Louis, Greenberg, D. C., Coleman, M. P., Woods, Laura, Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Gavin, A., Black, R. J., Brewster, D. H., Steward, J. A., and Usel, Massimo

Subjects
Oncology, Ependymoma, Adult, Male, medicine.medical_specialty, Pathology, Cancer Research, Adolescent, Central Nervous System Neoplasms/mortality, Population, survival, NO, Benign tumor, Central Nervous System Neoplasms, Young Adult, Sex Factors, Internal medicine, morphology, medicine, 80 and over, Humans, Registries, Young adult, central nervous system tumors, Europe, Age Factors, Aged, Aged, 80 and over, Female, Middle Aged, Survival Rate, education, Survival rate, ddc:613, Medulloblastoma, education.field_of_study, Relative survival, business.industry, Cancer survival, Cancer, central nervous system tumors, survival, morphology, Europe, medicine.disease, business
Abstract

We present estimates of population-based 5-year relative survival for adult Europeans diagnosed with central nervous system tumors, by morphology (14 categories based on cell lineage and malignancy grade), sex, age at diagnosis and region (UK and Ireland, Northern, Central, Eastern and Southern Europe) for the most recent period with available data (2000-2002). Sources were 39 EUROCARE cancer registries with continuous data from 1996 to 2002. Survival time trends (1988 to 2002) were estimated from 24 cancer registries with continuous data from 1988. Overall 5-year relative survival was 85.0% for benign, 19.9% for malignant tumors. Benign tumor survival ranged from 90.6% (Northern Europe) to 77.4% (UK and Ireland); for malignant tumors the range was 25.1% (Northern Europe) to 15.6% (UK and Ireland). Survival decreased with age at diagnosis and was slightly better for women (malignant tumors only). For glial tumors, survival varied from 83.5% (ependymoma and choroid plexus) to 2.7% (glioblastoma); and for non-glioma tumors from 96.5% (neurinoma) to 44.9% (primitive neuroectoderm tumor/medulloblastoma). Survival differences between regions narrowed after adjustment for morphology and age, and were mainly attributable to differences in morphology mix; however UK and Ireland and Eastern Europe patients still had 40% and 30% higher excess risk of death, respectively, than Northern Europe patients (reference). Survival for benign tumors increased from 69.3% (1988-1990) to 77.1% (2000-2002); but survival for malignant tumors did not improve indicating no useful advances in treatment over the 14-year study period, notwithstanding major improvement in the diagnosis and treatment of other solid cancers.

Published
2011

46. Incidence of hematologic malignancies in Europe by morphologic subtype: Results of the HAEMACARE project

Author

Sant, M., Allemani, C., Tereanu, C., De Angelis, R., Capocaccia, R., Visser, O., Marcos Gragera, R., Maynadié, M., Simonetti, A., Lutz, J. M., Berrino, F., Hackl, M., Holub, J., Maynadie, M., Holleczek, B., Tryggvadottir, L., Comber, H., Bellù, F., Giacomin, A., Ferretti, S., Crocetti, E., Serraino, D., Vercelli, M., Federico, Massimo, Fusco, M., Michiara, M., Tumino, R., Mangone, L., Falcini, F., Iannelli, A., Budroni, M., Zanetti, R., Piffer, S., La Rosa, F., Zambon, P., Sowe, S., England, K., Langmark, F., Rachtan, J., Mezyk, R., Zwierko, M., Ondrusova, M., Primic Žakelj, M., Khan, S., Jundt, G., Usel, M., Ess, S. M., Bordoni, A., Otter, R., Coebergh, J. W., Siesling, S., Greenberg, D., Easey, N., Roche, M., Lawrence, G., Gavin, A., Brewster, D. H., and Steward, J.

Subjects
Male, medicine.medical_specialty, Pathology, Childhood leukemia, Hematologic malignant, Europe, morphologic subtype, international comparison, population-based cancer registry, Immunology, Population, UNITED-STATES, ALCOHOL, Biochemistry, NO, Myelodysplastic–myeloproliferative diseases, Internal medicine, Epidemiology, morphology, medicine, LYMPHOMA, Humans, EPIDEMIOLOGY, Registries, EXPOSURE, education, RISK, education.field_of_study, TOBACCO, haematologic malignancies, business.industry, Incidence (epidemiology), Incidence, leukemia, Myeloid leukemia, Cell Biology, Hematology, Hematologic malignancies, Plasma cell neoplasm, medicine.disease, Myelodysplastic-Myeloproliferative Diseases, Lymphoma, CANCER INCIDENCE, Hematologic Neoplasms, cancer incidence, tobacco, alcohol, epidemiology, leukemia, risk, exposure, CHILDHOOD LEUKEMIA, Female, business
Abstract

Changing definitions and classifications of hematologic malignancies (HMs) complicate incidence comparisons. HAEMACARE classified HMs into groupings consistent with the latest World Health Organization classification and useful for epidemiologic and public health purposes. We present crude, age-specific and age-standardized incidence rates for European HMs according to these groupings, estimated from 66 371 lymphoid malignancies (LMs) and 21 796 myeloid malignancies (MMs) registered in 2000-2002 by 44 European cancer registries, grouped into 5 regions. Age-standardized incidence rates were 24.5 (per 100 000) for LMs and 7.55 for MMs. The commonest LMs were plasma cell neoplasms (4.62), small B-cell lymphocytic lymphoma/chronic lymphatic leukemia (3.79), diffuse B-cell lymphoma (3.13), and Hodgkin lymphoma (2.41). The commonest MMs were acute myeloid leukemia (2.96), other myeloproliferative neoplasms (1.76), and myelodysplastic syndrome (1.24). Unknown morphology LMs were commonest in Northern Europe (7.53); unknown morphology MMs were commonest in Southern Europe (0.73). Overall incidence was lowest in Eastern Europe and lower in women than in men. For most LMs, incidence was highest in Southern Europe; for MMs incidence was highest in the United Kingdom and Ireland. Differences in diagnostic and registration criteria are an important cause of incidence variation; however, different distribution of HM risk factors also contributes. The quality of population-based HM data needs further improvement.

Published
2010

47. Improving automata efficiency by stretching and jamming

Author

Beijer, de, N., Cleophas, L.G.W.A., Kourie, D.G., Watson, B.W., Holub, J., and Zdarek, J.

Abstract

In recent years, the range of alphabet sizes typically used in applications of finite automata has grown considerably, now ranging from DNA alphabets—whose symbols are representable using 2 bits—to Unicode alphabets—whose symbol representation may take up to 32 bits. As automata traditionally use symbol encodings taking 8 bits, the different alphabet and symbol sizes bring up the question whether they may be exploited to either decrease memory use for the automata’s transition tables or to decrease string processing time. In [3], stretching and jamming were introduced as transformations on finite automata. Given a finite automaton, we can stretch it by splitting each single transition into two or more sequential transitions, thereby introducing additional intermediate states. Jamming is the inverse transformation, in which two or more successive transitions are joined into a single transition, thereby removing redundant intermediate states. In this paper, we only consider a restricted form of stretching and jamming, in which a fixed factor is used to stretch (jam) transitions (transition paths) in a given automaton, and in which transition symbols are assumed to be encoded as bit strings. We consider improved versions of the algorithms that were presented in [3] for this particular form of stretching and jamming. The algorithms were implemented in c++ and used to benchmark the transformations. The results of this benchmarking indicate that, under certain conditions, stretching may be beneficial to memory use to the detriment of processing time, while jamming may be beneficial to processing time to the detriment of memory use. The latter seems potentially useful in the case of DNA processing, while the former may be for Unicode processing. Keywords: finite automata; transformation; split transition; join transition; transition table size; string processing time

Published
2010

48. Survival trends in European cancer patients diagnosed from 1988 to 1999

Author

Verdecchia, Arduino, Guzzinati, Stefano, Francisci, Silvia, De Angelis, Roberta, Bray, Freddie, Allemani, Claudia, Tavilla, Andrea, Santaquilani, Mariano, Sant, Milena, Gavin, A., Black, R. J., Brewster, D. H., Steward, J. A., Oberaigner, W., Hackl, M., Van Eycken, E., Verstreken, Martine, Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hã©delin, G., Velten, M., Tron, I., Le Gall, E., Launoy, G., Guizard, A. V., Faivre, J., Bouvier, A. M., Carli, P. M., Maynadiã©, M., Danzon, A., Buemi, A., Tretarre, B., Lacour, B., Desandes, E., Colonna, M., Moliniã©, F., Bara, S., Schvartz, C., Ganry, O., Grosclaude, P., Brenner, H., Kaatsch, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Ciampichini, R., Ciccolallo, L., Gatta, G., Micheli, A., Sant, M., Sowe, S., Zigon, G., Tagliabue, G., Contiero, P., Bellã¹, F., Giacomin, A., Ferretti, S., Dal Maso, D. Serraino L., De Dottori, M., De Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Pannelli, F., Federico, M., Rashid, I., Cirilli, C., Fusco, M., Traina, A., De Lisi, V., Bozzani, F., Magnani, C., Pastore, G., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Zanetti, R., Patriarca, S., Rosso, S., Piffer, S., Franchini, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Zambon, P., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gã³åºdåº, S., Siudowska, U., Mè©zyk, R., Bielska-Lasota, M., Zwierko, M., Pinheiro, P. S., Primic-Žakelj, M. P. -. Z., Mateos, A., Izarzugaza, I., Torrella-Ramos, A., Zurriaga, Oscar, Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Martinez-Garcia, C., Sã¡nchez, M. J., Navarro, C., Chirlaque, M. D., Peris-Bonet, R., Ardanaz, E., Moreno, C., Galceran, J., Klint, Ã. …., Talbã¤ck, M., Jundt, G., Usel, M., Frick, H., Ess, S. M., Bordoni, A., Luthi, J. C., Konzelmann, I., Probst, N., Lutz, J. M., Pury, P., Visser, O., Otter, R., Schaapveld, M., Coebergh, J. W. W., Janssen-Heijnen, M. L., Van Der Heijden, Louis, Greenberg, D. C., Coleman, M. P., Woods, Laura, Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Stiller, C., Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanita [Rome], Department of Preventive and Predictive Medicine, Unit of Etiological Epidemiology and Prevention, Istituto Nazionale per lo Studio e la Cura dei Tumori, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), and Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC )

Subjects
Male, Cancer Research, Survival, MESH : Mortality, MESH : Age Distribution, MESH : Aged, Colonoscopy, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 0302 clinical medicine, MESH: Aged, 80 and over, Prostate, Residence Characteristics, Neoplasms, 80 and over, MESH : Female, MESH: Neoplasms, 030212 general & internal medicine, MESH: Residence Characteristics, Young adult, cancer survival, MESH : Sex Distribution, Aged, 80 and over, MESH: Aged, MESH: Middle Aged, medicine.diagnostic_test, Relative survival, Europe, Population registries, Time trends, Adolescent, Adult, Age Distribution, Aged, Female, Humans, Middle Aged, Mortality, Sex Distribution, Survival Analysis, Young Adult, Oncology, MESH: Sex Distribution, MESH : Adult, 3. Good health, medicine.anatomical_structure, MESH: Young Adult, 030220 oncology & carcinogenesis, MESH: Survival Analysis, MESH : Residence Characteristics, medicine.medical_specialty, MESH : Male, MESH : Europe, MESH : Young Adult, Socio-culturale, Rectum, [SDV.CAN]Life Sciences [q-bio]/Cancer, 03 medical and health sciences, Internal medicine, MESH : Adolescent, medicine, MESH : Middle Aged, MESH : Aged, 80 and over, Cervix, MESH: Age Distribution, Survival analysis, MESH: Adolescent, MESH: Humans, MESH: Mortality, business.industry, MESH : Humans, Cancer, MESH: Adult, medicine.disease, MESH : Neoplasms, MESH: Male, Surgery, MESH: Europe, MESH : Survival Analysis, business, MESH: Female
Abstract

International audience; We analysed data from 49 cancer registries in 18 European countries over the period 1988-1999 to delineate time trends in cancer survival. Survival increased in Europe over the study period for all cancer sites that were considered. There were major survival increases in 5 year age-adjusted relative survival for prostate (from 58% to 79%), colon and rectum (from 48% to 54% men and women), and breast (from 74% to 83%). Improvements were also significant for stomach (from 22% to 24%), male larynx (from 62% to 64%), skin melanoma (from 78% to 83%), Hodgkin disease (from 77% to 83%), non-Hodgkin lymphoma (from 49% to 56%), leukaemias (from 37% to 42%), and for all cancers combined (from 34% to 39% in men, and from 52% to 59% in women). Survival did not change significantly for female larynx, lung, cervix or ovary. The largest increases in survival typically occurred in countries with the lowest survival, and contributed to the overall reduction of survival disparities across Europe over the study period. Differences in the extent of PSA testing and mammographic screening, and increasing use of colonoscopy and faecal blood testing together with improving cancer care are probably the major underlying reasons for the improvements in survival for cancers of prostate, breast, colon and rectum. The marked survival improvements in countries with poor survival may indicate that these countries have made efforts to adopt the new diagnostic procedures and the standardised therapeutic protocols in use in more affluent countries.

Published
2009

49. The EUROCARE-4 database on cancer survival in Europe: data standardisation, quality control and methods of statistical analysis

Author

De Angelis, Roberta, Francisci, Silvia, Baili, Paolo, Marchesi, Francesca, Roazzi, Paolo, Belot, Aurã©lien, Crocetti, Emanuele, Pury, Pierre, Knijn, Arnold, Coleman, Michel, Capocaccia, Riccardo, Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hã©delin, G., Velten, M., Tron, I., Le Gall, E., Launoy, G., Guizard, A. V., Faivre, J., Bouvier, A. M., Carli, P. M., Maynadiã©, M., Danzon, A., Buemi, A., Tretarre, B., Lacour, B., Desandes, E., Colonna, M., Moliniã©, F., Bara, S., Schvartz, C., Ganry, O., Grosclaude, P., Brenner, H., Kaatsch, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Ciampichini, R., Ciccolallo, L., Gatta, G., Micheli, A., Sant, M., Sowe, S., Zigon, G., Tagliabue, G., Contiero, P., Bellã¹, F., Giacomin, A., Ferretti, S., Dal Maso, D. Serraino L., De Dottori, M., De Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Pannelli, F., Federico, M., Rashid, I., Cirilli, C., Fusco, M., Traina, A., De Lisi, V., Bozzani, F., Magnani, C., Pastore, G., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Zanetti, R., Patriarca, S., Rosso, S., Piffer, S., Franchini, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Zambon, P., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gã³åºdåº, S., Siudowska, U., Mè©zyk, R., Bielska-Lasota, M., Zwierko, M., Pinheiro, P. S., Primic-Žakelj, M. P. -. Z., Mateos, A., Izarzugaza, I., Torrella-Ramos, A., Zurriaga, Oscar, Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Martinez-Garcia, C., Sã¡nchez, M. J., Navarro, C., Chirlaque, M. D., Peris-Bonet, R., Ardanaz, E., Moreno, C., Galceran, J., Klint, Ã. …., Talbã¤ck, M., Jundt, G., Usel, M., Frick, H., Ess, S. M., Bordoni, A., Luthi, J. C., Konzelmann, I., Probst, N., Lutz, J. M., Pury, P., Visser, O., Otter, R., Schaapveld, M., Coebergh, J. W. W., Janssen-Heijnen, M. L., Van Der Heijden, Louis, Greenberg, D. C., Coleman, M. P., Woods, Laura, Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Stiller, C., Gavin, A., Black, R. J., Brewster, D. H., Steward, J. A., Oberaigner, W., Hackl, M., Van Eycken, E., Verstreken, Martine, Service de Biostatistique, Hospices Civils de Lyon ( HCL ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Département des maladies chroniques et traumatismes, Institut de Veille Sanitaire (INVS), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ), Hospices Civils de Lyon (HCL), Biostatistiques santé, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (UR 3181) (CEF2P / CARCINO), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)

Subjects
Cancer Research, MESH: Quality Control, computer.software_genre, MESH: Epidemiologic Methods, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 0302 clinical medicine, Neoplasms, Medicine, MESH: Neoplasms, 030212 general & internal medicine, cancer survival, education.field_of_study, Database, Relative survival, Incidence (epidemiology), Europe, Population registries, Survival analysis, Vital statistics, Databases as Topic, Epidemiologic Methods, Humans, Quality Control, Oncology, MESH : Quality Control, 3. Good health, 030220 oncology & carcinogenesis, Population, MESH : Europe, MEDLINE, Socio-culturale, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH : Epidemiologic Methods, 03 medical and health sciences, education, MESH: Humans, business.industry, MESH : Humans, Cancer, medicine.disease, MESH : Neoplasms, Data quality, MESH: Europe, MESH : Databases as Topic, business, computer, MESH: Databases as Topic, International Classification of Diseases for Oncology
Abstract

International audience; This paper describes the collection, standardisation and checking of cancer survival data included in the EUROCARE-4 database. Methods for estimating relative survival are also described. Incidence and vital status data on newly diagnosed European cancer cases were received from 93 cancer registries in 23 countries, covering 151,400,000 people (35% of the participating country population). The third revision of the International Classification of Diseases for Oncology was used to specify tumour topography and morphology. Records were extensively checked for consistency and compatibility using multiple routines; flagged records were sent back for correction. An algorithm assigned standardised sequence numbers to multiple cancers. Only first malignant cancers were used to estimate relative survival from registry, year, sex and age-specific life tables. Age-adjusted and Europe-wide survival were also estimated. The database contains 13,814,573 cases diagnosed in 1978-2002; 92% malignant. A negligible proportion of records was excluded for major errors. Of 5,753,934 malignant adult cases diagnosed in 1995-2002, 5.3% were second or later cancers, 2.7% were known from death certificates only and 0.4% were discovered at autopsy. The remaining 5,278,670 cases entered the survival analyses, 90% of these had microscopic confirmation and 1.3% were censored alive after less than five years' follow-up. These indicators suggest satisfactory data quality that has improved since EUROCARE-3.

Published
2009

50. EUROCARE-4. Survival of cancer patients diagnosed in 1995-1999. Results and commentary

Author

Sant, Milena, Allemani, Claudia, Santaquilani, Mariano, Knijn, Arnold, Marchesi, Francesca, Capocaccia, Riccardo, Stiller, C., Gavin, A., Black, R. J., Brewster, D. H., Steward, J. A., Oberaigner, W., Hackl, M., Van Eycken, E., Verstreken, Martine, Holub, J., Jurickova, L., Storm, H. H., Engholm, G., Hakulinen, T., Belot, A., Hã©delin, G., Velten, M., Tron, I., Le Gall, E., Launoy, G., Guizard, A. V., Faivre, J., Bouvier, A. M., Carli, P. M., Maynadiã©, M., Danzon, A., Buemi, A., Tretarre, B., Lacour, B., Desandes, E., Colonna, M., Moliniã©, F., Bara, S., Schvartz, C., Ganry, O., Grosclaude, P., Brenner, H., Kaatsch, P., Ziegler, H., Tryggvadottir, L., Comber, H., Berrino, F., Allemani, C., Baili, P., Ciampichini, R., Ciccolallo, L., Gatta, G., Micheli, A., Sant, M., Sowe, S., Zigon, G., Tagliabue, G., Contiero, P., Bellã¹, F., Giacomin, A., Ferretti, S., Dal Maso, D. Serraino L., De Dottori, M., De Paoli, A., Zanier, L., Vercelli, M., Orengo, M. A., Casella, C., Quaglia, A., Pannelli, F., Federico, M., Rashid, I., Cirilli, C., Fusco, M., Traina, A., De Lisi, V., Bozzani, F., Magnani, C., Pastore, G., Tumino, R., La Rosa, M. G., Spata, E., Sigona, A., Mangone, L., Falcini, F., Foca, F., Giorgetti, S., Senatore, G., Iannelli, A., Budroni, M., Zanetti, R., Patriarca, S., Rosso, S., Piffer, S., Franchini, S., Paci, E., Crocetti, E., La Rosa, F., Stracci, F., Cassetti, T., Zambon, P., Guzzinati, S., Caldora, M., Capocaccia, R., Carrani, E., De Angelis, R., Francisci, S., Grande, E., Inghelmann, R., Lenz, H., Martina, L., Roazzi, P., Santaquilani, M., Simonetti, A., Tavilla, A., Verdecchia, A., Dalmas, M., Langmark, F., Bray, F., Johannesen, T. B., Rachtan, J., Gã³åºdåº, S., Siudowska, U., Mè©zyk, R., Bielska-Lasota, M., Zwierko, M., Pinheiro, P. S., Primic-Žakelj, M. P. -. Z., Mateos, A., Izarzugaza, I., Torrella-Ramos, A., Zurriaga, Oscar, Marcos-Gragera, R., Vilardell, M. L., Izquierdo, A., Martinez-Garcia, C., Sã¡nchez, M. J., Navarro, C., Chirlaque, M. D., Peris-Bonet, R., Ardanaz, E., Moreno, C., Galceran, J., Klint, Ã. …., Talbã¤ck, M., Jundt, G., Usel, M., Frick, H., Ess, S. M., Bordoni, A., Luthi, J. C., Konzelmann, I., Probst, N., Lutz, J. M., Pury, P., Visser, O., Otter, R., Schaapveld, M., Coebergh, J. W. W., Janssen-Heijnen, M. L., Van Der Heijden, Louis, Greenberg, D. C., Coleman, M. P., Woods, Laura, Moran, T., Forman, D., Cooper, N., Roche, M., Verne, J., Mã¸ller, H., Meechan, D., Poole, J., Lawrence, G., Department of Preventive and Predictive Medicine, Unit of Etiological Epidemiology and Prevention, Istituto Nazionale per lo Studio e la Cura dei Tumori, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), and Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC )

Subjects
Male, Cancer Research, MESH : Age Distribution, MESH : Aged, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 0302 clinical medicine, Neoplasms, Epidemiology, Medicine, MESH : Female, MESH: Neoplasms, 030212 general & internal medicine, MESH : Sex Distribution, MESH: Aged, MESH: Middle Aged, Relative survival, MESH: Sex Distribution, Population-based cancer registries, Middle Aged, MESH : Adult, Cancer survival, EUROCARE, Adolescent, Adult, Age Distribution, Aged, Europe, Female, Humans, Sex Distribution, Survival Analysis, Oncology, 3. Good health, 030220 oncology & carcinogenesis, MESH: Survival Analysis, Skin melanoma, Stage at diagnosis, medicine.medical_specialty, MESH : Male, MESH : Europe, Socio-culturale, [SDV.CAN]Life Sciences [q-bio]/Cancer, Age and sex, 03 medical and health sciences, MESH : Adolescent, MESH : Middle Aged, MESH: Age Distribution, Survival analysis, MESH: Adolescent, MESH: Humans, business.industry, Advanced stage, MESH : Humans, Cancer, MESH: Adult, medicine.disease, MESH : Neoplasms, MESH: Male, MESH: Europe, MESH : Survival Analysis, business, MESH: Female, Demography
Abstract

International audience; EUROCARE-4 analysed about three million adult cancer cases from 82 cancer registries in 23 European countries, diagnosed in 1995-1999 and followed to December 2003. For each cancer site, the mean European area-weighted observed and relative survival at 1-, 3-, and 5-years by age and sex are presented. Country-specific 1- and 5-year relative survival is also shown, together with 5-year relative survival conditional to surviving 1-year. Within-country variation in survival is analysed for selected cancers. Survival for most solid cancers, whose prognosis depends largely on stage at diagnosis (breast, colorectum, stomach, skin melanoma), was highest in Finland, Sweden, Norway and Iceland, lower in the UK and Denmark, and lowest in the Czech Republic, Poland and Slovenia. France, Switzerland and Italy generally had high survival, slightly below that in the northern countries. There were between-region differences in the survival for haematologic malignancies, possibly due to differences in the availability of effective treatments. Survival of elderly patients was low probably due to advanced stage at diagnosis, comorbidities, difficult access or lack of availability of appropriate care. For all cancers, 5-year survival conditional to surviving 1-year was higher and varied less with region, than the overall relative survival.

Published
2009

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