Browsing by Subject "reproducibility"

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  • Gutiérrez, José Manuel; Maraun, Douglas; Widmann, Martin; Huth, Radan; Hertig, Elke; Benestad, Rasmus; Rössler, Ole; Wibig, Joanna; Wilcke, Renate; Kotlarski, Sven; San Martin, Daniel; Herrera, Sixto; Bedia, Joaquin; Casanueva, Ana; Manzanas, Rodrigo; Iturbide, Maialen; Vrac, Mathieu; Dubrovsky, Martin; Ribalaygua, Jamie; Pórtoles, Javier; Räty, Olle Einari; Räisänen, Jouni Antero; Hingray, Benoît; Raynaud, Damien; Casado, María; Ramos, Petra; Zerenner, Tanja; Turco, Marco; Bosshard, Thomas; Stepanek, Petr; Bartholy, Judit; Pongracz, Rita; Keller, Denise; Fischer, Andreas; Cardoso, Rita; Soares, Pedro; Czernecki, Bartosz; Pagé, Christian (2019)
    VALUE is an open European collaboration to intercompare downscaling approaches for climate change research, focusing on different validation aspects (marginal, temporal, extremes, spatial, process‐based, etc.). Here we describe the participating methods and first results from the first experiment, using “perfect” reanalysis (and reanalysis‐driven regional climate model (RCM)) predictors to assess the intrinsic performance of the methods for downscaling precipitation and temperatures over a set of 86 stations representative of the main climatic regions in Europe. This study constitutes the largest and most comprehensive to date intercomparison of statistical downscaling methods, covering the three common downscaling approaches (perfect prognosis, model output statistics—including bias correction—and weather generators) with a total of over 50 downscaling methods representative of the most common techniques. Overall, most of the downscaling methods greatly improve (reanalysis or RCM) raw model biases and no approach or technique seems to be superior in general, because there is a large method‐to‐method variability. The main factors most influencing the results are the seasonal calibration of the methods (e.g., using a moving window) and their stochastic nature. The particular predictors used also play an important role in cases where the comparison was possible, both for the validation results and for the strength of the predictor–predictand link, indicating the local variability explained. However, the present study cannot give a conclusive assessment of the skill of the methods to simulate regional future climates, and further experiments will be soon performed in the framework of the EURO‐CORDEX initiative (where VALUE activities have merged and follow on). Finally, research transparency and reproducibility has been a major concern and substantive steps have been taken. In particular, the necessary data to run the experiments are provided at http://www.value‐ and data and validation results are available from the VALUE validation portal for further investigation: http://www.value‐
  • Åhlgren, Johanna; Voikar, Vootele (2019)
    Individually ventilated caging (IVC) systems for rodents are increasingly common in laboratory animal facilities. However, the impact of such substantial change in housing conditions on animal physiology and behavior is still debated. Most importantly, there arise the questions regarding reproducibility and comparison of previous or new phenotypes between the IVC and open cages. The present study was set up for detailed and systematic comparison of behavioral phenotypes in male and female mice of three widely used inbred strains (C57BL/6JRccHsd, DBA/2JRccHsd, 129S2/SvHSd) after being kept in two housing environments (IVC and open cages) for 6?weeks (since 4?weeks of age) before behavioral testing. The tests addressed exploratory, anxiety-like and stress-related behavior (light-dark box, open field, forced swim test, stress-induced hyperthermia), social approach and species-specific behavior (nest building, marble burying). In all tests, large and expected strain differences were found. Somewhat surprisingly, the most striking effect of environment was found for basal body temperature and weight loss after one night of single housing in respective cages. In addition, the performance in light-dark box and open field was affected by environment. Several parameters in different tests showed significant interaction between housing and genetic background. In summary, the IVC housing did not invalidate the well-known differences between the mouse strains which have been established by previous studies. However, within the strains the results can be influenced by sex and housing system depending on the behavioral tasks applied. The bottom-line is that the environmental conditions should be described explicitly in all publications.
  • Julkunen, Anna; Terna, Emma; Numminen, Jura; Markkola, Antti; Dastidar, Prasun; Karjalainen, Matti; Huhtala, Heini; Rautiainen, Markus; Meurman, Jukka; Toppila-Salmi, Sanna (2017)
    Conclusion: The study demonstrated considerable inter-observer variation in certain surgically important structures. This would indicate the significance for consultation when evaluating sinus CT scans of CRS patients for planned advanced sinus surgery. Objectives: After the failure of medical treatment of chronic rhinosinusitis (CRS), the need for surgery and the pre-operative planning of safe surgery is based on computed tomography (CT) findings. The aim of this prospective study was to compare inter-observer agreement of anatomical and surgical structures of sinus CT scans. The hypothesis was that the agreement between observers is good. Methods: Of these 57 CRS patients, Lund-Mackay (LM) scores and 43 other structural parameters were analyzed blinded. The reproducibility of the findings between three observers, a radiologist, an Ear, nose and throat (ENT) surgeon, and an ENT resident, were compared. Results: In general, there was moderate inter-observer agreement of the structures by Cohen's kappa coefficient. Poor reproducibility was observed in the following structures: optic nerve, insertion of the uncinated process, anterior ethmoidal artery, and Keros class.
  • Thery, Clotilde; Witwer, Kenneth W.; Aikawa, Elena; Jose Alcaraz, Maria; Anderson, Johnathon D.; Andriantsitohaina, Ramaroson; Antoniou, Anna; Arab, Tanina; Archer, Fabienne; Atkin-Smith, Georgia K.; Ayre, D. Craig; Bach, Jean-Marie; Bachurski, Daniel; Baharvand, Hossein; Balaj, Leonora; Baldacchino, Shawn; Bauer, Natalie N.; Baxter, Amy A.; Bebawy, Mary; Beckham, Carla; Zavec, Apolonija Bedina; Benmoussa, Abderrahim; Berardi, Anna C.; Bergese, Paolo; Bielska, Ewa; Blenkiron, Cherie; Bobis-Wozowicz, Sylwia; Boilard, Eric; Boireau, Wilfrid; Bongiovanni, Antonella; Borras, Francesc E.; Bosch, Steffi; Boulanger, Chantal M.; Breakefield, Xandra; Breglio, Andrew M.; Brennan, Meadhbh A.; Brigstock, David R.; Brisson, Alain; Broekman, Marike L. D.; Bromberg, Jacqueline F.; Bryl-Gorecka, Paulina; Buch, Shilpa; Buck, Amy H.; Burger, Dylan; Busatto, Sara; Buschmann, Dominik; Bussolati, Benedetta; Buzas, Edit; Byrd, James Bryan; Camussi, Giovanni; Carter, David R. F.; Caruso, Sarah; Chamley, Lawrence W.; Chang, Yu-Ting; Chaudhuri, Amrita Datta; Chen, Chihchen; Chen, Shuai; Cheng, Lesley; Chin, Andrew R.; Clayton, Aled; Clerici, Stefano P.; Cocks, Alex; Cocucci, Emanuele; Coffey, Robert J.; Cordeiro-da-Silva, Anabela; Couch, Yvonne; Coumans, Frank A. W.; Coyle, Beth; Crescitelli, Rossella; Criado, Miria Ferreira; D'Souza-Schorey, Crislyn; Das, Saumya; de Candia, Paola; De Santana Junior, Eliezer F.; De Wever, Olivier; del Portillo, Hernando A.; Demaret, Tanguy; Deville, Sarah; Devitt, Andrew; Dhondt, Bert; Di Vizio, Dolores; Dieterich, Lothar C.; Dolo, Vincenza; Dominguez Rubio, Ana Paula; Dominici, Massimo; Dourado, Mauricio R.; Driedonks, Tom A. P.; Duarte, Filipe; Duncan, Heather M.; Eichenberger, Ramon M.; Ekstrom, Karin; Andaloussi, Samir E. L.; Elie-Caille, Celine; Erdbrugger, Uta; Falcon-Perez, Juan M.; Fatima, Farah; Fish, Jason E.; Flores-Bellver, Miguel; Forsonits, Andras; Frelet-Barrand, Annie; Fricke, Fabia; Fuhrmann, Gregor; Gabrielsson, Susanne; Gamez-Valero, Ana; Gardiner, Chris; Gaertner, Kathrin; Gaudin, Raphael; Gho, Yong Song; Giebel, Bernd; Gilbert, Caroline; Gimona, Mario; Giusti, Ilaria; Goberdhan, Deborah C.; Goergens, Andre; Gorski, Sharon M.; Greening, David W.; Gross, Julia Christina; Gualerzi, Alice; Gupta, Gopal N.; Gustafson, Dakota; Handberg, Aase; Haraszti, Reka A.; Harrison, Paul; Hegyesi, Hargita; Hendrix, An; Hill, Andrew F.; Hochberg, Fred H.; Hoffmann, Karl F.; Holder, Beth; Holthofer, Harry; Hosseinkhani, Baharak; Hu, Guoku; Huang, Yiyao; Huber, Veronica; Hunt, Stuart; Ibrahim, Ahmed Gamal-Eldin; Ikezu, Tsuneya; Inal, Jameel M.; Isin, Mustafa; Ivanova, Alena; Jackson, Hannah K.; Jacobsen, Soren; Jay, Steven M.; Jayachandran, Muthuvel; Jenster, Guido; Jiang, Lanzhou; Johnson, Suzanne M.; Jones, Jennifer C.; Jong, Ambrose; Jovanovic-Talisman, Tijana; Jung, Stephanie; Kalluri, Raghu; Kano, Shin-ichi; Kaur, Sukhbir; Kawamura, Yumi; Keller, Evan T.; Khamari, Delaram; Khomyakova, Elena; Khvorova, Anastasia; Kierulf, Peter; Kim, Kwang Pyo; Kislinger, Thomas; Klingeborn, Mikael; Klinke, David J.; Kornek, Miroslaw; Kosanovic, Maja M.; Kovacs, Arpad Ferenc; Kraemer-Albers, Eva-Maria; Krasemann, Susanne; Krause, Mirja; Kurochkin, Igor; Kusuma, Gina D.; Kuypers, Soren; Laitinen, Saara; Langevin, Scott M.; Languino, Lucia R.; Lannigan, Joanne; Lasser, Cecilia; Laurent, Louise C.; Lavieu, Gregory; Lazaro-Ibanez, Elisa; Le Lay, Soazig; Lee, Myung-Shin; Lee, Yi Xin Fiona; Lemos, Debora S.; Lenassi, Metka; Leszczynska, Aleksandra; Li, Isaac T. S.; Liao, Ke; Libregts, Sten F.; Ligeti, Erzsebet; Lim, Rebecca; Lim, Sai Kiang; Line, Aija; Linnemannstoens, Karen; Llorente, Alicia; Lombard, Catherine A.; Lorenowicz, Magdalena J.; Lorincz, Akos M.; Lotvall, Jan; Lovett, Jason; Lowry, Michelle C.; Loyer, Xavier; Lu, Quan; Lukomska, Barbara; Lunavat, Taral R.; Maas, Sybren L. N.; Malhi, Harmeet; Marcilla, Antonio; Mariani, Jacopo; Mariscal, Javier; Martens-Uzunova, Elena S.; Martin-Jaular, Lorena; Martinez, M. Carmen; Martins, Vilma Regina; Mathieu, Mathilde; Mathivanan, Suresh; Maugeri, Marco; McGinnis, Lynda K.; McVey, Mark J.; Meckes, David G.; Meehan, Katie L.; Mertens, Inge; Minciacchi, Valentina R.; Moller, Andreas; Jorgensen, Malene Moller; Morales-Kastresana, Aizea; Morhayim, Jess; Mullier, Francois; Muraca, Maurizio; Musante, Luca; Mussack, Veronika; Muth, Dillon C.; Myburgh, Kathryn H.; Najrana, Tanbir; Nawaz, Muhammad; Nazarenko, Irina; Nejsum, Peter; Neri, Christian; Neri, Tommaso; Nieuwland, Rienk; Nimrichter, Leonardo; Nolan, John P.; Hoen, Esther N. M. Nolte-'t; Hooten, Nicole Noren; O'Driscoll, Lorraine; O'Grady, Tina; O'Loghlen, Ana; Ochiya, Takahiro; Olivier, Martin; Ortiz, Alberto; Ortiz, Luis A.; Osteikoetxea, Xabier; Ostegaard, Ole; Ostrowski, Matias; Park, Jaesung; Pegtel, D. Michiel; Peinado, Hector; Perut, Francesca; Pfaffl, Michael W.; Phinney, Donald G.; Pieters, Bartijn C. H.; Pink, Ryan C.; Pisetsky, David S.; von Strandmann, Elke Pogge; Polakovicova, Iva; Poon, Ivan K. H.; Powell, Bonita H.; Prada, Ilaria; Pulliam, Lynn; Quesenberry, Peter; Radeghieri, Annalisa; Raffai, Robert L.; Raimondo, Stefania; Rak, Janusz; Ramirez, Marcel; Raposo, Graca; Rayyan, Morsi S.; Regev-Rudzki, Neta; Ricklefs, Franz L.; Robbins, Paul D.; Roberts, David D.; Rodrigues, Silvia C.; Rohde, Eva; Rome, Sophie; Rouschop, Kasper M. A.; Rughetti, Aurelia; Russell, Ashley E.; Saa, Paula; Sahoo, Susmita; Salas-Huenuleo, Edison; Sanchez, Catherine; Saugstad, Julie A.; Saul, Meike J.; Schiffelers, Raymond M.; Schneider, Raphael; Schoyen, Tine Hiorth; Scott, Aaron; Shahaj, Eriomina; Sharma, Shivani; Shatnyeva, Olga; Shekari, Faezeh; Shelke, Ganesh Vilas; Shetty, Ashok K.; Shiba, Kiyotaka; Siljander, Pia R-M; Silva, Andreia M.; Skowronek, Agata; Snyder, Orman L.; Soares, Rodrigo Pedro; Sodar, Barbara W.; Soekmadji, Carolina; Sotillo, Javier; Stahl, Philip D.; Stoorvogel, Willem; Stott, Shannon L.; Strasser, Erwin F.; Swift, Simon; Tahara, Hidetoshi; Tewari, Muneesh; Timms, Kate; Tiwari, Swasti; Tixeira, Rochelle; Tkach, Mercedes; Toh, Wei Seong; Tomasini, Richard; Torrecilhas, Ana Claudia; Pablo Tosar, Juan; Toxavidis, Vasilis; Urbanelli, Lorena; Vader, Pieter; van Balkom, Bas W. M.; van der Grein, Susanne G.; Van Deun, Jan; van Herwijnen, Martijn J. C.; Van Keuren-Jensen, Kendall; van Niel, Guillaume; van Royen, Martin E.; van Wijnen, Andre J.; Helena Vasconcelos, M.; Vechetti, Ivan J.; Veit, Tiago D.; Vella, Laura J.; Velot, Emilie; Verweij, Frederik J.; Vestad, Beate; Vinas, Jose L.; Visnovitz, Tamas; Vukman, Krisztina V.; Wahlgren, Jessica; Watson, Dionysios C.; Wauben, Marca H. M.; Weaver, Alissa; Webber, Jason P.; Weber, Viktoria; Wehman, Ann M.; Weiss, Daniel J.; Welsh, Joshua A.; Wendt, Sebastian; Wheelock, Asa M.; Wiener, Zoltan; Witte, Leonie; Wolfram, Joy; Xagorari, Angeliki; Xander, Patricia; Xu, Jing; Yan, Xiaomei; Yanez-Mo, Maria; Yin, Hang; Yuana, Yuana; Zappulli, Valentina; Zarubova, Jana; Zekas, Vytautas; Zhang, Jian-ye; Zhao, Zezhou; Zheng, Lei; Zheutlin, Alexander R.; Zickler, Antje M.; Zimmermann, Pascale; Zivkovic, Angela M.; Zocco, Davide; Zuba-Surma, Ewa K. (2018)
    The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
  • Jaiswal, Alok; Gautam, Prson; Pietilä, Elina A; Timonen, Sanna; Nordström, Nora; Akimov, Yevhen; Sipari, Nina; Tanoli, Ziaurrehman; Fleischer, Thomas; Lehti, Kaisa; Wennerberg, Krister; Aittokallio, Tero (2021)
    Molecular and functional profiling of cancer cell lines is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer cell lines for reliable biological discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics studies across 12 research laboratories for 2,018 cell lines. To account for a relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. The multi-modal meta-analysis approach also identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient endometrial cancer cells on RNA helicases.
  • Šimko, Tibor; Heinrich, Lukas Alexander; Lange, Clemens; Lintuluoto, Adelina Eleonora; MacDonell, Danika Marina; Mečionis, Audrius; Rodriguez, Diego Rodriguez; Shandilya, Parth (2021)
    We describe a novel approach for experimental High-Energy Physics (HEP) data analyses that is centred around the declarative rather than imperative paradigm when describing analysis computational tasks. The analysis process can be structured in the form of a Directed Acyclic Graph (DAG), where each graph vertex represents a unit of computation with its inputs and outputs, and the graph edges describe the interconnection of various computational steps. We have developed REANA, a platform for reproducible data analyses, that supports several such DAG workflow specifications. The REANA platform parses the analysis workflow and dispatches its computational steps to various supported computing backends (Kubernetes, HTCondor, Slurm). The focus on declarative rather than imperative programming enables researchers to concentrate on the problem domain at hand without having to think about implementation details such as scalable job orchestration. The declarative programming approach is further exemplified by a multi-level job cascading paradigm that was implemented in the Yadage workflow specification language. We present two recent LHC particle physics analyses, ATLAS searches for dark matter and CMS jet energy correction pipelines, where the declarative approach was successfully applied. We argue that the declarative approach to data analyses, combined with recent advancements in container technology, facilitates the portability of computational data analyses to various compute backends, enhancing the reproducibility and the knowledge preservation behind particle physics data analyses.
  • Lintuluoto, Adelina Eleonora (Helsingin yliopisto, 2021)
    At the Compact Muon Solenoid (CMS) experiment at CERN (European Organization for Nuclear Research), the building blocks of the Universe are investigated by analysing the observed final-state particles resulting from high-energy proton-proton collisions. However, direct detection of final-state quarks and gluons is not possible due to a phenomenon known as colour confinement. Instead, event properties with a close correspondence with their distributions are studied. These event properties are known as jets. Jets are central to particle physics analysis and our understanding of them, and hence of our Universe, is dependent upon our ability to accurately measure their energy. Unfortunately, current detector technology is imprecise, necessitating downstream correction of measurement discrepancies. To achieve this, the CMS experiment employs a sequential multi-step jet calibration process. The process is performed several times per year, and more often during periods of data collection. Automating the jet calibration would increase the efficiency of the CMS experiment. By automating the code execution, the workflow could be performed independently of the analyst. This in turn, would speed up the analysis and reduce analyst workload. In addition, automation facilitates higher levels of reproducibility. In this thesis, a novel method for automating the derivation of jet energy corrections from simulation is presented. To achieve automation, the methodology utilises declarative programming. The analyst is simply required to express what should be executed, and no longer needs to determine how to execute it. To successfully automate the computation of jet energy corrections, it is necessary to capture detailed information concerning both the computational steps and the computational environment. The former is achieved with a computational workflow, and the latter using container technology. This allows a portable and scalable workflow to be achieved, which is easy to maintain and compare to previous runs. The results of this thesis strongly suggest that capturing complex experimental particle physics analyses with declarative workflow languages is both achievable and advantageous. The productivity of the analyst was improved, and reproducibility facilitated. However, the method is not without its challenges. Declarative programming requires the analyst to think differently about the problem at hand. As a result there are some sociological challenges to methodological uptake. However, once the extensive benefits are understood, we anticipate widespread adoption of this approach.
  • Barim, Estela Maria; McLellan, Kátia Cristina Portero; Ribeiro, Rogerio Silicani; de Carvalho, José Antonio Maluf; Lindström, Jaana; Tuomilehto, Jaakko; Corrente, José Eduardo; Murta-Nascimento, Cristiane (2020)
    Introduction: The Finnish Diabetes Risk Score (FINDRISC) is a tool that was initially developed to predict the risk of developing type 2 diabetes mellitus in adults. This tool is simple, quick to apply, non-invasive, and low-cost. The aims of this study were to perform a translation and cultural adaptation of the original version of FINDRISC into Brazilian Portuguese and to assess test-retest reliability. Methodology: This work was done following the ISPOR Principles of Good Practice for the Translation and Cultural Adaptation Process for Patient-Reported Outcomes Measures. Once the final Brazilian Portuguese version (FINDRISC-Br) was developed, the reliability assessment was performed using a non-random sample of 83 individuals attending a primary care health center. Each participant was interviewed by trained registered dieticians on two occasions with a mean interval of 14 days. The reliability assessment was performed by analyzing the level of agreement between the test-retest responses of FINDRISC-Br using Cohen’s kappa coefficient and the intraclass correlation coefficient (ICC). Results: The steps of ISPOR guidelines were consecutively followed without major problems. Regarding the reliability assessment, the questionnaire as a whole presented adequate reliability (Cohen’s kappa = 0.82, 95%CI 0.72 – 0.92 and ICC = 0.94, 95%CI 0.91 – 0.96). Conclusion: FINDRISC was translated into Brazilian Portuguese and culturally adapted following standard procedures. FINDRISC-Br has thus become available for use and has potential as a screening tool in different Brazilian settings and applications. © 2020 Associação Brasileira de Saúde Coletiva.
  • Waldenström macroglobulinemia Group (2018)
    Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40–31.03, P = 1.36 × 10 −54 ) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45–6.96, P = 8.75 × 10 −19 ). Both risk alleles are observed at a low frequency among controls (~2–3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy. © 2018, The Author(s).