24 research outputs found
Cortical mechanisms underlying low-level motion processing in the visual system of human and non-human primates
No full textIncluding Item Characteristics in the Probabilistic Latent Semantic Analysis Model for Collaborative Filtering
No full textWe propose a new hybrid recommender system that combines some advantages of collaborative and content-based recommender systems. While it uses ratings data of all users, as do collaborative recommender systems, it is also able to recommend new items and provide an explanation of its recommendations, as do content-based systems. Our approach is based on the idea that there are communities of users that find the same characteristics important to like or dislike a product. This model is an extension of the probabilistic latent semantic model for collaborative filtering with ideas based on clusterwise linear regression. On a movie data set, we show that the model is competitive to other recommenders and can be used to explain the recommendations to the users.algorithms;probabilistic latent semantic analysis;hybrid recommender systems;recommender systems
Untersuchungen zu Diagnostik und Therapie des Buruli Ulkus mittels tropenadaptierter Labormethoden in endemischen Regionen
No full textFrom process understanding to process control: application of PAT on the cultivation of Bordetella pertussis for a whole cell vaccine
No full textDe kwaliteit van farmaceutische producten wordt geborgd door een op Good Manufacturing Practice gebaseerd kwaliteits systeem, waarbij kwaliteitscontrole van het eindproduct een belangrijke rol vervult. Recentelijk is hierin verandering gekomen en vragen regelgevers bij overheden steeds meer om een kwaliteitssysteem dat al tijdens het proces operationeel is. Voor chemische farmaca wordt dit al steeds meer door de industrie toegepast, maar voor biologische producten blijkt die nog steeds moeilijk. In dit proefschrift wordt een methode beschreven die on line monitoring en kwaliteitscontrole voor een complex biologisch product (een cellulair vaccin) mogelijk maakt. Door te identificeren welke procesparameters invloed hebben op de kritieke eigenschappen van het product, kan een controle systeem worden ingericht dat deze kritische parameters tijdens het proces monitort en beheerst. Hiermee verschuift de kwaliteitscontrole van achteraf naar tijdens het proces. Dit maakt de productie van vaccins flexibeler, goedkoper en bovenal veiliger voor de patient
Implementation of a National Reference Laboratory for Buruli Ulcer Disease in Togo
No full textBackground: In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease (BUD) from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as effort and time associated with shipment of PCR samples necessitated the implementation of stringent EQA measures and availability of local laboratory capacity. This study describes the approach to implementation of a national BUD reference laboratory in Togo. Methodology: Large scale outreach activities accompanied by regular training programs for health care professionals were conducted in the regions "Maritime'' and "Central,'' standard operating procedures defined all processes in participating laboratories (regional, national and external reference laboratories) as well as the interaction between laboratories and partners in the field. Microscopy was conducted at regional level and slides were subjected to EQA at national and external reference laboratories. For PCR analysis, sample pairs were collected and subjected to a dry-reagent-based IS2404-PCR (DRB-PCR) at national level and standard IS2404 PCR followed by IS2404 qPCR analysis of negative samples at the external reference laboratory. Principal Findings: The inter-laboratory concordance rates for microscopy ranged from 89% to 94%; overall, microscopy confirmed 50% of all suspected BUD cases. The inter-laboratory concordance rate for PCR was 96% with an overall PCR case confirmation rate of 78%. Compared to a previous study, the rate of BUD patients with non-ulcerative lesions increased from 37% to 50%, the mean duration of disease before clinical diagnosis decreased significantly from 182.6 to 82.1 days among patients with ulcerative lesions, and the percentage of category III lesions decreased from 30.3% to 19.2%. Conclusions: High inter-laboratory concordance rates as well as case confirmation rates of 50% (microscopy), 71% (PCR at national level), and 78% (including qPCR confirmation at external reference laboratory) suggest high standards of BUD diagnostics. The increase of non-ulcerative lesions, as well as the decrease in diagnostic delay and category III lesions, prove the effect of comprehensive EQA and training measures involving also procedures outside the laboratory
Event Management for Sensing Enterprises with Decision Support Systems
No full textThe final publication is available at Springer via http://dx.doi.org/10.1007/s40745-015-0034-z[EN] Sensing enterprises make use of new technologies to capture real-time information and fed constantly the decision making process. Decision support systems (DSS) are exposed to these real-time events and it is possible to start the decision process from scratch in case any unexpected internal and external events take place. Thus, an event monitoring and management system should interact with the DSS to manage events that might affect their decisions. It should act as a supra-system to identify when decisions made are still valid or need to be reanalysed. The traditional configuration of DSS (where they collect internal and external information of the organization and the decision-maker is involved in the decision-making process) should be extended to treat event management using a monitoring and management system, which monitors internal and external information and facilitate the introduction of no monitored events. This monitor and manager systems become more and more necessary due to the incessant incorporation of new technologies that enables the companies to be more context-sensitive. Furthermore, this new and/or more accurate information, which is obtained for the organization, requires a proper management.This research has been carried out in the framework of the project PAID-06-21Universitat Politècnica de València (Sistema de ayuda a la toma de decisiones ante decisiones no programadas en la planificación jerárquica de la producción) and GV/2014/010 Generalitat Valenciana (Identificación de la información proporcionada por los nuevos sistemas de detección accesibles mediante internet en el ámbito de las “sensing enterprises” para la mejora de la toma de decisiones en la planificación de la producción).Boza, A.; Alemany Díaz, MDM.; Cuenca, L.; Ortiz Bas, Á. (2015). Event Management for Sensing Enterprises with Decision Support Systems. Annals of Data Science. 2(1):103-109. https://doi.org/10.1007/s40745-015-0034-zS10310921Estupinyà P (2010) El ladrón de cerebros: Compartiendo el conocimiento científico de las mentes más brillantes. Penguin Random House Grupo Editorial EspañaVicens E, Alemany ME, Andrés C, Guarch JJ (2001) A design and application methodology for hierarchical production planning decision support systems in an enterprise integration context. Int J Prod Econ 74:5–20. doi: 10.1016/S0925-5273(01)00103-7Van Wezel W, Van Donk DP, Gaalman G (2006) The planning flexibility bottleneck in food processing industries. J Oper Manag 24:287–300. doi: 10.1016/j.jom.2004.11.001Winter R (1994) Multi-stage production controlling based on continuous, flexible abstraction hierarchies. IEPMÖzdamar L, Bozyel MA, Birbil SI (1998) A hierarchical decision support system for production planning (with case study). Eur J Oper Res 104:403–422. doi: 10.1016/S0377-2217(97)00016-7FInES FIESC (2012) FInES Research Roadmap 2025Shamsuzzoha Ah, Rintala S, Cunha PF, Ferreira PS, Kankaanpää T, Maia Carneiro L (2013) Event monitoring and management process in a non-hierarchical business network. In: Poler R, Carneiro L, Jasinski T, Zolghadri rc, Pedrazzoli P (eds) Intelligent non-hierarchical manufacturing networks. Wiley, New York, pp 349–374Committee of Sponsoring Organizations of the Treadway Commission (2004) COSO enterprise risk management-integrated framework: application techniques. Committee of Sponsoring Organizations of the Treadway CommissionSantucci G, Martinez C, Vlad-Câlcic D (2012) The sensing enterprise. FInES workshop at FIA 2012Vargas A, Cuenca L, Boza A, Sacala I, Moisescu M (2014) Towards the development of the framework for inter sensing enterprise architecture, J Intell Manuf, 1–18Anthony RN (1965) Planning and control systems: a framework for analysis. Harvard University, CambridgeSimon HA (1960) The new science of management decision. Harper & Brothers, New YorkShim JP, Warkentin M, Courtney JF, Power DJ, Sharda R, Carlsson C (2002) Past, present, and future of decision support technology. Decis Support Syst 33:111–126. doi: 10.1016/S0167-9236(01)00139-7Peng Y, Kou G, Shi Y, Chen ZA (2008) Descriptive framework for the field of data mining and knowledge discovery. Int J Inf Technol Decis Mak 7:639–682. doi: 10.1142/S0219622008003204Alarcón F, Alemany MME, Lario FC, Oltra RF (2011) La falta de homogeneidad del producto (FHP) en las empresas cerámicas y su impacto en la reasignación del inventario. Boletín de la Sociedad Española de Cerámica y Vidrio 50:49–58. doi: 10.3989/cyv.072011Cegarra J, van Wezel W (2011) A comparison of task analysis methods for planning and scheduling. In: Fransoo JC, Waefler T, Wilson JR (eds) Behavioral operations in planning and scheduling. Springer, Berlin Heidelberg, pp 323–338FP7-ICT (2012) ICT: Information and Communication Technologies: work programme 2013Barash G, Bartolini C, Wu L (2007) Measuring and improving the performance of an IT support organization in managing service incidents. In: 2nd IEEE/IFIP international workshop on business-driven IT management, BDIM ’07, pp 11–18Bartolini C, Stefanelli C, Tortonesi M (2010) SYMIAN: analysis and performance improvement of the IT incident management process. IEEE Trans Netw Serv Manag 7:132–144. doi: 10.1109/TNSM.2010.1009.I9P0321Boza A, Alemany MME, Alarcón F, Cuenca L (2013) A model-driven DSS architecture for delivery management in collaborative supply chains with lack of homogeneity in products. Prod Plan Control 25:650–661. doi: 10.1080/09537287.2013.798085Boza A, Ortiz A, Vicens E, Poler R (2009) A framework for a decision support system in a hierarchical extended enterprise decision context. In: Poler R, van Sinderen M, Sanchis R (eds) Enterprise interoperability. Springer, Berlin Heidelberg, pp 113–124Grefen P, Dijkman R (2013) Hybrid control of supply chains: a structured exploration from a systems perspective. Int J Prod Manag Eng 1:39–5
Germline NPAT inactivating variants as cause of hereditary colorectal cancer
No full textTwo independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene that encodes a cyclin E/CDK2 effector required for S phase entry and a coactivator of histone transcription, in two families with multiple members affected with colorectal cancer. Enrichment of loss-of-function and predicted deleterious NPAT variants was identified in familial/early-onset colorectal cancer patients compared to non-cancer gnomAD individuals, further supporting the association with the disease. Previous studies in Drosophila models showed that NPAT abrogation results in chromosomal instability, increase of double strand breaks, and induction of tumour formation. In line with these results, colorectal cancers with NPAT somatic variants and no DNA repair defects have significantly higher aneuploidy levels than NPAT-wildtype colorectal cancers. In conclusion, our findings suggest that constitutional inactivating NPAT variants predispose to mismatch repair-proficient nonpolyposis colorectal cancer.This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00(LV)]; Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV, GC)]; Government of Catalonia [AGAUR 2021SGR01112 (LV, GC), CERCA Program for institutional support (IDIBELL)]; Scientific Foundation “Asociación Española Contra el Cáncer” [AECC Investigador(MT)]; the Dutch Digestive Foundation [MLDS FP13-13 (TvW)]; Stichting Sacha Swarttouw-Hijmans (TvW); Fight Colorectal Cancer-Michael’s Mission-AACR Fellowship in Young Onset, Late-Stage Colorectal Cancer Research 2015 [15-40-1645-DEMI (NFCCdM)], the KWF Bas Mulder Award UL [2015-7664 (NFCCdM)] and the ZonMw Veni grant [016.176.l44(NFCCdM)]Peer Reviewed"Article signat per 16 autors/es: Mariona Terradas, Stephanie A. Schubert, Julen Viana-Errasti, Dina Ruano, Gemma Aiza, Maartje Nielsen, Paula Marciel, Carli M. Tops, Genís Parra, Hans Morreau, David Torrents, Monique E. van Leerdam, Gabriel Capellá, Noel F. C. C. de Miranda, Laura Valle & Tom van Wezel"Postprint (author's final draft
patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening
No full textpeer reviewedNon-target analysis (NTA) via chromatography coupled to high resolution mass spectrometry (HRMS) is used to monitor and identify organic chemicals in the environment. Biotic and abiotic processes can transform original chemicals (parents) into transformation products (TPs). These TPs can be of equal or more concern than their parent compounds and are therefore critical to monitor and identify in the environment (Escher & Fenner, 2011; Farré et al., 2008), often with NTA. Given the amount of data generated by NTA, advanced automated data processing workflows are essential. The open-source, R-based (R Core Team, 2021) platform patRoon (Helmus, ter Laak, et al., 2021) offers automated, straightforward, flexible and comprehensive NTA workflows.
This article describes improvements introduced in patRoon 2.0, including extensive TP screening and simultaneous processing of positive and negative HRMS data. The updated documentation and code are available via https://rickhelmus.github.io/patRoon and archived in Helmus, Velde, et al. (2021)
patRoon 2.0: Non-target screening workflows for automated transformation product screening and other major improvements
No full textPoster presentation about the patRoon 2.0/2.1 release presented during the IMSC 2022 conference in Maastrich
Dealing with the heterogeneous presentations of freezing of gait: how reliable are the freezing index and heart rate for freezing detection?
No full textAbstract Background Freezing of gait (FOG) is an unpredictable gait arrest that hampers the lives of 40% of people with Parkinson’s disease. Because the symptom is heterogeneous in phenotypical presentation (it can present as trembling/shuffling, or akinesia) and manifests during various circumstances (it can be triggered by e.g. turning, passing doors, and dual-tasking), it is particularly difficult to detect with motion sensors. The freezing index (FI) is one of the most frequently used accelerometer-based methods for FOG detection. However, it might not adequately distinguish FOG from voluntary stops, certainly for the akinetic type of FOG. Interestingly, a previous study showed that heart rate signals could distinguish FOG from stopping and turning movements. This study aimed to investigate for which phenotypes and evoking circumstances the FI and heart rate might provide reliable signals for FOG detection. Methods Sixteen people with Parkinson’s disease and daily freezing completed a gait trajectory designed to provoke FOG including turns, narrow passages, starting, and stopping, with and without a cognitive or motor dual-task. We compared the FI and heart rate of 378 FOG events to baseline levels, and to stopping and normal gait events (i.e. turns and narrow passages without FOG) using mixed-effects models. We specifically evaluated the influence of different types of FOG (trembling vs akinesia) and triggering situations (turning vs narrow passages; no dual-task vs cognitive dual-task vs motor dual-task) on both outcome measures. Results The FI increased significantly during trembling and akinetic FOG, but increased similarly during stopping and was therefore not significantly different from FOG. In contrast, heart rate change during FOG was for all types and during all triggering situations statistically different from stopping, but not from normal gait events. Conclusion When the power in the locomotion band (0.5–3 Hz) decreases, the FI increases and is unable to specify whether a stop is voluntary or involuntary (i.e. trembling or akinetic FOG). In contrast, the heart rate can reveal whether there is the intention to move, thus distinguishing FOG from stopping. We suggest that the combination of a motion sensor and a heart rate monitor may be promising for future FOG detection
