Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

Evaluating replicability of laboratory experiments in economics

The reproducibility of scientific findings has been called into question. To contribute data about reproducibility in economics, we replicate 18 studies published in the American Economic Review and the Quarterly Journal of Economics in 2011-2014. All replications follow predefined analysis plans publicly posted prior to the replications, and have a statistical power of at least 90% to detect the original effect size at the 5% significance level. We find a significant effect in the same direction as the original study for 11 replications (61%); on average the replicated effect size is 66% of the original. The reproducibility rate varies between 67% and 78% for four additional reproducibility indicators, including a prediction market measure of peer beliefs

Novetats

Ressenyes sobre novetats editorials dels anys 2005 i 200

Properties of Corn Screenings

Inspection data from 1988 to 1990 validated a previous prediction equation for corn particle size distribution and showed the relative distribution to be independent of market location, BCFM level, and other grade factor data. Samples (62) of corn screenings obtained from country elevators were size-separated in 2/64-in. increments, from 4.5/64 in. to 16/64 in. Smaller particles had lower bulk density, higher particle density, more mycotoxins, higher protein, and lower starch than larger particles. About 17% of the material was larger than 12/64-in., which means it would not have been classed as broken corn-foreign material in the grades. Removal efficiency for commercial cleaners was estimated, by size increment, as a function of removal efficiency for BCFM

Global ionospheric maps : estimation and assessment in post-processing and real-time

The research of this paper-based dissertation is focused on Global Ionospheric Maps (GIM) generation and assessment. In summary, the novelty and thematic unity in this works relies on four different but complementary topics: 1. Defining a systematic procedure to validate and quantify the quality of GIMs based on independent data sources or techniques. 2. Applying this methodology to not only the GIMs computed at UPC, but also to most of the currently open accessible GIMs inside the scientific community. 3.Including newly available Global Navigation Satellite Systems (GNSS) data to the processing of UPC's GIMs. 4. Assessment and distribution also of real-time GIMs. More in detail, my first contribution has been to the definition of a complete GIM validation procedure. This procedure is based on two methods: direct VTEC (Vertical Total Electron Content) altimeter and GNSS difference of slant TEC (Total Electron Content), both of them giving complementary information of the GIM performance. The main advantage of using satellite altimeter data is the fact that we are using a truly independent information source with regard to the input data used for GIM generation. This allows assessing the TEC from a entirely different point-of-view, fully different and independent to any error that may affect GNSS systems and its processing. The second technique, relies on using the same type of input data but in this case from permanent GNSS stations not participating in the GIM generation. The main advantages of this second technique is twofold: first, it allows to asses the GIMs on land; and second its a low latency direct assessment of the GIM, given a more direct information about the processing and interpolation done with the GNSS input data. Afterwards, a second contribution has been to use the previously defined methodology to validate all the GIMs generated by the International GNSS Service (IGS) Associated Analysis Centers (IAAC), and some other candidates to join them, for a more than a full solar cycle (starting from end of 2001 to beginning of 2017). As a side result, it is also demonstrated that while the time interval of the GIM has little influence on its overall quality, the interpolation technique used by the IAACs has an important role. Finally, this work also lead to the acceptance of the previously mentioned IAAC candidates since it demonstrated the good quality of their GIMs. Another contribution has been, as part of the European GRC project, improving the currently in production UPC's TOMION (TOMographic IONospheric) software used to generate the UQRG (UPC's rapid GIM) map. The software input source data was restricted to GPS L1 and L2. Now it allows processing all current frequencies available for GPS, Galileo and Beidou. This software has been internally tested for some specific days with the previously explained altimeter method giving results with improved quality for specific combinations of GNSS systems and frequencies. Using this work flow but focused on single frequency processing, a last article was published analysing the ionospheric footprint of the solar eclipse over North America during 2017. Finally, another contribution has been to improve the data acquisition and distribution system for the real-time GIM generation processing chain. Furthermore, as part of UPC contribution to the Real Time Ionospheric Monitoring Working Group (RTIM-WG) of the International Association of Geodesy (IAG) and following the previously explained methodology, an assessment of the GIMs generated by the members of this sub-commission have been performed. As a result of all these efforts, UPC has been leading inside the IGS frame, and made a first implementation, of a new real-time combined map.La recerca realitzada en aquesta tesis en format compendi d’articles esta enfocada en la generació i validació de mapes ionosfèrics globals (GIM, del angles Global Ionospheric Maps). En resum, la novetat i unitat temàtica d’aquesta tesis esta basada en quatre temes diferents però complementaris: • Definició d’un procediment sistemàtic per validar i quantificar la qualitat dels GIMs basada en fonts de dades o tècniques independents. • Aplicar aquesta metodologia no nomes als GIMs generats a UPC, sinó també a la resta de GIMs d’accés obert actualment existent dintre la comunitat científica internacional. • Incloure en el processat per generar els GIMs de UPC dades de les noves constel·lacions GNSS (del angles Global Navigation Satellite Systems) disponibles. • Validació i distribució també dels GIMs en temps real. Com a conseqüència, també s’ha aconseguit generar un primer GIM combinat en temps real. Mes en detall, la meva primera contribució va ser definir un procediment complet de validació de GIM. Aquest procediment esta basat en dos mètodes: obtenció directa del contingut vertical total d’electrons (VTEC, del angles, Vertical Total Electron Content) a partir de dades d’altimetria i per diferencies del contingut total d’electrons (TEC, del angles Total Electron Content) inclinat de dades GNSS. Els dos donen informació complementaria de la qualitat dels GIM. L’avantatge principal d’utilitzar dades de satèl·lits altimètrics es que es una font de dades completament diferent de les que s’utilitzen per la generació dels GIMs. Aquest fet ens permet verificar el TEC des d’una perspectiva diferent, plenament independent de qualsevol font d’error que pugui afectar al propi sistema GNSS o el seu processat. El segon mètode, es basa en la mateix tipus de dades que s’utilitzen pel càlcul dels GIM però en aquest cas amb dades d’estacions permanent GNSS no involucrades en la generació dels GIMs a avaluar. L’avantatge principal d’aquest segon mètodes es doble: primer, permet avaluar el GIM sobre els continents; i segon, permet fer la anàlisis directa de baixa latència del GIM, a mes a mes donant informació directa sobre el processat i la interpolació aplicada sobre les dades GNSS. Seguidament, la meva segona contribució va ser utilitzar la metodologia prèviament definida per validar tots els GIM generats per part dels centres d’anàlisis associats al Servei Internacional de GNSS (IGS, del angles International GNSS Service) i altres centres candidats a unir-se a IGS, per mes d’un cicle solar (des de finals del 2001 fins al inici del 2017). Com a resultat secundari, també va permetre demostrar que per una banda l’interval temporal dels GIM te poca influencia sobre la seva qualitat global, però per altra banda la tècnica d’interpolació emprada per part dels centres te un impacte molt important. Finalment, aquest article va portar a l’admissió d’aquests candidats prèviament mencionats a centres d’anàlisis associats a IGS donat que es va demostrar la bona qualitat dels seus GIMs. Una altra contribució important va ser, com a part del projecte europeu GRC, millorar el software TOMION (TOMographic IONospheric) de UPC, actualment en producció generant el GIM UQRG (GIM ràpid de UPC). Aquest software nomes permetia utilitzar dades de GPS L1 i L2. Les millores realitzades durant aquesta tesis permeten processar totes les freqüències actualment existent de GPS, Galileo i Beidou. El software ha estat internament validat per certs dies específics amb el mètode explicat prèviament d’altimetria millorant els resultats en comparació a la versió anterior per certes combinacions de constel·lacions GNSS i freqüències. Utilitzant aquesta nova metodologia de processat aplicada a una sola freqüència, un últim article va ser publicat analitzant l’empremta ionosfèrica de l’eclipsi solar sobre Amèrica del nord durant el 2017. Finalment, una altre contribució va ser millorar el mètode d’adquisició i distribució del sistema de processat del GIM en temps real. Es mes, com a part de la contribució de la UPC, es va realitzar una validació dels GIMs generats pels participants del grup de treball de monitorització en temps real de la ionosfera (RTIM-WG, del angles Real Time Ionospheric Monitoring Working Group) de l’Associació Internacional de Geodèsia (IAG, del angles International Association of Geodesy) seguint la metodologia anteriorment citada. Com a resultat d’aquestes tasques la UPC ha liderat i mplementat un nou mapa combinat en temps real, en el marc de IGS.Postprint (published version

High-resolution ionosphere corrections for single-frequency positioning

The ionosphere is one of the main error sources in positioning and navigation; thus, information about the ionosphere is mandatory for precise modern Global Navigation Satellite System (GNSS) applications. The International GNSS Service (IGS) and its Ionosphere Associated Analysis Centers (IAAC) routinely provide ionospheric information in terms of global ionosphere maps (final GIM). Typically, these products are modeled using series expansion in terms of spherical harmonics (SHs) with a maximum degree of n=15 and are based on post processed observations from Global Navigation Satellite Systems (GNSS), as well as final satellite orbits. However, precise applications such as autonomous driving or precision agriculture require real-time (RT) information about the ionospheric electron content with high spectral and spatial resolution. Ionospheric RT-GIMs are disseminated via Ntrip protocol using the SSR VTEC message of the RTCM. This message can be streamed in RT, but it is limited for the dissemination of coefficients of SHs of lower degrees only. It allows the dissemination of SH coefficients up to a degree of n=16. This suits to most the SH models of the IAACs, but higher spectral degrees or models in terms of B-spline basis functions, voxels, splines and many more cannot be considered. In addition to the SHs, several alternative approaches, e.g., B-splines or Voxels, have proven to be appropriate basis functions for modeling the ionosphere with an enhanced resolution. Providing them using the SSR VTEC message requires a transfer to SHs. In this context, the following questions are discussed based on data of a B-spline model with high spectral resolution; (1) How can the B-spline model be transformed to SHs in order to fit to the RTCM requirements and (2) what is the loss of detail when the B-spline model is converted to SHs of degree of n=16? Furthermore, we discuss (3) what is the maximum necessary SH degree n to convert the given B-spline model and (4) how can the transformation be performed to make it applicable for real-time applications? For a final assessment, we perform both, the dSTEC analysis and a single-frequency positioning in kinematic mode, using the transformed GIMs for correcting the ionospheric delay. The assessment shows that the converted GIMs with degrees n=30 coincide with the original B-spline model and improve the positioning accuracy significantly.Peer ReviewedPostprint (published version

The cooperative IGS RT-GIMs: a reliable estimation of the global ionospheric electron content distribution in real time

The Real-Time Working Group (RTWG) of the International GNSS Service (IGS) is dedicated to providing high-quality data and high-accuracy products for Global Navigation Satellite System (GNSS) positioning, navigation, timing and Earth observations. As one part of real-time products, the IGS combined Real-Time Global Ionosphere Map (RT-GIM) has been generated by the real-time weighting of the RT-GIMs from IGS real-time ionosphere centers including the Chinese Academy of Sciences (CAS), Centre National d'Etudes Spatiales (CNES), Universitat Politècnica de Catalunya (UPC) and Wuhan University (WHU). The performance of global vertical total electron content (VTEC) representation in all of the RT-GIMs has been assessed by VTEC from Jason-3 altimeter for 3 months over oceans and dSTEC-GPS technique with 2¿d observations over continental regions. According to the Jason-3 VTEC and dSTEC-GPS assessment, the real-time weighting technique is sensitive to the accuracy of RT-GIMs. Compared with the performance of post-processed rapid global ionosphere maps (GIMs) and IGS combined final GIM (igsg) during the testing period, the accuracy of UPC RT-GIM (after the improvement of the interpolation technique) and IGS combined RT-GIM (IRTG) is equivalent to the rapid GIMs and reaches around 2.7 and 3.0 TECU (TEC unit, 1016¿el¿m-2) over oceans and continental regions, respectively. The accuracy of CAS RT-GIM and CNES RT-GIM is slightly worse than the rapid GIMs, while WHU RT-GIM requires a further upgrade to obtain similar performance. In addition, a strong response to the recent geomagnetic storms has been found in the global electron content (GEC) of IGS RT-GIMs (especially UPC RT-GIM and IGS combined RT-GIM). The IGS RT-GIMs turn out to be reliable sources of real-time global VTEC information and have great potential for real-time applications including range error correction for transionospheric radio signals, the monitoring of space weather, and detection of natural hazards on a global scale. All the IGS combined RT-GIMs generated and analyzed during the testing period are available at https://doi.org/10.5281/zenodo.5042622 (Liu et al., 2021b).his research has been supported by the China Scholarship Council (CSC). The contribution from UPC- IonSAT authors was partially supported by the European Union- funded project PITHIA-NRF (grant no. 101007599) and by the ESSP/ICAO-funded project TEC4SpaW. The work of An- drzej Krankowski is supported by the National Centre for Research and Development, Poland, through grant ARTEMIS (grant nos. DWM/PL-CHN/97/2019 and WPC1/ARTEMIS/2019)Peer ReviewedPostprint (published version