Fitting and selecting scattering data

The main purpose of scattering experiments is to unveil the underlying structure of the colliding particles and their interaction. Typically one measures scattering observables (cross sections and polarizations) at discrete angles and energies and mutually consistent data may validate or falsify proposed theories or models. However, the accumulation of data from different laboratories while potentially improves the statistical significance it may sometimes generate mutually inconsistent data as a side-effect. Thus, some decision has to be made on what are the maximal amount of data which are mutually compatible. We show elastic $\pi N$ and $NN$ scattering as prominent examples where this selection is called for. We discuss how it can be done in a self-consistent manner invoking a principle of maximal consensus of the database and with the help of a sufficiently flexible model involving a minimal number of theoretical assumptions. In the NN case this has become possible with a combination of long distance field theoretical constraints at the hadronic level such as pion exchanges and electromagnetic effects and a coarse graining of the unknown interaction over the shortest de Broglie wavelength being probed in the scattering process.Comment: 7 pages, 5 figures, talk presented by ERA at XVII International Conference on Hadron Spectroscopy and Structure - Hadron2017, Salamanca, 25-29 September 201

Uncertainty quantification and falsification of Chiral Nuclear Potentials

Are chiral theories at present describing experimental NN scattering data satisfactorily ?. Will the chiral approach offer a framework where fitting and selecting the existing np and pp data can be done without theoretical bias ?. While predictive power in theoretical nuclear physics has been a major concern in the study of nuclear structure and reactions, the Effective Field Theory (EFT) based on chiral expansions has emerged after Weinberg as a model independent hierarchy for many body forces and much progress has been achieved over the last decades. We review some of the issues involved which point to being close to the solution, but also that work remains still to be done to validate the theory. We analyze several examples including zero energy NN scattering and perturbative counterterm -- free peripheral scattering where one would expect these methods to work best and unveil relevant systematic discrepancies when a fair comparison to the Granada-2013 NN-database and partial wave analysis (PWA) based on coarse graining the interaction is undertaken.Comment: Prepared for the special issue of "The tower of effective (field) theories and the emergence of nuclear phenomena"; 20 pages, 7 figure

Amplification of the Gene Ontology annotation of Affymetrix probe sets

BACKGROUND: The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable for microarray experiment evaluation. RESULTS: Here we present a protocol to amplify the set of Gene Ontology annotations associated to Affymetrix DNA microarray probe sets using information from related databases. CONCLUSION: Predicted novel annotations and the evidence producing them can be accessed at Probe2GO: . Scripts are available on demand

Propuesta de herramienta para la detección de necesidades de formación docente; a partir del análisis de la relación entre los principales factores que inciden en la motivación académica de sus estudiantes, y el tipo de formación docente del personal de la Escuela de Biología del TEC.

Proyecto de Graduación (Licenciatura en Educación Técnica) Instituto Tecnológico de Costa Rica, Escuela de Educación Técnica, 2021El presente estudio se realizó en el Tecnológico de Costa Rica en su sede central ubicada en el cantón central de Cartago, específicamente la Escuela de Biología. La unidad de análisis fueron la población de personas estudiantes y profesores empadronados en la carrera de Ingeniería en Biotecnología grado Bachillerato en al menos un curso del sexto semestre del plan de estudios IB-1053 durante el II semestre del año 2020. La Escuela de Biología, está en procesos de acreditación; se sabe que requiere un constante monitoreo y evaluación de sus prácticas docentes. A raíz de ello nace la necesidad de esta propuesta de investigación, ante la pregunta ¿Existe una relación entre el tipo de formación docente del personal de la Escuela de Biología, y el grado de motivación de sus estudiantes durante el proceso de enseñanza-aprendizaje? Antes de contestar dicha pregunta se determinó los cinco principales factores que inciden en la motivación (estrategias didácticas, trato a la persona estudiante, pasión por enseñar, planeamiento didáctico y herramientas de evaluación), y es necesario indicar que la percepción de los estudiantes difiere respecto a la formación recibida por las personas docentes, al menos en cuatro de los cinco factores. A pesar de que se determinó que no existe una relación directa entre la formación recibida y la motivación académica, se sugiere utilizar la herramienta para generar un perfil con aspectos de mejora para las personas docentes. Se concluye que la Escuela de Biología podría fortalecer la capacitación de sus docentes principalmente en dos de los cinco factores mencionados en el párrafo anterior (herramientas de evaluación y estrategias didácticas), por medio de un plan de formación en conjunto con el CEDA considerando las necesidades de formación detectadas en este trabajo.The present study was carried out at Costa Rica Institute of Technology located Cartago, in the Biology Department. The unit of analysis was the population of students and professors registered in the Bachelor's degree in Biotechnology Engineering in at least one course of the sixth semester of the IB-1053 curriculum during the second semester of 2020. The School of Biology is in the accreditation process; it is known that it requires constant monitoring and evaluation of their teaching practices. As a result of this, the need for this research proposal arises, when faced with the question: Is there a relationship between the type of teacher training of the teaching staff of the School of Biology, and the degree of motivation of its students during the teaching-learning process? Before answering this question, the five factors that affect motivation the most were determined (didactic strategies, student treatment, passion for teaching, didactic planning and evaluation tools), and we must acknowledge that students perception differs from the training received by teachers in four out of five factors. Although it was determined that there is no direct relationship between the training received and academic motivation, it is suggested to use the tool to generate a profile with aspects of improvement for teachers. It is concluded that the School of Biology could strengthen the training of its teachers mainly in two of the five factors mentioned (evaluation tools and didactic strategies), through a training plan in conjunction with CEDA considering the training needs detected in this work

Worldwide impact of economic cycles on suicide trends over 3 decades: Differences according to level of development. A mixed effect model study

Objectives: To investigate the trends and correlations of gross domestic product (GDP) adjusted for purchasing power parity (PPP) per capita on suicide rates in 10 WHO regions during the past 30 years. Design: Analyses of databases of PPP-adjusted GDP per capita and suicide rates. Countries were grouped according to the Global Burden of Disease regional classification system. Data sources: World Bank’s official website and WHO’s mortality database. Statistical analyses: After graphically displaying PPP-adjusted GDP per capita and suicide rates, mixed effect models were used for representing and analysing clustered data. Results: Three different groups of countries, based on the correlation between the PPP-adjusted GDP per capita and suicide rates, are reported: (1) positive correlation: developing (lower middle and upper middle income) Latin-American and Caribbean countries, developing countries in the South East Asian Region including India, some countries in the Western Pacific Region (such as China and South Korea) and high-income Asian countries, including Japan; (2) negative correlation: high-income and developing European countries, Canada, Australia and New Zealand and (3) no correlation was found in an African country. Conclusions: PPP-adjusted GDP per capita may offer a simple measure for designing the type of preventive interventions aimed at lowering suicide rates that can be used across countries. Public health interventions might be more suitable for developing countries. In high-income countries, however, preventive measures based on the medical model might prove more usefulAll authors have completed the Unified Competing Interest form. Dr. Blasco-Fontecilla acknowledges the Spanish Ministry of Health (Rio Hortega CMO8/00170; SAF2010-21849), Alicia Koplowitz Foundation and Conchita Rabago Foundation for funding his post-doctoral stage at CHRU, Montpellier, France

Recent developments in StemBase: a tool to study gene expression in human and murine stem cells

<p>Abstract</p> <p>Background</p> <p>Currently one of the largest online repositories for human and mouse stem cell gene expression data, StemBase was first designed as a simple web-interface to DNA microarray data generated by the Canadian Stem Cell Network to facilitate the discovery of gene functions relevant to stem cell control and differentiation.</p> <p>Findings</p> <p>Since its creation, StemBase has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. As of September 1, 2008, StemBase contains gene expression data (microarray and Serial Analysis of Gene Expression) from 210 stem cell samples in 60 different experiments.</p> <p>Conclusion</p> <p>StemBase can be used to study gene expression in human and murine stem cells and is available at <url>http://www.stembase.ca</url>.</p

Gene function in early mouse embryonic stem cell differentiation

BACKGROUND: Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determinants of mouse embryonic stem cell (mESC) differentiation, we have generated and analyzed 11-point time-series of DNA microarray data for three biologically equivalent but genetically distinct mESC lines (R1, J1, and V6.5) undergoing undirected differentiation into embryoid bodies (EBs) over a period of two weeks. RESULTS: We identified the initial 12 hour period as reflecting the early stages of mESC differentiation and studied probe sets showing consistent changes of gene expression in that period. Gene function analysis indicated significant up-regulation of genes related to regulation of transcription and mRNA splicing, and down-regulation of genes related to intracellular signaling. Phylogenetic analysis indicated that the genes showing the largest expression changes were more likely to have originated in metazoans. The probe sets with the most consistent gene changes in the three cell lines represented 24 down-regulated and 12 up-regulated genes, all with closely related human homologues. Whereas some of these genes are known to be involved in embryonic developmental processes (e.g. Klf4, Otx2, Smn1, Socs3, Tagln, Tdgf1), our analysis points to others (such as transcription factor Phf21a, extracellular matrix related Lama1 and Cyr61, or endoplasmic reticulum related Sc4mol and Scd2) that have not been previously related to mESC function. The majority of identified functions were related to transcriptional regulation, intracellular signaling, and cytoskeleton. Genes involved in other cellular functions important in ESC differentiation such as chromatin remodeling and transmembrane receptors were not observed in this set. CONCLUSION: Our analysis profiles for the first time gene expression at a very early stage of mESC differentiation, and identifies a functional and phylogenetic signature for the genes involved. The data generated constitute a valuable resource for further studies. All DNA microarray data used in this study are available in the StemBase database of stem cell gene expression data [1] and in the NCBI's GEO database

Radio definida por software y docencia en línea: experiencia en el Grado en Ingeniería Telemática

[EN] Devices based on software defined radio have been used in the last 6 years as motivating elements in the laboratory practices of digital communications courses at the Degree in Telematics Engineering of the University of Valencia. However, the development of these practices requires giving access to some hardware devices that are physically located in the laboratories of the School of Engineering. In this contribution, taking into account the current situation of hybrid learning and a possible transition to remote learning due to the COVID-19 pandemic, a system that allows the remote interaction with the software defined radio devices is proposed. This remote access system, in addition to allowing these devices to be used in laboratory practices even in a remote learning context, would allow students to access them outside laboratory practice hours. The results obtained in the Digital Communications Theory course demonstrate the high potential for motivation and increased academic involvement provided by the use of these devices, especially in contexts with low academic involvement, such as the 2020-2021 academic year.[ES] Los dispositivos de radio definida por software se han utilizado en los últimos 6 años como elementos dinamizadores de las prácticas de laboratorio en las asignaturas de la materia de comunicaciones digitales del Grado en Ingeniería Telemática de la Universitat de València. Sin embargo, el desarrollo de estas prácticas requiere el acceso a unos dispositivos hardware que están localizados físicamente en los laboratorios de la Escuela Técnica Superior de Ingeniería. En esta contribución, atendiendo a la actual situación de docencia semipresencial y de un posible paso a docencia en línea debido a la pandemia de COVID-19, se plantea establecer un sistema que permita la interacción remota con los dispositivos de radio definida por software. Este sistema de acceso remoto, además de permitir que se sigan utilizando estos dispositivos en las prácticas de laboratorio aún en un contexto de docencia en línea, permitiría el acceso del alumnado a ellos fuera del horario de prácticas de laboratorio. Los resultados obtenidos en la asignatura de Teoría de la Comunicación demuestran el alto potencial de motivación y de aumento de la implicación académica que presentan estos dispositivos, especialmente en contextos con una implicación académica baja, como es el curso académico 2020-2021.Este trabajo ha sido financiado por el “Vicerectorat d’Ocupació i Programes Formatius” de la Universitat de València a través del proyecto UV-SFPIE PID-1353656. Sandra Roger agradece la finaciación recibida a través del contrato postdoctoral RYC-2017-22101 y el proyecto GV/2020/046.Botella Mascarell, C.; Roger, S.; Soriano Asensi, A.; Perez, J.; Segura Garcia, J.; Felici Castell, S.; Navarro Camba, EA. (2021). Radio definida por software y docencia en línea: experiencia en el Grado en Ingeniería Telemática. En IN-RED 2021: VII Congreso de Innovación Edicativa y Docencia en Red. Editorial Universitat Politècnica de València. 267-277. https://doi.org/10.4995/INRED2021.2021.13687OCS26727

A correlative biomarker study and integrative prognostic model in chemotherapy-naïve metastatic castration-resistant prostate cancer treated with enzalutamide

There is a considerable need to incorporate biomarkers of resistance to new antiandrogen agents in the management of castration-resistant prostate cancer (CRPC). We conducted a phase II trial of enzalutamide in first-line chemo-naïve asymptomatic or minimally symptomatic mCRPC and analyzed the prognostic value of TMPRSS2-ERG and other biomarkers, including circulating tumor cells (CTCs), androgen receptor splice variant (AR-V7) in CTCs and plasma Androgen Receptor copy number gain (AR-gain). These biomarkers were correlated with treatment response and survival outcomes and developed a clinical-molecular prognostic model using penalized cox-proportional hazard model. This model was validated in an independent cohort. Ninety-eight patients were included. TMPRSS2-ERG fusion gene was detected in 32 patients with no differences observed in efficacy outcomes. CTC detection was associated with worse outcome and AR-V7 in CTCs was associated with increased rate of progression as best response. Plasma AR gain was strongly associated with an adverse outcome, with worse median prostate specific antigen (PSA)-PFS (4.2 vs. 14.7 m; p < 0.0001), rad-PFS (4.5 vs. 27.6 m; p < 0.0001), and OS (12.7 vs. 38.1 m; p < 0.0001). The clinical prognostic model developed in PREVAIL was validated (C-Index 0.70) and the addition of plasma AR (C-Index 0.79; p < 0.001) increased its prognostic ability. We generated a parsimonious model including alkaline phosphatase (ALP); PSA and AR gain (C-index 0.78) that was validated in an independent cohort. TMPRSS2-ERG detection did not correlate with differential activity of enzalutamide in first-line mCRPC. However, we observed that CTCs and plasma AR gain were the most relevant biomarkers

MedlineRanker: flexible ranking of biomedical literature

The biomedical literature is represented by millions of abstracts available in the Medline database. These abstracts can be queried with the PubMed interface, which provides a keyword-based Boolean search engine. This approach shows limitations in the retrieval of abstracts related to very specific topics, as it is difficult for a non-expert user to find all of the most relevant keywords related to a biomedical topic. Additionally, when searching for more general topics, the same approach may return hundreds of unranked references. To address these issues, text mining tools have been developed to help scientists focus on relevant abstracts. We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker