Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

DNA Damage Response to Ionizing Radiation Defective in the Invasive Cancer Phenotype

The purpose of this study was to determine the differences in DNA damage responses (DDRs) between immortalized normal prostate epithelial cells (PrEC) and prostate cancer cells (DU145). To study the DDRs, two protein markers were used. The first, phosphorylated KRAB Associated Protein 1 (pKAP-1) activates target genes involved in the DDR. The second, phosphorylated H2AX (pH2AX) is required for the assembly of damaged chromatin as well as for activation of checkpoints proteins. Ionizing Radiation (IR) was used to induce DNA damage. Flow Cytometry and Western Blot analyses were used to measure the levels of the proteins when exposed to various doses of IR (0, 2, 4, 8 Gy). In both cell lines, there was a clear dose dependent increase in pH2AX and pKAP-1, however error bars showed that with the pH2AX protein, only the later doses showed significant differences. Fluorescence staining was used to examine the localization of the proteins. Both cell lines showed punctate staining of pH2AX in the nuclei at 8Gy and no staining in unirradiated cells. With pKAP-1, the PrEC cells had punctate staining in the nuclei with 8Gy of radiation whereas the DU145 cells had a diffuse pattern in the nuclei

Reporte Final PAP Primavera 2020: Playas región costa sur, Mezcala y UMAS, gestión integral de residuos del Estado de Jalisco, incorrecta disposición de los residuos líquidos denominados vinazas,CONAFOR y SEMADET

El proyecto de aplicación personal sobre el cual versa el presente reporte tiene con objetivo ser un vínculo de observancia de procuración de justicia ambiental, de tal forma, que, mediante este, se busca que los alumnos se conviertan en actores activos de las problemáticas ambientales que se gestan tanto en el nivel local, estatal y nacional. Para lograr esto, el equipo de alumnos se conforma por estudiantes de diversas carreras universitarias con la finalidad de generar un dialogo interseccional que permita generar el conocimiento y los insumos suficientes para generar estrategias y soluciones a problemas complejos, siempre buscando tener como eje rector la justicia ambiental. Para lograr el propósito de que los alumnos conozcan, desarrollen y propongan soluciones es que se genera un proceso de colaboración con una diversidad de actores relacionados dentro de la sociedad, de esta forma, buscando que el análisis crítico de la problemática ambiental que aborda al estado de Jalisco y las posibles soluciones para el apoyo de dichos grupos vulnerables. Este proyecto de aplicación profesional busca adentrar a los alumnos desde tres perspectivas distintas como lo son la academia, el sector privado y la administración pública buscando con esto dar a conocer el contexto de la complejidad del Derecho Ambiental a través de su aplicación desde una visión de procuración de justicia y la justiciabilidad. Dando como resultado una experiencia en donde el contacto con distintos sectores de la población, la aplicación de los conocimientos adquiridos durante la carrera y el análisis crítico de la realidad de los conflictos ambientales desde una perspectiva Ignaciana den como resultado la ejecución de mecanismos de procuración de justicia sobre la problemática ambiental que vive nuestro estado.ITESO, A.C

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press