Automatic Publication of Open Data from OGC Services: the Use Case of TRAFAIR Project

This work proposes a workflow for the publication of Open Spatial Data. The main contribution of this work is the automatic generation of metadata extracted from OGC spatial services providing access to feature types and coverages. Besides, this work adopts the GeoDCAT-AP metadata profile for the description of datasets because it allows for an appropriate crosswalk between the annotation requirements in the spatial domain and the metadata models accepted in general Open Data portals. The feasibility of the proposed workflow has been tested within the framework of the TRAFAIR project to publish monitoring and forecasting air quality data

Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data

BACKGROUND: We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the participation of a given gene in more than one cluster. Genes assigned to each cluster are used for the detection of pathways predominantly activated in that cluster by finding statistically significant associated GO terms. We tested the approach with a published dataset of microarray experiments in yeast. Upon validation with the yeast dataset, we applied the technique to a prostate cancer dataset. RESULTS: Two major pathways are shown to be activated in organ-confined, non-metastatic prostate cancer: those regulated by the androgen receptor and by receptor tyrosine kinases. A number of gene markers (HER3, IQGAP2 and POR1) highlighted by the software and related to the later pathway have been validated experimentally a posteriori on independent samples. CONCLUSION: Using a new microarray analysis tool followed by a posteriori experimental validation of the results, we have confirmed several putative markers of malignancy associated with peptide growth factor signalling in prostate cancer and revealed others, most notably ERRB3 (HER3). Our study suggest that, in primary prostate cancer, HER3, together or not with HER4, rather than in receptor complexes involving HER2, could play an important role in the biology of these tumors. These results provide new evidence for the role of receptor tyrosine kinases in the establishment and progression of prostate cancer

Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data

BACKGROUND: We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the participation of a given gene in more than one cluster. Genes assigned to each cluster are used for the detection of pathways predominantly activated in that cluster by finding statistically significant associated GO terms. We tested the approach with a published dataset of microarray experiments in yeast. Upon validation with the yeast dataset, we applied the technique to a prostate cancer dataset. RESULTS: Two major pathways are shown to be activated in organ-confined, non-metastatic prostate cancer: those regulated by the androgen receptor and by receptor tyrosine kinases. A number of gene markers (HER3, IQGAP2 and POR1) highlighted by the software and related to the later pathway have been validated experimentally a posteriori on independent samples. CONCLUSION: Using a new microarray analysis tool followed by a posteriori experimental validation of the results, we have confirmed several putative markers of malignancy associated with peptide growth factor signalling in prostate cancer and revealed others, most notably ERRB3 (HER3). Our study suggest that, in primary prostate cancer, HER3, together or not with HER4, rather than in receptor complexes involving HER2, could play an important role in the biology of these tumors. These results provide new evidence for the role of receptor tyrosine kinases in the establishment and progression of prostate cancer

Highly sensitive molecular diagnosis of prostate cancer using surplus material washed off from biopsy needles

INTRODUCTION: Currently, final diagnosis of prostate cancer (PCa) is based on histopathological analysis of needle biopsies, but this process often bears uncertainties due to small sample size, tumour focality and pathologist’s subjective assessment. METHODS: Prostate cancer diagnostic signatures were generated by applying linear discriminant analysis to microarray and real-time RT–PCR (qRT–PCR) data from normal and tumoural prostate tissue samples. Additionally, after removal of biopsy tissues, material washed off from transrectal biopsy needles was used for molecular profiling and discriminant analysis. RESULTS: Linear discriminant analysis applied to microarray data for a set of 318 genes differentially expressed between non-tumoural and tumoural prostate samples produced 26 gene signatures, which classified the 84 samples used with 100% accuracy. To identify signatures potentially useful for the diagnosis of prostate biopsies, surplus material washed off from routine biopsy needles from 53 patients was used to generate qRT–PCR data for a subset of 11 genes. This analysis identified a six-gene signature that correctly assigned the biopsies as benign or tumoural in 92.6% of the cases, with 88.8% sensitivity and 96.1% specificity. CONCLUSION: Surplus material from prostate needle biopsies can be used for minimal-size gene signature analysis for sensitive and accurate discrimination between non-tumoural and tumoural prostates, without interference with current diagnostic procedures. This approach could be a useful adjunct to current procedures in PCa diagnosis. British Journal of Cancer (2011) 105, 1600–1607. doi:10.1038/bjc.2011.435 www.bjcancer.com Published online 18 October 2011 & 2011 Cancer Research UKMinisterio de Ciencia e Innovacion (PI080274), Fundación Marato TV3, Ministerio de Educacio´n (GEN2001-4856- C13, GEN2001-4865-C13-10 and SAF2005-05109), Ministerio de Sanidad (PI020231), Red Temática de Cáncer of the Instituto Carlos III (ISCIII-RETIC RD06/0020), Xarxa de Bancs de Tumors de Catalunya-ICO (XBTC) and Fundación Ramón Areces.Peer Reviewe

Secondary School Students' Knowledge and Opinions on Astrobiology Topics and Related Social Issues

Astrobiology is the study of the origin of life on Earth and the distribution of life in the Universe. Its multidisciplinary approach, social and philosophical implications, and appeal within the discipline and beyond make astrobiology a uniquely qualified subject for general science education. In this study, student knowledge and opinions on astrobiology topics were investigated. Eighty-nine students in their last year of compulsory education (age 15) completed a written questionnaire that consisted of 10 open questions on the topic of astrobiology. The results indicate that students have significant difficulties understanding the origin of life on Earth, despite exposure to the topic by way of the assigned textbooks. The students were often unaware of past or present achievements in the search for life within the Solar System and beyond, topics that are far less commonly seen in textbooks. Student questionnaire answers also indicated that students had problems in reasoning and critical thinking when asked for their opinions on issues such as the potential for life beyond Earth, the question of whether UFOs exist, or what our place is in the Universe. Astrobiology might help initiate student awareness as to current thinking on these matters and should be considered for general science educatio

Virus del dengue de serotipo 1 (DENV-1) de Colombia: su contribución a la presentación del dengue en el departamento de Santander

Introduction: Between 1998 and 2008 all dengue virus serotypes circulated in the Departamento de Santander, an endemic region in northeastern Colombia. No information is available as to the role of serotype 1 (DENV-1) with respect to epidemiology of dengue.Objective: To analyze the relationship between changes in DENV-1 predominance with respect to genetic diversity, prevalence of others serotypes and occurrence of severe dengue.Methods: Virus genetic diversity was studied by phylogenetic analysis comparing E gene sequences from 12 viral strains. Data about serotypes predominance obtained in previous studies and official data about dengue incidence were used for analysis.Results: Selected viruses grouped into genotype V together DENV-1 from Latin America countries, and segregation in four lineages was evidenced. Changes in virus predominance coincided with replacement of lineage, increase in prevalence of DENV-2 and DENV-3 and increase of severe dengue.Conclusion: Genetic divergence could have contributed to changes in DENV-1 predominance. The relationship of the virus with DENV-2 and DENV-3 could create scenarios that promote occurrence of severe cases. More studies are required to ascertain the precise role of serotypes in the epidemiology of dengue. doi: http://dx.doi.org/10.7705/biomedica.v33i0.717Introducción. Los cuatro serotipos del virus del dengue circularon en el departamento de Santander entre 1998 y 2008. No existe información sobre el papel del serotipo 1 (DENV-1) en la epidemiología de la enfermedad.Objetivo. Analizar la relación entre el cambio de predominancia del (DENV-1) con su diversificación genética, predominancia de los otros serotipos y presentación del dengue grave.Materiales y métodos. La diversificación genética se estudió por análisis filogenético usando la secuencia del gen E de 12 cepas del virus. Para el análisis se utilizaron datos sobre predominancia delos serotipos obtenidos en estudios previos y datos oficiales de incidencia del dengue.Resultados. Los virus seleccionados se agruparon en el genotipo V junto a (DENV-1) de países de Latinoamérica y se evidenció segregación en cuatro linajes. Los cambios en la predominancia del virus coincidieron con el reemplazo de linaje y esto, a su vez, con incremento en la prevalencia de DENV-2y DENV-3, e incremento del dengue grave.Conclusión. La diversificación genética podría contribuir a cambios de predominancia de (DENV-1), y la relación del virus con el DENV-2 y DENV-3 en situaciones que favorecen la presentación de casos graves. Se necesitan más estudios para precisar el papel de los serotipos en la epidemiología del dengue.doi: http://dx.doi.org/10.7705/biomedica.v33i0.717

Evaluation of monocytes as carriers for armed oncolytic adenoviruses in murine and Syrian hamster models of cancer

Replication-competent (oncolytic) adenoviruses (OAV) can be adapted as vectors for the delivery of therapeutic genes, with the aim of extending the antitumor effect beyond direct cytolysis. Transgene expression using these vectors is usually intense but short-lived, and repeated administrations are hampered by the rapid appearance of neutralizing antibodies (NAbs). We have studied the performance of monocytes as cell carriers to improve transgene expression in cancer models established in athymic mice and immunocompetent Syrian hamsters. Human and hamster monocytic cell lines (MonoMac6 and HM-1, respectively) were loaded with replication-competent adenovirus-expressing luciferase. Intravenous administration of these cells caused a modest increase in transgene expression in tumor xenografts, but this effect was virtually lost in hamsters. In contrast, intratumoral administration of HM-1 cells allowed repeated cycles of expression and achieved partial protection from NAbs in preimmunized hamsters bearing pancreatic tumors. To explore the therapeutic potential of this approach, HM-1 cells were loaded with a hypoxia-inducible OAV expressing the immunostimulatory cytokine interleukin-12 (IL-12). Three cycles of treatment achieved a significant antitumor effect in the hamster model, and transgene expression was detected following each administration, in contrast with the rapid neutralization of the free virus. We propose monocytes as carriers for multiple intratumoral administrations of armed OAVs

Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

<p>Abstract</p> <p>Background</p> <p>Transcriptional profiling of prostate cancer (PC) has unveiled new markers of neoplasia and allowed insights into mechanisms underlying this disease. Genomewide analyses have also identified new chromosomal abnormalities associated with PC. The combination of both classes of data for the same sample cohort might provide better criteria for identifying relevant factors involved in neoplasia. Here we describe transcriptional signatures identifying distinct normal and tumoral prostate tissue compartments, and the inference and demonstration of a new, highly recurrent copy number gain on chromosome 17q25.3.</p> <p>Methods</p> <p>We have applied transcriptional profiling to tumoral and non-tumoral prostate samples with relatively homogeneous epithelial representations as well as pure stromal tissue from peripheral prostate and cultured cell lines, followed by quantitative RT-PCR validations and immunohistochemical analysis. In addition, we have performed <it>in silico </it>colocalization analysis of co-regulated genes and validation by fluorescent in situ hybridization (FISH).</p> <p>Results</p> <p>The transcriptomic analysis has allowed us to identify signatures corresponding to non-tumoral luminal and tumoral epithelium, basal epithelial cells, and prostate stromal tissue. In addition, <it>in silico </it>analysis of co-regulated expression of physically linked genes has allowed us to predict the occurrence of a copy number gain at chromosomal region 17q25.3. This computational inference was validated by fluorescent <it>in situ </it>hybridization, which showed gains in this region in over 65% of primary and metastatic tumoral samples.</p> <p>Conclusion</p> <p>Our approach permits to directly link gene copy number variations with transcript co-regulation in association with neoplastic states. Therefore, transcriptomic studies of carefully selected samples can unveil new diagnostic markers and transcriptional signatures highly specific of PC, and lead to the discovery of novel genomic abnormalities that may provide additional insights into the causes and mechanisms of prostate cancer.</p

Potential use of high levels of vegetal proteins in diets for market-sized gilthead sea bream (Sparus aurata)

[EN] The effect of partial or total dietary substitution of fishmeal (FM) by vegetal protein sources on growth and feed efficiency was carried out in on-growing gilthead sea bream (mean initial weight 131 g). The Control diet (FM 100) contained FM as the primary protein source, while in Diets FM 25 and FM 0 the FM protein was replaced at 75% and 100%, respectively, by a vegetable protein mixture consisting of wheat gluten, soybean meal, rapeseed meal and crystalline amino acids. Diets FM 25 and FM 0 also contained krill meal at 47 g/kg in order to improve palatability. At the end of the trial (after 158 d), fish survival was above 90%. Final weight and the specific growth rate were statistically lower in fish fed the Control diet (361 g and 0.64%/d), compared with 390–396 g and 0.69–0.70%/d after feeding vegetal diets. No significant differences were found regarding feed intake and feed conversion ratio. The digestibility of protein and amino acids (determined with chromium oxide as indicator) was similar in all diets. The blood parameters were not significantly affected by treatments. The activity of trypsin and pepsin was significantly reduced after feeding Diet FM 0. In the distal intestine, the villi length in fish fed Diet FM 25 was significantly longer and the intestine of the fish fed the FM 100 diet showed a smaller number of goblet cells. In conclusion, a total FM substitution by a vegetal mix supplemented with synthetic amino acids in on-growing sea bream is feasible.This work was supported by the Vicerrectorat d'Investigacio, Innovacio i Transferencia - Universitat Politecnica de Valencia, Project Name: Aquaculture feed without fishmeal (SP20120603). URLs of funder:http://www.upv.es/entidades/VIIT/info/indexnormalc.htm. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Monge-Ortiz, R.; Martínez-Llorens, S.; Marquez, L.; Moyano-Lopez, FJ.; Jover Cerdá, M.; Tomas-Vidal, A. (2016). Potential use of high levels of vegetal proteins in diets for market-sized gilthead sea bream (Sparus aurata). Archives of Animal Nutrition. 70(2):155-172. https://doi.org/10.1080/1745039X.2016.1141743S15517270

Population based prostate cancer screening in north Mexico reveals a high prevalence of aggressive tumors in detected cases

Background: Prostate Cancer (PCa) is the second most frequent neoplasia in men worldwide. Previous reports suggest that the prevalence of PCa in Hispanic males is lower than in Africans (including communities with African ancestry) and Caucasians, but higher than in Asians. Despite these antecedents, there are few reports of open population screenings for PCa in Latin American communities. This article describes the results of three consecutive screenings in the urban population of Monterrey, Mexico. Methods: After receiving approval from our University Hospital's Internal Review Board (IRB), the screening was announced by radio, television, and press, and it was addressed to male subjects over 40 years old in general. Subjects who consented to participate were evaluated at the primary care clinics of the University Health Program at UANL, in the Metropolitan area of Monterrey. Blood samples were taken from each subject for prostate specific antigen (PSA) determination; they underwent a digital rectal examination (DRE), and were subsequently interviewed to obtain demographic and urologic data. Based on the PSA (>4.0 ng/ml) and DRE results, subjects were appointed for transrectal biopsy (TRB). Results: A total of 973 subjects were screened. Prostate biopsy was recommended to 125 men based on PSA values and DRE results, but it was performed in only 55 of them. 15 of these biopsied men were diagnosed with PCa, mostly with Gleason scores ≥ 7. Conclusion: Our results reflect a low prevalence of PCa in general, but a high occurrence of high grade lesions (Gleason ≥ 7) among patients that resulted positive for PCa. This observation remarks the importance of the PCa screening programs in our Mexican community and the need for strict follow-up campaigns