Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

<p>Abstract</p> <p>Background</p> <p>Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored.</p> <p>Results</p> <p>We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP) and sensitivity (ST) of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results.</p> <p>Conclusions</p> <p>The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.</p

POF-Based Solar Concentrators Incorporating Dyes and Europium Chelates

In this paper, useful models that enable time-efficient computational analyses of the performance of luminescent solar concentrators (LSCs) are developed and thoroughly described. These LSCs are based on polymer optical fibers codoped with organic dyes and/or europium chelates. The interest in such dopants lies in the availability of new dyes with higher quantum yields and in the photostability and suitable absorption and emission bands of europium chelates. Time-efficiency without compromising accuracy is especially important for the simulation of europium chelates, in which non-radiative energy transfers from the absorbing ligands to the europium ion and vice versa are so fast that the discretization in time, in the absence of some simplifying assumptions, would have to be very fine. Some available experimental results are also included for the sake of comparison.This research was funded by Gobierno de España, Ministerio de Economía y Competitividad, with grant RTI2018-094669-B-C31. They also acknowledge funding support from Departamento de Educación del Gobierno Vasco, Grant IT933-16, and SPRI ELKARTEK projects KK-2019/00101 (μ4Indust), and ELKARTEK KK-2019/00051 (SMARTRESNAK)

A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies

Inherited retinal diseases (IRD) are a heterogeneous group of diseases that mainly affect the retina; more than 250 genes have been linked to the disease and more than 20 different clinical phenotypes have been described. This heterogeneity both at the clinical and genetic levels complicates the identification of causative mutations. Therefore, a detailed genetic characterization is important for genetic counselling and decisions regarding treatment. In this study, we developed a method consisting on pooled targeted next generation sequencing (NGS) that we applied to 316 eye disease related genes, followed by High Resolution Melting and copy number variation analysis. DNA from 115 unrelated test samples was pooled and samples with known mutations were used as positive controls to assess the sensitivity of our approach. Causal mutations for IRDs were found in 36 patients achieving a detection rate of 31.3%. Overall, 49 likely causative mutations were identified in characterized patients, 14 of which were first described in this study (28.6%). Our study shows that this new approach is a cost-effective tool for detection of causative mutations in patients with inherited retinopathies.This work was supported by grants from the National Institute of Health Carlos III (Institute of Health Carlos III/ISCIII) (CP10/00572, PI13/02621 and RD16/0008/0027 to JRE, PI17/01413 to CI, and a Research Intensification Contract to ALdM); the Basque Government's Industry Department (SAIOTEK: SAIO11-PE11BN002; and SAIO12-PC12BN001 to JRE), a grant from the Mutua Madrilena Foundation and support from the Retinitis Pigmentosa Patients of Gipuzkoa Foundation (BEGISARE). JR-E is a Miguel Servet II Fellow, National Institute of Health Carlos III (ISCIII). MEI was supported by grants from the Basque Government's Department of Education (DEDUC14/309). OB is supported by funding from the Retinitis Pigmentosa Patients of Gipuzkoa Foundation (BEGISARE) and a grant from the Mutua Madrilena Foundation. AA was supported by grants from the Fundacion Jesus de Gangoiti Barrera and from the Basque Government's Departments of Industry and Education (SAIOTEK-11BN002/PC12BN001/DEPLC13/002). CI is partially supported by a Research Intensification Contract (INTBIO15/001). The authors are grateful to Xabier Elcoroaristizabal and Marta Fernandez-Mercado for their helpful advice on developing the base-calling setup. Maribel Gomez; Naiara Telletxea and Nahikari Pastoriza at the Basque Biobank for isolating DNA samples; and Dr. Carmen Ayuso for kindly providing control samples. We also give special thanks to all patients with IRD and their families involved in the study

Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

BACKGROUND: The development of a more refined prognostic methodology for early non-small cell lung cancer (NSCLC) is an unmet clinical need. An accurate prognostic tool might help to select patients at early stages for adjuvant therapies. RESULTS: A new integrated bioinformatics searching strategy, that combines gene copy number alterations and expression, together with clinical parameters was applied to derive two prognostic genomic signatures. The proposed methodology combines data from patients with and without clinical data with a priori information on the ability of a gene to be a prognostic marker. Two initial candidate sets of 513 and 150 genes for lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC), respectively, were generated by identifying genes which have both: a) significant correlation between copy number and gene expression, and b) significant prognostic value at the gene expression level in external databases. From these candidates, two panels of 7 (ADC) and 5 (SCC) genes were further identified via semi-supervised learning. These panels, together with clinical data (stage, age and sex), were used to construct the ADC and SCC hazard scores combining clinical and genomic data. The signatures were validated in two independent datasets (n = 73 for ADC, n = 97 for SCC), confirming that the prognostic value of both clinical-genomic models is robust, statistically significant (P = 0.008 for ADC and P = 0.019 for SCC) and outperforms both the clinical models (P = 0.060 for ADC and P = 0.121 for SCC) and the genomic models applied separately (P = 0.350 for ADC and P = 0.269 for SCC). CONCLUSION: The present work provides a methodology to generate a robust signature using copy number data that can be potentially used to any cancer. Using it, we found new prognostic scores based on tumor DNA that, jointly with clinical information, are able to predict overall survival (OS) in patients with early-stage ADC and SCC

Sistema de acceso a datos de proceso mediante plataforma Arduino para aplicaciones de automatización industrial

[ES]Este proyecto consiste en el desarrollo de un sistema que permita el acceso a datos de proceso, haciendo uso de la plataforma Arduino desde un PLC. Para ello, se hace uso del protocolo de comunicaciones Modbus TCP. Las aplicaciones se programarán mediante Codesys y se ejecutarán en un PC industrial con Codesys Control RTE, instalado en Windows 8.1 empotrado.[EU]Proiektu honek Arduinoren bitartez prozesuko datuetara sarbidea ematen duen sistemaren garapenean datza. Modbus TCP komunikazio protokoloa erabiltzen da horretarako. Aplikazioak Codesys-en programatuko dira eta Windows 8.1 Embedded-pean instalatutako Codesys Control RTE software-an exekutatuko dira.[EN]This Project consists of the development of a system which enables access to process data from a PLC. Modbus TCP communications protocol is used for that instance. Applications will be programmed in Codesys and they will be run in Codesys Control RTE, installed in Windows XP Embedded

CBDCs, ¿el próximo capítulo de la política monetaria?

En este trabajo se estudian los efectos que tendría la implementación de dinero digital emitido por el banco central (Digital Bank Digital Currency, CBDC). En el primer capítulo se estudia la naturaleza del dinero, las funciones de este; y como a lo largo de la historia la forma que ha adquirido ha ido evolucionando. Tras un breve resumen sobre las principales diferencias entre los diferentes proyectos criptográficos y las CBDCs; se analiza las funciones de la banca comercial y la banca central. El objetivo es entender el funcionamiento de los bancos comerciales y la banca central, para comprender como podría afectar este nuevo marco, donde el uso de dinero de banco central estaría abierto al público. Para ver la situación y las herramientas que tiene el banco central, se realiza un resumen histórico sobre los cambios en el paradigma de la política monetaria. Por último, se analiza el modelo (Jonas Grossa y Jonathan Schillerb, 2021) donde se estudian los efectos que tendría las CBDCs en un entorno de estrés financiero

Proximity-informed robot control through whole-body artificial skin

Human-Robot Interaction is the field of robotics dedicated to the understanding, design, and evaluation of robotic systems for use by or with humans. Safety is one of the most important aspects this field will have to deal with in the years to come. In this work, pre-contact safety is adressed through the use of an artificial skin developed in our lab that integrates proximiy sensing. Proximity sensor readings are transformed into 3D data, which will later inform the control algorithms. Two different avoidance controls have been implemented: “A Depth Space Approach to Human-Robot Collision Avoidance” [1] and “Collision Avoidance with Proximity Servoing for Redundant Serial Robot Manipulators” [2]. The implementations of these two controllers form, with the addition of a third controller that improves upon both of them, a framework for the comparison and improvement of the current state of art in safe robot controllers

Sistema de acceso a datos de proceso mediante plataforma Arduino para aplicaciones de automatización industrial

[ES]Este proyecto consiste en el desarrollo de un sistema que permita el acceso a datos de proceso, haciendo uso de la plataforma Arduino desde un PLC. Para ello, se hace uso del protocolo de comunicaciones Modbus TCP. Las aplicaciones se programarán mediante Codesys y se ejecutarán en un PC industrial con Codesys Control RTE, instalado en Windows 8.1 empotrado.[EU]Proiektu honek Arduinoren bitartez prozesuko datuetara sarbidea ematen duen sistemaren garapenean datza. Modbus TCP komunikazio protokoloa erabiltzen da horretarako. Aplikazioak Codesys-en programatuko dira eta Windows 8.1 Embedded-pean instalatutako Codesys Control RTE software-an exekutatuko dira.[EN]This Project consists of the development of a system which enables access to process data from a PLC. Modbus TCP communications protocol is used for that instance. Applications will be programmed in Codesys and they will be run in Codesys Control RTE, installed in Windows XP Embedded

Getting DNA copy numbers without control samples

Abstract Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons.</p

Lan arriskuen prebentzioak behar al du estandar pribaturik? ISO 45001 estandarra aztergai

El fenómeno de los estándares de gestión y de la autorregulación empresarial ha fraguado con éxito en las tres últimas décadas. Se trata de un fenómeno muy complejo que se produce en un contexto globalizador marcado por presiones para articular una verdadera cadena de suministro global y por la incapacidad de los estados para ejercer una regulación pública en determinados ámbitos de actuación, como el medioambiental o el relativo a los derechos de los trabajadores. Este fenómeno hace años que llegó al ámbito de la prevención de los riesgos laborales con el estándar OHSAS 18001, pero en estos días está experimentando un nuevo auge con el proyecto de lanzamiento de la nueva ISO 45001, un estándar privado que pretende regular los mencionados aspectos. El proceso de diseño, aceptación y lanzamiento de este estándar está siendo largo y conflictivo, aunque no esté siendo analizado debidamente desde el ámbito académico. Priman las aproximaciones de carácter «técnico» o los que muestran cierto seguidismo respecto al propio fenómeno objeto de estudio, sin analizar siquiera las distintas caras de un fenómeno muy complejo y en muchas ocasiones de conflicto social. Con el fin de satisfacer la citada laguna, este artículo pretende arrojar luz sobre la norma ISO 45001. Las conclusiones evidencian dos tipos de discrepancias principales. Por una parte, las discrepancias de forma y de contenidos concretos y, por otra, discrepancias de fondo como las que ponen en duda la razón de ser del propio estándar.The generation and dissemination process of standards for corporate self-regulation had been a successful phenomenon in the last three decades. It’s a very complex phenomenon fostered by the pressure to adopt global supply chains and in the context of the inability on the part of governments to pursue public regulation in certain areas of activity such as the environmental issues or the one of the rights and duties of workers. Indeed, several years ago, when the OHSAS 18001 was launched, this phenomenon arrives to the field of occupational health and safety. Nowadays, the process of design and launching of the ISO 45001 standard is turning out to be a complex issue and some discussions are definitely back. Nevertheless, the design and launching process of ISO 45001 has been an under researched issue in the scholarly literature as in the published analyses priority is given to those approaches of a ‘technical’ nature or to rather acritical perspectives that simply appear to rehash previous literature with regard to the phenomenon itself subject to study. In order to fulfill the mentioned gap this contribution aims at shedding light on the ISO 45001 standard. The article analyses the very different perspectives about the ISO 45001 standard by diverse stakeholders. Two main type of discrepancies could be pointed out. First, discrepancies in terms of form and specific content. Second, underlying discrepancies such as those that raise doubts about the final purpose of the ISO 45001 standard itself.Kudeaketa eta enpresa-autorregulaziorako estandarren fenomenoak bilakaera arrakastatsua izan du azken hiru hamarraldietan. Fenomeno oso konplexua da, horniketa-kate globala artikulatzeko presioek markatutakoa eta estatuek nazioarteko testuinguruan hainbat esparrutan —esaterako, ingurumenari edo langileen eskubideei buruzkoetan— arautzeko erakutsi duten gabeziaren argitan gertatzen ari dena. Badira hainbat urte fenomeno hori lan arriskuen prebentzioko esparrura iritsi zela, OHSAS 18001 estandarra sortu zenean, hain zuzen ere. Egun, lan arriskuen prebentziorako kudeaketa arautuko lukeen ISO 45001 estandarraren proiektuak gaiari buruzko ezbaia areagotu du. ISO 45001en diseinu eta onarpen prozesua luzea eta gatazkatsua suertatzen ari da, eta esparru akademikotik ez zaio behar bezalako arretarik eskaini. Balizko izaera «teknikoa» duten hurbilpen soilak edota aztergai den fenomenoari nolabaiteko jarraipen akritikoa ematen dietenak dira nagusi. Eta ikuspegi horiek muzin egiten diote izaera oso konplexua duen fenomeno honen zenbait aurpegi aztertzeari. Gabezia hori betetzeko asmoz ISO 45001 estandarraren nondik-norakoa aztertzea da artikulu honen helburua. Prozesuari buruz interes-talde desberdinek dituzten desadostasunak jasotzen ditu artikuluak; funtsean bi motatakoak. Batetik, forma eta eduki zehatzei dagozkien desadostasunak. Eta bestetik, sakonagoak: lan arriskuen prebentzioa gidatzeko estandar pribatu baten beharra bera ere zalantzan jartzen dutenak