isomiRdb: microRNA expression at isoform resolution

A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients’ samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9×1011 sequencing reads) and consistently analyzed them usingmiRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland. de/isomirdb.Saarland Universit

MirGeneDB 2.1: toward a complete sampling of all major animal phyla

B.F. is supported by the Tromso forskningsstiftelse (TFS) [20 SG BF `MIRevolution']; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F., W.K., E.M.-S. and M.R.F.); M.R.F. is additionally supported by ERC [758397 `miRCell']; South-Eastern Norway Regional Health Authority support is acknowledged [2018014 to E.H.]; P.J. Chabot is supported by the Junior Scholars Program (Dartmouth College); V.O.'s research funding was awarded to Dr Mary J. O'Connell (Associate Professor) from the School of Life Sciences University of Nottingham; M.H. is supported by the Spanish Government [AGL2017-88702C2-2-R]; University of Granada [A-BIO-481-UGR18, FEDER 18]; K.J.P. has been supported by the National Science Foundation; NASA Ames; Dartmouth College.We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.Tromso forskningsstiftelse (TFS) 20_SG_BFStrategic Research Area (SFO) program of the Swedish Research Council through Stockholm UniversityEuropean Research Council (ERC) European Commission 758397South-Eastern Norway Regional Health Authority 2018014Junior Scholars Program (Dartmouth College)School of Life Sciences University of NottinghamSpanish GovernmentEuropean Commission AGL2017-88702-C2-2-RUniversity of Granada A-BIO-481-UGR18 FEDER 18National Science Foundation (NSF)National Aeronautics & Space Administration (NASA)Dartmouth Colleg

Descripción y análisis del sistema de suministro de material medico-quirúrgico en el Complejo Hospitalario Dr. Arnulfo Arias Madrid año 1993

Cualquier profesional que desempeñe funciones de administración en alguna institución o establecimiento de salud debe afrontar, en el transcurso de su misión, una serie de dificultades y decisiones relacionadas con los Insumos que se necesitan para lograr cumplir con el propósito fundamental de brindar servicios de salud a la población. Como toda organización que produce servicios, los hospitales tienen que consumir recursos financieros y materiales sin los cuales la labor del recurso humano se hace casi imposible. El gerente (sea médico, técnico o profesional de la administración) es el llamado a garantizar esos Insumos y darle el uso más eficiente posible. El medio político, económico y social que rodea al funcionamiento institucional panameño, y por lo tanto las entidades de salud es inestable e Incierto. Ante ello sus gerentes tienen un gran compromiso y deben recurrir a todas las herramientas que la Salud Pública provee para enfrentar el reto de hacer uso racional de los recursos materiales y financieros que los asegurados le confieren

Desplegament d'un cluster Kubernetes altament disponible en Google Cloud Platform

[ES] El cloud computing, es un modelo tecnológico que se está implementando en la mayoría de empresas en los últimos años. Sus ventajas son obvias, ya sea porque se usa Software como servicio (SaaS), Plataforma como servicio (PaaS) o Infraestructura como servicio (IaaS). Ello supone para las empresas un ahorro de costes, espacios seguros, fácil accesibilidad y una personalización del servicio según los requisitos del cliente. El objeto de este trabajo es estudiar qué facilidades, herramientas y comodidades ofrece Google Cloud Platform a la hora de desplegar un clúster de Kubernetes altamente disponible, con el objetivo de que pueda ser comparado con sus competidores y ayudar a las empresas a seleccionar un servicio u otro según sus requisitos.[EN] Cloud computing is a technological model that has been implemented in most companies in recent years. Its advantages are obvious, whether it is Software as a Service (SaaS), Platform as a Service (PaaS) or Infrastructure as a Service (IaaS). This offers companies cost savings, secure spaces, easy accessibility and customisation of the service according to the client's requirements.The aim of this paper is to study what facilities, tools and conveniences Google Cloud Platform offers when deploying a highly available Kubernetes cluster, so that it can be compared with its competitors and help companies to select one service or another according to their requirements.Gaspar Aparicio, E. (2022). Despliegue de un cluster Kubernetes altamente disponible en Google Cloud Platform. Universitat Politècnica de València. http://hdl.handle.net/10251/18856

Balanced scorecard y competitividad en el sector gráfico, el caso: Corporación Gráfica Huascaran, 2013- 2014

Implementa un modelo de gestión basado en la herramienta de Balanced Scorecard para una empresa Pyme del sector gráfico, empresa en la que el problema planteado es resolver si es posible establecer indicadores estratégicos que puedan medir la gestión. Como hipótesis se establece si la implantación de un Balanced Scorecard en una empresa Pyme del sector gráfico permite la medición integral de la estrategia de dicha organización, en adición al uso de indicadores financieros tradicionales.Tesi

Study on Electro-mechanical Stability of REBCO Tape Lap Joints for Segmented Fabrication of High-Temperature Superconducting Fusion Magnets

Tohoku University橋爪秀利課

Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host

Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host’s hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for managing blood meals (storage and digestion) and protecting against host immunity and pathogen infections. Previous transcriptomic studies revealed the complexity of tick sialomes (salivary gland transcriptomes) and mialomes (midgut transcriptomes) which encode for protease inhibitors, lipocalins (histamine-binding proteins), disintegrins, enzymes, and several other tickspecific proteins. Several studies have demonstrated that mammalian hosts acquire tick resistance against repeated tick bites. Consequently, there is an urgent need to uncover how tick sialomes and mialomes respond to resistant hosts, as they may serve to develop novel tick control strategies and applications. Here, we mimicked natural repeated tick bites in a laboratory setting and analyzed gene expression dynamics in the salivary glands and midguts of adult female ticks. Rabbits were subjected to a primary (feeding on a naive host) and a secondary infestation of the same host (we re-exposed the hosts but to other ticks). We used single salivary glands and midguts dissected from individual siblings adult pathogen-free female Ixodes ricinus to reduce genetic variability between individual ticks. The comprehensive analysis of 88 obtained RNA-seq data sets allows us to provide high-quality annotated sialomes and mialomes from individual ticks. Comparisons between fed/ unfed, timepoints, and exposures yielded as many as 3000 putative differentially expressed genes (DEG). Interestingly, when classifying the exposure DEGs by means of a clustering approach we observed that the majority of these genes show increased expression at early feeding timepoints in the mid-gut of re-exposed ticks. The existence of clearly defined groups of genes with highly similar responses to re-exposure suggests the existence of molecular swiches. In silico functional analysis shows that these early feeding reexposure response genes form a dense interaction network at protein level being related to virtually all aspects of gene expression regulation and glycosylation. The processed data is available through an easy-to-use database-associated webpage (https://arn.ugr.es/IxoriDB/) that can serve as a valuable resource for tick research.Grant Agency of the Czech Republic 19-382 07247SERD Funds 384 CZ.02.1.01/0.0/0.0/16_019/0000759Programa Operativo FEDER de Andalucia A-BIO-481-UGR18European Union within ESIF in frame of Operational Programme Research, Development and Education CZ.02.2.69/0.0/0.0/20_079/001780

IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution

Besides canonical microRNAs (miRNAs), sequence-based variations called iso-miRs have biological relevance and diagnostic potential; however, accurate calling of these post-transcriptional modifications is challenging, especially for low input samples. Here, we present IsoSeek, a sequencing protocol that reduces ligation and PCR amplification bias and improves the accuracy of miRNA detection in low input samples. We describe steps for using randomized adapters combined with unique molecular identifiers (UMI), library quantification, and sequencing, followed by detailed procedures for data processing and analysis.Multiple grants awarded to D.M.P. including NWO Perspectief Cancer-ID, TKI-Health Holland AQrate, and Cancer Center Amsterdam Foundatio

miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations

MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/

Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced small RNA (sRNA) libraries from the leaves and roots of three wheat cultivars (Kukri, RAC875 and Excalibur) under water and drought conditions. A total of 636 known miRNAs and 294 novel miRNAs were identified, of which 34 miRNAs were tissue- or cultivar-specific. Among these, 314 were significantly regulated under drought conditions. miRNAs that were drought-regulated in all cultivars displayed notably higher expression than those that responded in a cultivar-specific manner. Cultivar-specific drought response miRNAs were mainly detected in roots and showed significantly different drought regulations between cultivars. By using wheat degradome library, 6619 target genes were identified. Many target genes were strongly enriched for protein domains, such as MEKHLA, that play roles in drought response. Targeting analysis showed that drought-downregulated miRNAs targeted more genes than droughtupregulated miRNAs. Furthermore, such genes had more important functions. Additionally, the genes targeted by drought-downregulated miRNAs had multiple interactions with each other, while the genes targeted by drought-upregulated miRNAs had no interactions. Our data provide valuable information on wheat miRNA expression profiles and potential functions in different tissues, cultivars and drought conditions