Expression Atlas update: insights from sequencing data at both bulk and single cell level.

Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.

The impact of a night float system on operative experience in neurosurgery residency.

OBJECTIVE: Since the Accreditation Council for Graduate Medical Education (ACGME) implemented duty-hour restrictions in 2003, many residency programs have adopted a night float system to comply with time constraints. However, some surgical subspecialities have been concerned that use of a night float system deprives residents of operative experience. In this study, the authors describe their training program's transition to a night float system and its impact on resident operative experience. METHODS: The authors conducted a single-program study of resident surgical case volume before and after implementing the night float system at 3 of their 5 hospitals from 2014 to 2020. The authors obtained surgical case numbers from the ACGME case log database. RESULTS: Junior residents received a concentrated educational experience, whereas senior residents saw a significant decrease from 112 calls/year to 17. Logged cases significantly increased after implementation of the night float system (8846 vs 10,547, p = 0.04), whereas cases at non-night float hospitals remained the same. This increase was concurrent with an increase in hospital cases. This difference was mainly driven by senior resident cases (p = 0.010), as junior and chief residents did not show significant differences in logged cases (p > 0.40). Lead resident cases increased significantly after implementation of the night float system (6852 vs 8860, p = 0.04). When normalized for increased hospital cases, resident case increases were not statistically significant. CONCLUSIONS: Transitioning to a night float call system at the authors' institution increased overall resident operative cases, particularly for lead resident surgeons. Based on the results of this study, the authors recommend the use of a night float call system to consolidate night calls, which increases junior resident-level educational opportunities and senior resident cases.

Established and Emerging Therapies in Acute Spinal Cord Injury.

Acute spinal cord injury (SCI) is devastating for patients and their caretakers and has an annual incidence of 20-50 per million people. Following initial assessment with appropriate physical examination and imaging, patients who are deemed surgical candidates should undergo decompression with stabilization. Earlier intervention can improve neurological recovery in the post-operative period while allowing earlier mobilization. Optimized medical management is paramount to improve outcomes. Emerging strategies for managing SCI in the acute period stem from an evolving understanding of the pathophysiology of the injury. General areas of focus include ischemia prevention, reduction of secondary injury due to inflammation, modulation of the cytotoxic and immune response, and promotion of cellular regeneration. In this article, we review established, emerging, and novel experimental therapies. Continued translational research on these methods will improve the feasibility of bench-to-bedside innovations in treating patients with acute SCI.

PathExNET: A tool for extracting pathway expression networks from gene expression statistics.

A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to provide a numeric characterization of pathways across different biological experiments, in the prospect to create unique footprints that may characterise a specific disease under study at a pathway network level. In this line we propose PathExNET, a web service that allows the creation of pathway-to-pathway expression networks that hold the over- and under expression information obtained from differential gene expression analyses. The unique numeric characterization of pathway expression status related to a specific biological experiment (or disease), as well as the creation of diverse combination of pathway networks generated by PathExNET, is expected to provide a concrete contribution towards the individualization of disease, and further lead to a more precise personalised medicine and management of treatment. PathExNET is available at: https://bioinformatics.cing.ac.cy/PathExNET and at https://pathexnet.cing-big.hpcf.cyi.ac.cy/.

Surgical Management of Postradiation, Dropped Head Spinal Deformity in Patients with Head and Neck Cancer.

BACKGROUND: Dropped head syndrome is a morbid condition that affects daily functionality, causing pain and dysphagia and respiratory compromise. Reported causes of dropped head syndrome include neuromuscular disorders, iatrogenic from cervical spine surgery, and idiopathic and postradiation for head and neck cancers. Management of this spinal disorder remains challenging, as the complication rates are high. We present our series of 7 patients who underwent surgical correction of dropped head syndrome, all resulting from radiation for head and neck cancers. METHODS: This was a retrospective review of 7 patients who underwent surgery between 2016 and 2019 for dropped head syndrome secondary to postradiation cervical spine deformity. Clinical variables were obtained from medical records. Radiographic parameters pre- and postsurgery including T1 slope, sagittal vertical axis, and C2-C7 cervical lordosis were examined. RESULTS: Seven patients were included in the study, with an average age 69 years. Two patients underwent traction preoperatively. Five patients had posterior fixation and fusion only and 2 patients had a combined anterior and posterior fixation and fusion. Overall, there was improvement in average pre/postoperative sagittal vertical axis (6.96 cm to 3.04 cm), T1 slope (33.61° to 24.34°), and C2-C7 lordosis (-21.65° to -0.03°). CONCLUSIONS: Surgical correction of postradiation dropped head spinal deformity involving anterior and posterior fixation with osteotomies provides improvement in functional and radiographic outcomes as shown in our series. These cases are technically challenging and have a high rate of perioperative complications. Approaches must be tailored to the patient with attention to their specific surgical and radiation history.

Training volume and amateur cyclists' health: a six-month follow-up from coinciding with a high-demand cycling event.

This study aimed to analyse the longitudinal association of amateur cycling training volume with health by comparing the proximity of participation in a high-demand cycling event. Variations in cycling training volume, behavioural cardiometabolic risk factors, and physical and psychosocial health were examined. Cyclists decreased their training volume by approximately 40% and their total physical activity volumes by approximately 20%, while controls maintained (~5%). A time*group interaction was found for men's physical conditioning, body mass index and anxiety and, independent of gender, for behavioural cardiometabolic risk factors. Variation in cycling training volume was positively correlated with variation in physical conditioning and total physical activity and negatively correlated with variation in body mass index. The high level of cycling training volume developed at the time coinciding with a high demand cycling event predisposes to better physical health and behavioural cardiometabolic risk factors, without negatively affect psychosocial health, compared with six month later.

Expression Atlas update: from tissues to single cells.

Expression Atlas is EMBL-EBI's resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.

Infundibular Epidermoid Cyst: Case Report and Systematic Review.

BACKGROUND: Intracranial epidermoid cysts are benign, congenital, keratinizing, squamous epithelial-lined cysts filled with keratin. They are uncommon and often pose a surgical challenge owing to the adherence to surrounding structures. They are typically found at the cerebellopontine angle or in the parasellar region, where they are associated with abnormal development of the Rathke pouch; involvement of the pituitary stalk is rare. CASE DESCRIPTION: The patient's electronic health record was queried for relevant data. A systematic review of the literature using dedicated search terms for cases of infundibular epidermoid cysts was conducted. We present a unique case of a 55-year-old male who presented with vision changes and was found to have a parasellar epidermoid cyst confined to the pituitary stalk. The patient underwent endoscopic transsphenoidal resection, and gross total resection was achieved. The patient's postoperative course was significant for possible chemical meningitis and the development of panhypopituitarism. The patient's vision subjectively improved after surgery. CONCLUSIONS: Although 3 other cases of epidermoid cysts involving the pituitary stalk were identified, our patient's tumor was unique in that it was confined to the stalk. Our patient's case highlights a surgical approach to parasellar epidermoid cysts and the possible complications associated therewith.

Pyrocarbon arthroplasty in acute unreconstructable radial head fractures: mid-term to long term results.

BACKGROUND: The aim of this study is to describe the mid-term radiological findings appearing in patients with a pyrocarbon radial head prosthesis, and to correlate them to patient symptoms. MATERIALS AND METHODS: We review 18 patients who underwent radial head implantation of the MoPyC prosthesis between 2004 and 2015, due to unreconstructible radial head fractures. The clinical outcomes were assessed with Mayo Elbow Performance Score (MEPS). Range of motion, pain, and elbow radiological assessments were recorded. A non-parametric, statistical analysis was carried out to assess the radiological findings with the clinical outcomes. RESULTS: We have found that after a mean follow-up of 6.5 years (2-11 years), patients have recovered a median flexion arch of 113°, therefore 77% are classed as satisfactory outcomes and the average MEPS score is 89.5. The presence of periprosthetic changes on X-ray is highly frequent-we found radiolucent lines in 38% of cases, radial neck re-absorption in 83%, and arthrosic changes in 78%. However, the differences found when correlating these changes with the clinical results have not been statistically significant (p > 0.05). CONCLUSIONS: Satisfactory outcomes can be expected midterm when using pyrocarbon prostheses in around 75% of the cases. We consider radial neck re-absorption to be a sign of good stem osteointegration, whereas progressive radiolucencies and loss of the ballooning of the stem legs are signs of bad prognosis in our series. LEVEL OF EVIDENCE: IV retrospective case series.

Expression Atlas: gene and protein expression across multiple studies and organisms.

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.

Plant Reactome: a resource for plant pathways and comparative analysis.

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.

Open Targets: a platform for therapeutic target identification and validation.

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org.

[Adherence to the Mediterranean diet in inactive adults, indoor cycling practitioners and amateur cyclists]. / Adherencia a la dieta mediterránea en adultos inactivos, practicantes de ciclo indoory ciclistas aficionados.

INTRODUCTION: There is limited information referred to the relationship between adherence to the Mediterranean Diet (AMD) and sports practice. OBJECTIVE: To determinate the association of cycling practice and cycling training volume with the AMD and the influence of the participation in a high-demand cyclist event on the AMD. MATERIAL AND METHODS: A first evaluation of AMD in 785 (84 women) amateur cyclists (volume: ≥ 7 hours/week), 514 (224 women) indoor cycling practitioners (volume: 2-6 hours/week) and 718 (411 women) inactive adults was conducted in May coinciding with the participation of cyclists in a cycling event. A subsample of 359 cyclists and 148 inactive subjects agreed to be retested in November, far from the cycling event date. The MEDAS-14 questionnaire was used to assess the AMD and a self-designed questionnaire was used to assess the volume of training. RESULTS: 40% of subjects showed high AMD. In both sexes, athletes showed higher AMD than inactive subjects, with the highest indexes for groups of cyclists (p < 0.001). The relationship between AMD and training volume was weak (men: r = 0.137, women: r = 0.173; p < 0.001). The AMD of cyclists decreased from May to November (p < 0.001) with no significant changes in inactive subjects (p = 0.535). CONCLUSIONS: Cycling is associated to higher values of AMD with a limited influence of training volume and transient positive effects of participation in a cycling endurance event.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.

Tumor de testículo enmascarado por una orquiepididimitis: presentación de un caso / Tumor of the testicle masked by an orchiepididymitis.: a case report

Paciente masculino, de la raza blanca, de 26 años de edad, que acude a la consulta externa de urología del Hospital General Docente «Abel Santamaría Cuadrado¼ en Pinar del Río, con un dolor en el testículo derecho y un aumento de volumen, aproximadamente dos año de evolución; fue tratado en múltiples ocasiones por el diagnóstico de orquiepididimitis, recibiendo tratamiento con antibióticos (ciprofloxacina, amoxicilina ) sin respuesta al tratamiento, es visto nuevamente; al examen físico se comprueba un aumento de volumen del escroto derecho, doloroso a la palpación, constatándose una tumoración de aproximadamente 2 cm, dura e irregular, en la cara anterior, y la parte media e inferior de dicho testículo. Se realizan los exámenes de laboratorios, los cuales se encuentran en rangos normales, además, ultrasonografía testicular donde se describe una tumoración de baja ecogenicidad que corresponde con el tumor sospechado, realizándose un tratamiento quirúrgico (orquiectomia derecha con ligadura alta del cordón) y biopsia, resultando ser un seminoma clásico. Actualmente asintomático.

A 26 year-old male, Caucasian patient came to the Urology Clinic at "Abel Santamaria Cuadrado" University Hospital in Pinar del Rio, complaining of a pain in the right testicle and an increase in its volume during two years of evolution approximately; the patient was treated several times having the diagnosis of orchiepididymitis, and underwent antibiotic therapy (ciprofloxacin, amoxicillin) without response, the patient was re-evaluated; physical examination corroborated an increase in the volume of the right testicle finding a tender, firm and irregular tumor of 2 cm approximately located in the anterior face and half-inferior part of such testicle. Laboratory tests showed normal ranges, the sonographic studies described a tumor of low echogenicity in correspondence with the suspected tumor in the testicle; surgical removal and biopsy were performed (right orchiectomy with upper ligature of the cord); which resulted in a classic seminoma, currently asymptomatic.

Reflujo vesico-ureteral primario. Tratamiento quirúrgico / Primary vesico- uretral reflux. A surgical procedure

En esta investigación se analiza el tratamiento quirúrgico empleado en los pacientes de edad pediátrica de la provincia de Pinar del Río en el período comprendido entre el 1ro de enero del 1995 al 31 de diciembre de 2005. Se registraron todos los pacientes que fueron atendidos en este período en el Policlínico de Especialidades Pediátricas de dicha provincia, los cuales requerían tratamiento quirúrgico. Se realizó un estudio longitudinal, descriptivo, retrospectivo. Los datos se expresan en tablas; determinando Chi cuadrado con un nivel de significación de 0.05. Se encontró como principales resultados que los pacientes que recibieron tratamiento quirúrgico fueron los del sexo femenino y de la raza blanca; todos en su mayoría con alteración en la gammagrafía renal y urograma descendente; en su generalidad hubo un predominio del reflujo vesico-ureteral en su forma bilateral, la técnica quirúrgica que más se empleó fue la de Cohen y más del 80% de los pacientes fueron curados al año del tratamiento quirúrgico.

In this investigation the surgical procedure used in pediatric-age patients in Pinar delRío province was analysed from January 1, 1995 to Dcember 31st. 2005. All patients being assisted during this period at Pediatric Out-patient Clinic were recorded, and all of them underwent a surgical procedure. A longitudinal, descriptive retrospective study was carried out. Data are expressed in Tables determining chi-square test with a significance level of 0,05. It was remarkable that those who received surgical procedure were females and white, having most of them a disorder in the renal scintigram and a descending urogram, a prevalence of bilateral vesico-ureteral reflux was observed generally, and the Cohen technique was the most used, and more than 80% of patients were healed 1 year after the surgical procedure.

Accidentes urológicos en gineco-obstetricia. Pinar del Río. 2001-2004 / Urologic accidents in gynecology and obstetrics

La cirugía ginecológica es la causa mas frecuente de accidentes urológicos en los Estados Unidos y en muchos otros países desarrollados en el mundo y la vejiga es el sitio más común de lesión del tractus urinario durante la cirugía ginecológica. En Gineco-obstetricia se cometen varios accidentes quirúrgicos que se convierten posteriormente en patologías urológicas que para su resolución la mayoría tienen que ser a través del acto quirúrgico. Se realizó un estudio longitudinal retrospectivo de enero del 2001 a diciembre del 2004 de todas las pacientes que habían sido atendidos en el servicio de Urología General del Hospital Universitario Abel Santamaría Cuadrado de la provincia de Pinar del Río por presentar patologías urológicas producto a intervenciones Gineco-obstétricas. Los resultados fueron expresados en tablas y a las mismas se le aplico Chi Cuadrado. Encontrando como principales resultados las fístulas vesico-vaginales como las principales patologías accidentales en histerectomías abdominales y vaginales, la ubicación de las fístulas eran a nivel post-trigonal, la mayoría se repararon a través de la fistelectomia abdominal con muy pocas complicaciones post-quirúrgicas.

The gynecological surgery is the most frequent cause of urologic insults in the United Status and in many other developed countries in the world and the bladder is the most common site of insults in the urinary tract during gynecological surgical procedure. During the procedure several surgical insults take place which will further become urologic pathologies whose solution is only posible through surgery. A longitudinal and retrospective study was carried out, from January 2001 to December 2004, with all the patients being assisted by the General Urologic Department at Abel Santamaría Cuadrado University Hospital in Pinar del Río Province. These patients had urologic pathologies because of gyneco-obstetric surgical procedures. Results were shown in tables and these tables were applied chi-square test. The main results included vesico-vaginal fistulas as the chief pathological insults in vaginal and abdominal hysterectomies. The location of the fistulas were at post trigonal level, most of them were restored through abdominal fistulectomy with very rare post-surgical uneventful experiences.