Elastofibroma Dorsi

Se realiza un estudio clínico-patológico de dos casos, mujeres de 57 y 45 años, de "elastofibroma dorsi" intervenidos quirúrgicamente. En una enferma apareció como una tumoracion asintomática y en otra asociada a dolor en el hombro irradiado a miembro superior derecho. Se describen las particularizadas clínicas, las exploraciones complementarias, los hallazgos quirúrgicos y las características histológicas de estos tumores de partes blandas cuyo origen debe referirse a una alteración del tejido fibroelástico. Se confronta nuestra experiencia con los casos anteriormente publicados confirmándose su aparición en mujeres adultas o añosas dedicadas a trabajos manuales rutinarios, que parecen estar implicados en la patogenia del elastofibroma dorsi. En uno de los casos, aunque localizado en el espacio anatómico escápulo-torácico, su situación era supraescapular frente a la típicamente infraescapular del elastofibroma dorsi, y la consideramos la primera observación de la literatura.A clinical-pathological study of two cases of elastofibroma dorsi was carried out. Both patients were female, 57 and 45 years old, and underwent surgical operation. One patients was sympton-free, while the other complained of pain in the shoulder which spread to the upper right arm. The autors describe the clinical details, the diagnostic methods employed, the results of surgery and the histopathological features of these tumours which must have originated in a modification of conective tissue, especially in elastic fibres. We compare our findings with those of previously published cases and can confirm the appearence of these tumours in adults or middle-aged women who carry out rutinary manual work, which seems to be connected with the pathogeny of the elastofibroma dorsi. These are normally found adjacent to the vertebral border of the escapula at its inferior angle, but in one case ot was located in the supra-escapular region and we believe this is the first evidence of this kind in the literature

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewedThe authors would like to acknowledge support from the Spanish Ministry of Economy and Competitiveness through grants BIO2013-44647-R and BIO2016-76400-R (AEI/ FEDER, UE), Comunidad Autonoma de Madrid through grant S2017/BMD-3817, Instituto de Salud Carlos III through grants PT13 /0001/0009 and PT17/0009/0010,the European Union (EU) and Horizon 2020 through West-Life (EINFRA- 2015-1, Proposal 675858), CORBEL (INFRADEV-1-2014-1, Proposal 654248), ELIXIR–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and the National Institutes of Health (P41 GM 103712) (IB

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded

Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package

Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors

<div><p>Benign neurofibromas, the main phenotypic manifestations of the rare neurological disorder neurofibromatosis type 1, degenerate to malignant tumors associated to poor prognosis in about 10% of patients. Despite efforts in the field of (epi)genomics, the lack of prognostic biomarkers with which to predict disease evolution frustrates the adoption of appropriate early therapeutic measures. To identify potential biomarkers of malignant neurofibroma transformation, we integrated four human experimental studies and one for mouse, using a gene score-based meta-analysis method, from which we obtained a score-ranked signature of 579 genes. Genes with the highest absolute scores were classified as promising disease biomarkers. By grouping genes with similar neurofibromatosis-related profiles, we derived panels of potential biomarkers. The addition of promoter methylation data to gene profiles indicated a panel of genes probably silenced by hypermethylation. To identify possible therapeutic treatments, we used the gene signature to query drug expression databases. Trichostatin A and other histone deacetylase inhibitors, as well as cantharidin and tamoxifen, were retrieved as putative therapeutic means to reverse the aberrant regulation that drives to malignant cell proliferation and metastasis. This <i>in silico</i> prediction corroborated reported experimental results that suggested the inclusion of these compounds in clinical trials. This experimental validation supported the suitability of the meta-analysis method used to integrate several sources of public genomic information, and the reliability of the gene signature associated to the malignant evolution of neurofibromas to generate working hypotheses for prognostic and drug-responsive biomarkers or therapeutic measures, thus showing the potential of this <i>in silico</i> approach for biomarker discovery.</p></div

Chromosome distribution of the MPNST vs. NF gene signature.

<p>The gene signature distribution was calculated from the 336 genes with positive score <b>(a)</b>, and from the 243 genes with negative score <b>(b)</b>. Bar diagrams compare the observed distribution of MPNST vs. NF gene percentage in the human chromosome arms (dark bars) with the expected distribution according to the human ENSEMBL database (light bars). Statistical significance of the gene signature over-represented chromosome arms is above the bars. Over-represented human chromosome bands in the MPNST vs. NF gene signature are shown below each chart. Their statistical significance is shown at the top right side of band names. (****) P(X≥x) < 0.0001, (***) 0.0001< P(X≥x) < 0.001, (**) 0.001< P(X≥x) < 0.01, (*) 0.01< P(X≥x) < 0.05.</p

Clustering of phenotype comparisons and of NF1-related genes.

<p>Comparisons among MPNST, NF and control phenotypes were grouped through hierarchical clustering. Cell culture and nerve tumor comparisons are shown on the top of the upper dendrogram, and the node height scale is detailed on the left of this tree. The hierarchical relationship among gene clusters obtained by grouping the logFC_m values of 2209 NF1-related genes by the Self-Organizing Tree Algorithm (SOTA) is represented by the dendrogram on the left. Clusters are described by their SOTA centroid vectors. Color scale of logFC_m values is shown below. The right side of the Fig details the number of genes in each cluster, the gene number of the MPNST vs. NF signature in each cluster (*, > 15 genes), the percentage of genes of this signature in each cluster (grey scale shown below), the number of biological process GO terms over-represented in each cluster, and the summary of the GO term enrichment as functional characterization of clusters. A complete list of terms is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178316#pone.0178316.s009" target="_blank">S9 Table</a>.</p

Microarray studies selected from public databases and included in the MPNST vs. NF meta-analysis.

<p>Microarray studies selected from public databases and included in the MPNST vs. NF meta-analysis.</p

Prisma flow diagram.

<p>Prisma flow diagram.</p

List of 20 genes with the highest and the lowest scores of the MPNST vs. NF signature¹.

<p>List of 20 genes with the highest and the lowest scores of the MPNST vs. NF signature<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178316#t002fn001" target="_blank">¹</a>.</p