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Abstract Background Coronary artery obstruction after percutaneous aortic replacement is a complication with high short-term mortality secondary to the lack of timely treatment. There are various predictors of coronary obstruction prior to valve placement such as the distance from the ostia, the degree of calcification, the distance from the sinuses; In such a situation some measures must be taken to prevent and treat coronary obstruction. Case presentation An 84-year-old male, with severe aortic stenosis and high surgical risk, who was treated with TAVR. However, during the deployment of the valve he presented hemodynamic instability secondary to LMCA obstruction. The intravascular image showed obstruction of the ostium secondary to the displacement of calcium that he was successfully treated with a chimney stent technique. Conclusions The high degree of calcification and the left ostium near the annulus are conditions for obstruction of the ostium at the time of valve release; In this context, provisional stenting prior to TAVR in patients at high risk of obstruction should be considered as a safe prevention strategy to achieve the success of the procedure.

El párpado es una estructura crítica para la protección y función del globo ocular, y parte primordial en la estética facial. Su reconstrucción está determinada por la extensión de la lesión y el compromiso de las diferentes capas. Siempre se preferirán tejidos loco-regionales debido a su mayor similitud y disposición. Los métodos de reanimación palpebral se pueden dividir en estáticos y dinámicos, considerando a estos últimos como el único medio para restaurar el parpadeo. Presentamos un caso de celulitis orbitaria preseptal con lesión de espesor total del párpado superior y su reconstrucción miofuncional utilizando un colgajo frontal. Este colgajo frontal miocutáneo logró la restauración funcional del párpado comprometido mediante la adición de fibras musculares y permitiendo el fenómeno de reinervación.

The moisture content variations in wood have a significant influence in wood’s physicochemical properties, as well as in its electromagnetic properties and to specific effects upon waves’ characteristics. In particular, this paper focuses on the analysis of the Ground-penetrating Radar’s (GPR) using an antenna of 1.6GHz central frequency capacity to register the velocity and the amplitude of the electromagnetic waves’ variation during the drying process of Pinus pinaster Ait timber joists. The results showed that when timber MC descends, the propagation velocity and amplitude of both the direct and the reflected wave increased. The high correlation found between the variables studied demonstrates GPR efficiency and the innovative application of this technique as a non-destructive evaluation tool for timber structures, particularly when studying its moisture content.

The influence of aerosols, both natural and anthropogenic, remains a major area of uncertainty when predicting the properties and behaviour of clouds and their influence on climate. In an attempt to better understand warm cloud formation in a tropical marine environment, a period of intensive measurements took place in December 2004 in Puerto Rico, using some of the latest developments in online instrumentation such as aerosol mass spectrometers, cloud condensation nuclei counters and a hygroscopicity tandem differential mobility analyser. Simultaneous online measurements of aerosol size distributions, composition, hygroscopicity and optical properties were made near the lighthouse of Cape San Juan in the north-eastern corner of the island and at the top of East Peak mountain (1040 m a.s.l.), the two sites separated by 17 km. Additional measurements of the cloud droplet residual and interstitial aerosol properties were made at the mountain site, accompanied by measurements of cloud droplet size distributions, liquid water content and the chemical composition of cloud and rain water samples. Both aerosol composition and cloud properties were found to be sensitive to wind sector. Air from the east-northeast (ENE) was mostly free of anthropogenic influences, the submicron fraction being mainly composed of non-sea salt sulphate, while that from the east-southeast (ESE) was found to be moderately influenced by populated islands upwind, adding smaller (−3, median volume diameter decreased from 20 to 14 μm and the liquid water content increased from 0.24 to 0.31 g m−3 when the winds shifted from the ENE to ESE. Larger numbers of interstitial particles were recorded, most notably at sizes greater than 100 nm, which were absent during clean conditions. The average size of the residual particles and concentrations of cloudwater nitrate, sulphate and insoluble material increased during polluted conditions. Previous studies in Puerto Rico had reported the presence of a significant non-anthropogenic organic fraction in the aerosols measured and concluded that this was a factor controlling the in situ cloud properties. However, this was not observed in our case. In contrast to the 1.00±0.14 μg m−3 of organic carbon measured in 1992 and 1995, the organic matter measured in the current study of 0.17±0.35 μg m−3 is many times lower, most of which can be attributed to anthropogenic sources. During clean conditions, the submicron aerosol was observed to be almost entirely inorganic, an observation supported by the hygroscopicity measurements. This suggests that organic aerosols from marine sources may not be completely ubiquitous (either spatially or temporally) in this environment and requires further investigation to quantify their true extent and implications, with more extensive, longer-term sampling in conjunction with wind field analyses.

Background: While sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack sufficient tools and methods that allow for an in-depth analysis of sex as a variable in biomedical research. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness., Description: MetaFun is a complete suite that allows the analysis of transcriptomics data and the exploration of the results at all levels, performing single-dataset exploratory analysis, differential gene expression, gene set functional enrichment, and finally, combining results in a functional meta-analysis. Which biological processes, molecular functions or cellular components are altered in a common pattern in different transcriptomic studies when comparing male and female patients? This and other biological questions of interest can be answered with the use of MetaFun. This tool is available at https://bioinfo.cipf.es/metafun while additional help can be found at https://gitlab.com/ubb-cipf/metafunweb/-/wikis/Summary ., Conclusions: Overall, Metafun is the first open-access web-based tool to identify consensus biological functions across multiple transcriptomic datasets, helping to elucidate sex differences in numerous diseases. Its use will facilitate the generation of novel biological knowledge that can be used in the research and application of Personalized Medicine considering the sex of patients., (© 2024. The Author(s).)

Objective: To study the suitability of costsensitive ordinal artificial intelligence-machine learning (AIML) strategies in the prognosis of SARS-CoV-2 pneumonia severity., Materials & Methods: Observational, retrospective, longitudinal, cohort study in 4 hospitals in Spain. Information regarding demographic and clinical status was supplemented by socioeconomic data and air pollution exposures. We proposed AI-ML algorithms for ordinal classification via ordinal decomposition and for cost-sensitive learning via resampling techniques. For performance-based model selection, we defined a custom score including per-class sensitivities and asymmetric misprognosis costs. 260 distinct AI-ML models were evaluated via 10 repetitions of 5×5 nested cross-validation with hyperparameter tuning. Model selection was followed by the calibration of predicted probabilities. Final overall performance was compared against five well-established clinical severity scores and against a 'standard' (non-cost sensitive, non-ordinal) AI-ML baseline. In our best model, we also evaluated its explainability with respect to each of the input variables., Results: The study enrolled n = 1548 patients: 712 experienced low, 238 medium, and 598 high clinical severity. d = 131 variables were collected, becoming d ' = 148 features after categorical encoding. Model selection resulted in our best-performing AI-ML pipeline having: a) no imputation of missing data, b) no feature selection (i.e. using the full set of d ' features), c) 'Ordered Partitions' ordinal decomposition, d) cost-based reimbalance, and e) a Histogram-based Gradient Boosting classifier. This best model (calibrated) obtained a median accuracy of 68.1% [67.3%, 68.8%] (95% confidence interval), a balanced accuracy of 57.0% [55.6%, 57.9%], and an overall area under the curve (AUC) 0.802 [0.795, 0.808]. In our dataset, it outperformed all five clinical severity scores and the 'standard' AI-ML baseline., Discussion & Conclusion: We conducted an exhaustive exploration of AI-ML methods designed for both ordinal and cost-sensitive classification, motivated by a real-world application domain (clinical severity prognosis) in which these topics arise naturally. Our model with the best classification performance exploited successfully the ordering information of ground truth classes, coping with imbalance and asymmetric costs. However, these ordinal and cost-sensitive aspects are seldom explored in the literature.

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that appears in adult FMR1 premutation carriers. The neuropathological hallmark of FXTAS is an intranuclear inclusion in neurons and astrocytes. Nearly 200 different proteins have been identified in FXTAS inclusions, being the small ubiquitin-related modifier 2 (SUMO2), ubiquitin and p62 the most highly abundant. These proteins are components of the protein degradation machinery. This study aimed to characterize SUMO2/3 expression levels and autophagy process in human postmortem brain samples and skin fibroblast cultures from FXTAS patients. Results revealed that FXTAS postmortem brain samples are positive for SUMO2/3 conjugates and supported the idea that SUMO2/3 accumulation is involved in inclusion formation. Insights from RNA-sequencing data indicated that SUMOylation processes are significantly upregulated in FXTAS samples. In addition, the analysis of the autophagy flux showed the accumulation of p62 protein levels and autophagosomes in skin fibroblasts from FXTAS patients. Similarly, gene set analysis evidenced a significant downregulation in gene ontology terms related to autophagy in FXTAS samples. Overall, this study provides new evidence supporting the role of SUMOylation and autophagic processes in the pathogenic mechanisms underlying FXTAS.

Blood sampling in rodents is common practice in scientific studies. Some of the refined methods widely used are the puncture of the saphenous vein or tail vein, or even tail docking. The handling needs of these different blood sampling methods are different and can directly affect stress, increasing the variability of the study. Moreover, there is less aversion and stress if the animal is accustomed to the environment, handling and technique. Therefore, our study aimed to assess the influence of these three blood sampling techniques (saphenous puncture, tail vein puncture and tail vein docking) and the use of previous acclimation on different indicators of animal stress, assessing blood glucose concentrations and faecal corticosterone metabolites (FCMs). Twenty-four young adult male and female C57Bl6/J mice were divided in three groups by sampling method: tail docking (TD), saphenous vein puncture (SV) and caudal vein puncture (CV) groups. All mice were studied with and without acclimation, which was performed during 9 consecutive days. The results showed that both males and females present very similar responses to the different handling and sampling methods without significant differences. Nevertheless, acclimation in all sampling methods decreased glucose and FCM levels significantly. The method that obtained the lowest glucose and FCM levels with significance was saphenous vein puncture. Therefore, we can say that it causes less stress when performing prior acclimation, even when this involves greater handling of the animal. Our results contribute to refinement within the 3R concept and could serve researchers to programme and select a good handling technique and a welfare-friendly blood sampling method for their experiments.

Background: As the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable., Methods: In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues (AT) of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the expression stability of all genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes (suHKG) suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to identify any sexual dimorphisms in mRNA expression stability in AT and to properly validate potential candidates., Results: Just above half of the considered studies informed properly about the sex of the human samples, however, not enough female mouse samples were found to be included in this analysis. We found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. We propose a suHKG signature including experimentally validated classical HKG like PPIA and RPL19 and novel potential markers for human AT and discarding others like the extensively used 18S gene due to a sex-based variability display in adipose tissue. Orthologs have also been assayed and proposed for mouse WAT suHKG signature. All results generated during this study are readily available by accessing an open web resource ( https://bioinfo.cipf.es/metafun-HKG ) for consultation and reuse in further studies., Conclusions: This sex-based research proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB., (© 2023. The Author(s).)

Background: There is an inverse association between cardiorespiratory fitness and general anxiety levels in adolescents. Obesity also is associated with a higher risk of anxiety in this population. However, little is known about the association between other health-related fitness elements with anxiety symptoms in this population. The authors explored the relationship between health-related fitness and anxiety symptoms in a large sample of Brazilian youth., Methods: This was an observational cross-sectional study with a sample comprised of 257 school adolescents, who were 136 girls (52.9%) and 121 boys (47.1%). The health-related fitness elements were evaluated by FitnessGram® test and anxiety levels by Multidimensional Anxiety Scale for Children - 39. Hierarchical regression analyses were used to determine the association between health-related fitness elements and anxiety symptoms in both sexes., Results: In male adolescents, only the cardiorespiratory fitness was significantly associated with anxiety symptoms ( F (1, 119) = 6.472; P = 0.012; R 2 = 0.052; adjusted R 2 = 0.044). In turn, the anxiety symptoms showed an inverse small relationship with cardiorespiratory fitness ( r = - 0.227; P < 0.01). However, in female adolescents, no association was found between health-related fitness elements and anxiety symptoms., Conclusion: The level of cardiorespiratory fitness may represent a marker of anxiety in male adolescents., Competing Interests: Eric Murillo-Rodriguez is Editorial Advisory Board of Clinical Practice & Epidemiology in Mental Health Antonio Egidio Nardi is Editorial Advisory Board of Clinical Practice & Epidemiology in Mental Health Sergio Machado is Editorial Advisory Board of Clinical Practice & Epidemiology in Mental Health, (© 2022 Legey et al.)

The objective of this study is to describe the alterations occurring during the neurodegenerative process in skin fibroblast cultures from C9orf72 patients. We characterized the oxidative stress, autophagy flux, small ubiquitin-related protein SUMO2/3 levels as well as the mitochondrial function in skin fibroblast cultures from C9orf72 patients. All metabolic and bioenergetic findings were further correlated with gene expression data obtained from RNA sequencing analysis. Fibroblasts from C9orf72 patients showed a 30% reduced expression of C9orf72, ~3-fold increased levels of oxidative stress and impaired mitochondrial function obtained by measuring the enzymatic activities of mitochondrial respiratory chain complexes, specifically of complex III activity. Furthermore, the results also reveal that C9orf72 patients showed an accumulation of p62 protein levels, suggesting the alteration of the autophagy process, and significantly higher protein levels of SUMO2/3 ( p = 0.03). Our results provide new data reinforcing that C9orf72 cells suffer from elevated oxidative damage to biomolecules and organelles and from increased protein loads, leading to insufficient autophagy and an increase in SUMOylation processes.

Objective: To determine the molecular functions of genes exhibiting altered expression in the endometrium of women with uterine disorders affecting fertility., Design: Retrospective analysis integrating case and control data from multiple cohorts with endometrium gene expression in women with uterine disorders., Setting: Infertility research department affiliated with a university hospital., Patient(s): Two hundred and forty women, 121 of whom were controls, 119 of whom had endometrial adenocarcinoma (ADC), recurrent implantation failure (RIF), recurrent pregnancy loss (RPL), or stage II-IV endometriosis., Intervention(s): None., Main Outcome Measure(s): Genomewide gene expression and altered molecular functions in the endometrium of each uterine disorder., Result(s): Using robust analysis methods, we identified statistically significantly altered endometrial functions in all the uterine disorders. Cell cycle alterations were shared among all the pathologies investigated. Endometriosis was characterized by the down-regulation of ciliary processes. Among the endometriosis, ADC, and RIF samples, mitochondrial dysfunction and protein degradation were shared dysregulated processes. In addition, RPL had the most distinct functional profile, and 95% of affected functions were down-regulated., Conclusion(s): The most robust functions dysregulated in the endometrium of patients with uterine disorders across sample cohorts implicated an endometrial factor at the gene expression level. This shared endometrial factor affects endometrial receptivity processes., (Copyright © 2020 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.)

Coronary trifurcation lesions are a complex subset of lesions and are substantially more complex than bifurcations when treated with percutaneous coronary intervention (PCI) because of higher rates of acute periprocedural complications (dissection, myocardial infarction, acute vessel closure) and less effective long-term outcomes (stent thrombosis, restenosis) as compared to non-bifurcation lesions. We present the case of a 73-year-old man who was admitted to our hospital with symptomatic severe aortic stenosis who was found to have a distal left main trifurcation disease as well as porcelain aorta on work-up. Given the high risk of stroke during surgical aortic valve replacement and coronary artery bypass grafting, the patient was accepted by the heart team to proceed with percutaneous coronary intervention (PCI) and trans-catheter aortic valve replacement (TAVR). We describe a successful double mini-crush stenting technique approach for this case., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Congenital disorders of glycosylation (CDG) are a heterogeneous and rapidly growing group of diseases caused by abnormal glycosylation of proteins and/or lipids. Mutations in genes involved in the homeostasis of the endoplasmic reticulum (ER), the Golgi apparatus (GA), and the vesicular trafficking from the ER to the ER-Golgi intermediate compartment (ERGIC) have been found to be associated with CDG. Here, we report a patient with defects in both N- and O-glycosylation combined with a delayed vesicular transport in the GA due to mutations in TRAPPC11, a subunit of the TRAPPIII complex. TRAPPIII is implicated in the anterograde transport from the ER to the ERGIC as well as in the vesicle export from the GA. This report expands the spectrum of genetic alterations associated with CDG, providing new insights for the diagnosis and the understanding of the physiopathological mechanisms underlying glycosylation disorders., (© 2016 WILEY PERIODICALS, INC.)

Motivation: Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.Here, we propose an enhanced methodology that builds on the well-established gene set analysis paradigm. Evidence for differential expression at the miRNA level is transferred to a gene differential inhibition score which is easily interpretable in terms of gene sets or pathways. Such transferred indexes account for the additive effect of several miRNAs targeting the same gene, and also incorporate cancellation effects between cases and controls. Together, these two desirable characteristics allow for more accurate modeling of regulatory processes., Results: We analyze high-throughput sequencing data from 20 different cancer types and provide exhaustive reports of gene and Gene Ontology-term deregulation by miRNA action., Availability and Implementation: The proposed methodology was implemented in the Bioconductor library mdgsa http://bioconductor.org/packages/mdgsa For the purpose of reproducibility all of the scripts are available at https://github.com/dmontaner-papers/gsa4mirna, Contact: : david.montaner@gmail.com, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press.)

Opitz C trigonocephaly (or Opitz C syndrome, OTCS) and Bohring-Opitz syndrome (BOS or C-like syndrome) are two rare genetic disorders with phenotypic overlap. The genetic causes of these diseases are not understood. However, two genes have been associated with OTCS or BOS with dominantly inherited de novo mutations. Whereas CD96 has been related to OTCS (one case) and to BOS (one case), ASXL1 has been related to BOS only (several cases). In this study we analyze CD96 and ASXL1 in a group of 11 affected individuals, including 2 sibs, 10 of them were diagnosed with OTCS, and one had a BOS phenotype. Exome sequences were available on six patients with OTCS and three parent pairs. Thus, we could analyze the CD96 and ASXL1 sequences in these patients bioinformatically. Sanger sequencing of all exons of CD96 and ASXL1 was carried out in the remaining patients. Detailed scrutiny of the sequences and assessment of variants allowed us to exclude putative pathogenic and private mutations in all but one of the patients. In this patient (with BOS) we identified a de novo mutation in ASXL1 (c.2100dupT). By nature and location within the gene, this mutation resembles those previously described in other BOS patients and we conclude that it may be responsible for the condition. Our results indicate that in 10 of 11, the disease (OTCS or BOS) cannot be explained by small changes in CD96 or ASXL1. However, the cohort is too small to make generalizations about the genetic etiology of these diseases., (© 2015 Wiley Periodicals, Inc.)

FMR1 premutation female carriers are at risk for Fragile X-associated primary ovarian insufficiency (FXPOI). Insights from knock-in mouse model have recently demonstrated that FXPOI is due to an increased rate of follicle depletion or an impaired development of the growing follicles. Molecular mechanisms responsible for this reduced viability are still unknown. In an attempt to provide new data on the mechanisms that lead to FXPOI, we report the first investigation involving transcription profiling of total blood from FMR1 premutation female carriers with and without FXPOI. A total of 16 unrelated female individuals (6 FMR1 premutated females with FXPOI; 6 FMR1 premutated females without FXPOI; and 4 no-FXPOI females) were studied by whole human genome oligonucleotide microarray (Agilent Technologies). Fold change analysis did not show any genes with significant differential gene expression. However, functional profiling by gene set analysis showed large number of statistically significant deregulated GO annotations as well as numerous KEGG pathways in FXPOI females. These results suggest that the impairment of fertility in these females might be due to a generalized deregulation of key signaling pathways involved in oocyte maturation. In particular, the vasoendotelial growth factor signaling, the inositol phosphate metabolism, the cell cycle, and the MAPK signaling pathways were found to be down-regulated in FXPOI females. Furthermore, a high statistical enrichment of biological processes involved in cell death and survival were found deregulated among FXPOI females. Our results provide new strategic approaches to further investigate the molecular mechanisms and potential therapeutic targets for FXPOI not focused in a single gene but rather in the set of genes involved in these pathways., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype-phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358&#95;359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Babelomics has been running for more than one decade offering a user-friendly interface for the functional analysis of gene expression and genomic data. Here we present its fifth release, which includes support for Next Generation Sequencing data including gene expression (RNA-seq), exome or genome resequencing. Babelomics has simplified its interface, being now more intuitive. Improved visualization options, such as a genome viewer as well as an interactive network viewer, have been implemented. New technical enhancements at both, client and server sides, makes the user experience faster and more dynamic. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a variety of tests for different experimental designs and (iii) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context. In addition to the public server, local copies of Babelomics can be downloaded and installed. Babelomics is freely available at: http://www.babelomics.org., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The striking similarity displayed at the mechanistic level between tumorigenesis and the generation of induced pluripotent stem cells and the fact that genes and pathways relevant for embryonic development are reactivated during tumor progression highlights the link between pluripotency and cancer. Based on these observations, we tested whether it is possible to use a pluripotency-associated transcriptional reporter, whose activation is driven by the SRR2 enhancer from the Sox2 gene promoter (named S4+ reporter), to isolate cancer stem cells (CSCs) from breast cancer cell lines. The S4+ pluripotency transcriptional reporter allows the isolation of cells with enhanced tumorigenic potential and its activation was switched on and off in the cell lines studied, reflecting a plastic cellular process. Microarray analysis comparing the populations in which the reporter construct is active versus inactive showed that positive cells expressed higher mRNA levels of cytokines (IL-8, IL-6, TNF) and genes (such as ATF3, SNAI2, and KLF6) previously related with the CSC phenotype in breast cancer.

Majocchi's granuloma is a persistent supurative folliculitis, associated with a deep granulomatous reaction induced by dermatophytes. There are two clinical forms of Majocchi's granuloma: the superficial form that appears in healthy individuals after localized trauma; and the nodular form, which occurs in inmunocompromised patients. We present a case of nodular Majocchi's granuloma on the forearm of an immunocompetent patient. Microbiological culture and examination of a deep aspiration sample identified Trichophyton rubrum. Collecting a deep sample of tissue is essential in achieving a good diagnostic performance.

Disease targeted sequencing is gaining importance as a powerful and cost-effective application of high throughput sequencing technologies to the diagnosis. However, the lack of proper tools to process the data hinders its extensive adoption. Here we present TEAM, an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient's variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD-public, HUMSAVAR, ClinVar and COSMIC.) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions. TEAM is freely available at: http://team.babelomics.org., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Whole-exome sequencing has become a fundamental tool for the discovery of disease-related genes of familial diseases and the identification of somatic driver variants in cancer. However, finding the causal mutation among the enormous background of individual variability in a small number of samples is still a big challenge. Here we describe a web-based tool, BiERapp, which efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research in Rare Diseases (CIBERER) in which more than 800 exomes have been analyzed. BiERapp is freely available at: http://bierapp.babelomics.org/, (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Germline mutations in CDKN2A and/or red hair color variants in MC1R genes are associated with an increased susceptibility to develop cutaneous melanoma or non melanoma skin cancer. We studied the impact of the CDKN2A germinal mutation p.G101W and MC1R variants on gene expression and transcription profiles associated with skin cancer. To this end we set-up primary skin cell co-cultures from siblings of melanoma prone-families that were later analyzed using the expression array approach. As a result, we found that 1535 transcripts were deregulated in CDKN2A mutated cells, with over-expression of immunity-related genes (HLA-DPB1, CLEC2B, IFI44, IFI44L, IFI27, IFIT1, IFIT2, SP110 and IFNK) and down-regulation of genes playing a role in the Notch signaling pathway. 3570 transcripts were deregulated in MC1R variant carriers. In particular, genes related to oxidative stress and DNA damage pathways were up-regulated as well as genes associated with neurodegenerative diseases such as Parkinson's, Alzheimer and Huntington. Finally, we observed that the expression signatures indentified in phenotypically normal cells carrying CDKN2A mutations or MC1R variants are maintained in skin cancer tumors (melanoma and squamous cell carcinoma). These results indicate that transcriptome deregulation represents an early event critical for skin cancer development.