A note on minimal resolutions of vector-spread Borel ideals

We consider vector-spread Borel ideals. We show that these ideals have linear quotients and thereby we determine the graded Betti numbers and the bigraded Poincaré series. A characterization of the extremal Betti numbers of such a class of ideals is given. Finally, we classify all Cohen-Macaulay vector-spread Borel ideals

A Multi-Cloud Warm-Absorber Model for NGC 4051

A multi-cloud model is presented which explains the soft X-ray excess in NGC 4051 and, consistently, the optical line spectrum and the SED of the continuum. The clouds are heated and ionized by the photoionizing flux from the active center and by shocks. Diffuse radiation, partly absorbed throughout the clouds, nicely fits the bump in the soft X-ray domain, while bremsstrahlung radiation from the gaseous clouds contribute to the fit of the continuum SED. Debris of high density fragmented clouds are necessary to explain the absorption oxygen throats observed at 0.87 keV and 0.74 keV. The debris are heated by shocks of about 200-300 km/s. Low velocity (100 km/s)-density (100 cm-3) clouds contribute to the line and continuum spectra, as well as high velocity (1000 km/s)-density (8000 cm-3) clouds which are revealed by the FWHM of the line profiles. The SED in the IR is explained by reradiation of dust, however, the dust-to-gas ratio is not particularly high. Radio emission is well fitted by synchrotron radiation created at the shock front by Fermi mechanism.Comment: 19 pages + 3 figures PostScrip

Identifying the oncogenic potential of gene fusions exploiting miRNAs

It is estimated that oncogenic gene fusions cause about 20% of human cancer morbidity. Identifying potentially oncogenic gene fusions may improve affected patients’ diagnosis and treatment. Previous approaches to this issue included exploiting specific gene-related information, such as gene function and regulation. Here we propose a model that profits from the previous findings and includes the microRNAs in the oncogenic assessment. We present ChimerDriver, a tool to classify gene fusions as oncogenic or not oncogenic. ChimerDriver is based on a specifically designed neural network and trained on genetic and post-transcriptional information to obtain a reliable classification. The designed neural network integrates information related to transcription factors, gene ontologies, microRNAs and other detailed information related to the functions of the genes involved in the fusion and the gene fusion structure. As a result, the performances on the test set reached 0.83 f1-score and 96% recall. The comparison with state-of-the-art tools returned comparable or higher results. Moreover, ChimerDriver performed well in a real-world case where 21 out of 24 validated gene fusion samples were detected by the gene fusion detection tool Starfusion. ChimerDriver integrates transcriptional and post-transcriptional information in an ad-hoc designed neural network to effectively discriminate oncogenic gene fusions from passenger ones. ChimerDriver source code is freely available at https://github.com/martalovino/ChimerDriver

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification

Metaplastic carcinoma with extensive dendritic cell differentiation: a previously unrecognised type of triple-negative breast cancer

The case of a metaplastic carcinoma of the breast exhibiting dendritic cell differentiation is described. The clinico-pathologic and immunohistochemical features are reported, together with the differential diagnosis

Correction to: inflammation is a target of medical treatment for lower urinary tract symptoms associated with benign prostatic hyperplasia

The article “Inflammation is a target of medical treatment for lower urinary tract symptoms associated with benign prostatic hyperplasia”, written by Cosimo De Nunzio, Andrea Salonia, Mauro Gacci and Vincenzo Ficarra was originally published electronically on the publisher’s internet portal on 14 February 2020 without open access

Inflammation is a target of medical treatment for lower urinary tract symptoms associated with benign prostatic hyperplasia

Purpose: To review the role of a persistent prostatic inflammatory status (PIS) in the development and progression of benign prostatic hyperplasia (BPH) associated with lower urinary tract symptoms (LUTS) and which medical therapies approved for LUTS/BPH may reduce persistent PIS. Methods: Literature search in PubMed up to July 2019. Results: The cause of histologically defined persistent PIS or chronic prostatic inflammation is multifactorial. It is evident in many men with LUTS/BPH, particularly in older men and in men with a large prostate volume or more severe (storage) LUTS. Additionally, persistent PIS is associated with an increased risk of acute urinary retention and symptom worsening. Of medical therapies approved for LUTS/BPH, the current evidence for a reduction of persistent PIS is greatest for the hexanic extract of Serenoa repens (HESr). This treatment relieves LUTS to the same extent as α1-adrenoceptor antagonists and short-term 5α-reductase inhibitors. Limited evidence is available on the effect of other mainstream LUTS/BPH treatments on persistent PIS. Conclusions: Persistent PIS plays a central role in both the development and progression of LUTS/BPH. In men with LUTS/BPH who have a high chance of harbouring persistent PIS, HESr will not only improve LUTS, but also reduce (underlying) inflammation. Well-designed clinical studies, with a good level of evidence, are required to better evaluate the impact of BPH/LUTS medical therapies on persistent PIS

A novel Gaussian fitting approach for 2D gel electrophoresis saturated protein spots

Analysis of 2D-GE images is a hot topic in bioinformatics research, since currently available commercial and academic software has proven to be not really effective and not completely automatic, often requiring manual revision of spots detection and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, it reveals overexposed areas where spots may be truncated, and plateau regions caused by smeared and overlapped spots. As next, the correct distribution of pixel values in the overexposed areas and plateau regions is recovered by a two-dimensional fitting based on a generalized Gaussian distribution approximating the spots volume. Pixel correction according to the generalized Gaussian curve in saturated and smeared spots allows more accurate quantifications, providing more reliable image analysis results. As validation, we process highly exposed 2D-GE image, containing saturate spots, with respect to the corresponding non-saturated image, confirming that the method can effectively fix the saturated spots and enable correct spots quantification