BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments

<p>Abstract</p> <p>Background</p> <p>It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gene. It is widely recognized that a breakdown in AS mechanisms plays an important role in cellular differentiation and pathologies. Polymerase Chain Reactions, microarrays and sequencing technologies have been applied to the study of transcript diversity arising from alternative expression. Last generation Affymetrix GeneChip Human Exon 1.0 ST Arrays offer a more detailed view of the gene expression profile providing information on the AS patterns. The exon array technology, with more than five million data points, can detect approximately one million exons, and it allows performing analyses at both gene and exon level. In this paper we describe BEAT, an integrated user-friendly bioinformatics framework to store, analyze and visualize exon arrays datasets. It combines a data warehouse approach with some rigorous statistical methods for assessing the AS of genes involved in diseases. Meta statistics are proposed as a novel approach to explore the analysis results. BEAT is available at <url>http://beat.ba.itb.cnr.it</url>.</p> <p>Results</p> <p>BEAT is a web tool which allows uploading and analyzing exon array datasets using standard statistical methods and an easy-to-use graphical web front-end. BEAT has been tested on a dataset with 173 samples and tuned using new datasets of exon array experiments from 28 colorectal cancer and 26 renal cell cancer samples produced at the Medical Genetics Unit of IRCCS Casa Sollievo della Sofferenza.</p> <p>To highlight all possible AS events, alternative names, accession Ids, Gene Ontology terms and biochemical pathways annotations are integrated with exon and gene level expression plots. The user can customize the results choosing custom thresholds for the statistical parameters and exploiting the available clinical data of the samples for a multivariate AS analysis.</p> <p>Conclusions</p> <p>Despite exon array chips being widely used for transcriptomics studies, there is a lack of analysis tools offering advanced statistical features and requiring no programming knowledge. BEAT provides a user-friendly platform for a comprehensive study of AS events in human diseases, displaying the analysis results with easily interpretable and interactive tables and graphics.</p

Stable Photocatalytic Paints Prepared from Hybrid Core-Shell Fluorinated/Acrylic/TiO2 Waterborne Dispersions

The contamination of air and water is one of the major concerns towards the development of a sustainable world in the 21st century. In this context many efforts are devoted to the design of photocatalytic paints able to degrade chemical and biological impurities present in air and water. In this work, the photocatalytic activity of hybrid films formed from the blends of pure acrylic or core/ shell fluorinated/ acrylic waterborne dispersions and photocatalytic titanium dioxide (TiO2) nanoparticle dispersions was first assessed. The films show photocatalytic activity (inactivation of the Escherichia coli bacteria under UV irradiation) at the substrate-film interface, but very reduced activity in the air-film interface due to the substantially lower amount of the TiO2 nanoparticles in the vicinity of this interface. In a second step, the fluorinated/(meth) acrylic core-shell hybrid dispersions were used as binders in the formulation of waterborne photocatalytic paints and the stability of the paints, in terms of gloss retain and color change, was assessed during 5000 hours of accelerated weathering tests (QUV-B). Although a decrease in gloss retention and increased color change occurs during the first 1000 hours of exposure, no further change of these properties takes place, which is an excellent indication of stable photocatalytic paints.Financial support from the European Union (Limpid project FP7NMP-2012-2.2-6-310177), Ministerio de Economia y Competitividad (MEC, Ref. CTQ2014-59016-P), the Basque Government (GV IT-303-10) and Gipuzkoako Foru Aldundia (EXP 55/14) is gratefully acknowledged. The SGIKER UPV/EHU for the electron microscopy facilities of the Gipuzkoa unit is also acknowledged. G.P. Leal is acknowledged for the SEM analysis. The Swiss National Science Foundation (SNF) Project No 200021-143283/1 is also gratefully aknowledged

Designing and implementing a multi-scalar approach to Maritime Spatial Planning: The case study of Italy

The Italian coastal and marine space includes areas with remarkable differences in terms of oceanographic characteristics, maritime uses, natural habitats, species distribution, landscape and cultural heritage. In Italy, coastal and marine management competencies are shared among national, regional, and for some aspects even local authorities. This geographic heterogeneity and governance complexity required the adoption of a multiscalar approach to Maritime Spatial Planning (MSP). Such an approach aims at implementing decision-making and spatial planning at multiple and nested scales. In the case of Italy, the multi-scalar approach included the definition of national guidelines and the development of three maritime spatial (MS) plans, one for each maritime area (Adriatic, Ionian and Central Mediterranean, and Tyrrhenian and Western Mediterranean), including subareas and nested planning units. The development of the MS plans involved competent Ministries, the coastal Regions and several researchers. Based on the description of the adopted six-phase methodology and the exemplification of results of the Italian MSP process, this paper discusses the most relevant features and common challenges of multi-scalar MSP (i.e. co-planning, vertical and horizontal integration, multi-level governance, scalability, flexibility, integration of data and knowledge with different resolution, multi-scalar stakeholder engagement). Finally, the paper reflects on some novel aspects of the adopted multi-scalar approach and identifies actions to grant efficacy to this approach during the next phases of the Italian MSP proces

JLB: a flexible and effective device in critical patients. Review of clinical cases

JLB catheter (Deltamed Inc) is an alternative way to manage difficult venous access; it is placed under US-guidance in large bore veins, with an easy-sterile approach. Internal jugular vein (IJV) is the first choice for cannulation, followed by subclavian or deep upper-arm veins. The catheter is available in different lengths and gauges, it allows high flow rates and can be left in place up to 30 days. From June 2015 to March 2017, JLB has been positioned in 409 patients: in 354 as primary access in IJV, brachial or subclavian vein; in 55 cases JLB became an introducing line for the Seldinger guidewire and further CVC positioning. All clinical cases were reviewed selecting those with greater clinical relevance. We report 8 cases in which JLB resulted determinant for the patient treatment: a 16 years old obese girl born with perinatal distress, a 78 years old obese woman with hemorrhagic shock caused by gastrointestinal bleeding, a 40 years old man with severe hypokalemia, a 30 years old man with severe sepsis, a 40 years old man with Becker’s muscular dystrophy and severe sepsis, a 40 years old man with multiple myeloma who had to carry out cycles of chemotherapy, a 76 years old man with CMV pancolitis and myelofibrosis who needed parenteral nutrition, antiviral therapy and frequent blood and platelets transfusion. Moreover, it has been useful in elderly patients who needed to carry out palliative care for seniority or cancer lasting up to 30 days . In our experience the JLB catheter is safe, easy to place, quick and cost –effective. It is a valid solution either in unstable patients requiring an immediate access in emergency and stable patients with difficult venous access, in which invasive devices can be considered an over-treatment

Effect of systemic therapies or best supportive care after disease progression to both nivolumab and cabozantinib in metastatic renal cell carcinoma: The Meet‐Uro 19BEYOND study

Background Nivolumab and cabozantinib are currently approved agents in metastatic renal cell carcinoma (mRCC) but there are no data available for patients progressing to both treatments. The aim of this study was to compare active therapeutic options and best supportive care (BSC) after progression to nivolumab and cabozantinib in mRCC. Methods In this retrospective study, we selected 50 patients from eight Italian centers. The primary endpoint of the study was the overall survival (OS) of patients on active treatment versus BSC. Secondary endpoints were the progression-free survival (PFS) and objective response rate (ORR). The efficacy of active therapy was also investigated. Results After progression to both nivolumab and cabozantinib, 57.1% of patients were given active treatment (mainly everolimus and sorafenib) while 42.9% received BSC. The median OS was 13 months (95% CI: 4-NR) in actively treated patients and 3 months (95% CI: 2–4) in BSC patients (p = 0.001). Patients treated with sorafenib had better disease control than those treated with everolimus (stable disease: 71.4% vs. 16.7%, progression disease: 14.3% vs. 58.3%; p = 0.03), with no significant differences in PFS (5 and 3 months, 95% CI: 1–6 vs. 2–5; p = 0.6) and OS (12 and 4 months, 95% CI: 3-NR vs. 2-NR; p = 0.2). Conclusion After treatment with both nivolumab and cabozantinib, the choice of a safe active systemic therapy offered better outcomes than BSC

Prednisone vs high-dose dexamethasone in newly diagnosed adult primary immune thrombocytopenia: a randomized trial

A debate exists regarding which type of corticosteroids (standard-dose prednisone [PDN] or high-dose dexamethasone [HD-DXM]) is the best first-line treatment for adult patients with newly diagnosed untreated primary immune thrombocytopenia (pITP). An ad hoc study compared PDN with HD-DXM in newly diagnosed untreated patients with pITP (aged &gt;= 18 but &lt;= 80 years, platelet count of &lt;= 20 or &gt;20 but &lt;50 x 10(9)/L, and bleeding score of &gt;= 8). Patients were randomised to receive PDN 1 mg/kg per day from days 0 to 28 (Arm A) or HD-DXM 40 mg per day for 4 days, every 14 days, for 3 consecutive courses (Arm B). Fifty-nine of 113 patients (52.2%) were randomized to Arm A and 54 of 113 (47.8%) to Arm B. In evaluable patients, total initial responses (complete response [CR], partial response [PR], minimal response [MR]) were 44 of 56 (78.57%) in Arm A and 46 of 49 (93.88%) in Arm B at days 42 and 46, respectively (P = 0.0284). Total final responses (at day 180 from initial response) were 26 of 43 (60.47%) in Arm A and 23 of 39 (58.97%) in Arm B (P = 0.8907). Total persistent responses (at 12 months from initial response) were 25 of 31 (80.65%) in Arm A and 20 of 36 (55.56%) in Arm B (P = 0.0292). Seven relapses occurred. Median follow-up was 44.4 months. Overall survival was 100% at 48 months, overall disease-free survival was 81.11% at 48 months from day 180. PDN and pulsed HD-DXM were well tolerated; HD-DXM allows effective initial responses but less long lasting than PDN. This trial was registered at www.clinicaltrials.gov as #NCT00657410

Convenio de cooperación CONAE-CNEA: desarrollo, fabricación y ensayo de paneles solares para misiones satelitales argentinas

Con el fin de proveer total o parcialmente los módulos fotovoltaicos para las futuras misiones satelitales previstas en el Plan Espacial Nacional, la Comisión Nacional de Actividades Espaciales (CONAE) y la Comisión Nacional de Energía Atómica (CNEA) suscribieron, en marzo de 2001, un Convenio Específico de colaboración cuyos objetivos son: (i) montaje de un laboratorio para la integración de paneles solares, (ii) diseño y elaboración de celdas solares de silicio cristalino, (iii) desarrollo de los procesos de interconexión de las celdas y su integración al panel solar, y (iv) identificación y/o montaje de laboratorios para ensayos. En este trabajo se describen las principales características del proyecto, el cual tendrá una duración de 36 meses, analizándose el estado actual de desarrollo de los diferentes temas. Asimismo, se presentan las características del área limpia diseñada para el laboratorio de integración.In order to supply in the future the power requirements (totally or partially) of missions programmed in the Argentine National Space Plan, the National Commission for Space Activities (CONAE) and the National Atomic Energy Commission (CNEA) signed in March 2001 a Cooperation Agreement for: (i) the installation of a clean room laboratory for the integration of solar panels, (ii) the design and fabrication of monocrystalline silicon solar cells, (iii) the development of the techniques associated with the interconnection of the solar cells and the integration of the solar panel, (iv) the identification or installation of testing facilities. The main goals of the project are presented and the activities being performed at present are analyzed. Moreover, the characteristics of the clean room facility are described.Asociación Argentina de Energías Renovables y Medio Ambiente (ASADES