Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma.

Extensive genome-wide analyses of deregulated gene expression have now been performed for many types of cancer. However, most studies have focused on deregulation at the gene-level, which may overlook the alterations of specific transcripts for a given gene. Clear cell renal cell carcinoma (ccRCC) is one of the best-characterized and most pervasive renal cancers, and ccRCCs are well-documented to have aberrant RNA processing. In the present study, we examine the extent of aberrant isoform-specific RNA expression by reporting a comprehensive transcript-level analysis, using the new kallisto-sleuth-RATs pipeline, investigating coding and non-coding differential transcript expression in ccRCC. We analyzed 50 ccRCC tumors and their matched normal samples from The Cancer Genome Altas datasets. We identified 7,339 differentially expressed transcripts and 94 genes exhibiting differential transcript isoform usage in ccRCC. Additionally, transcript-level coexpression network analyses identified vasculature development and the tricarboxylic acid cycle as the most significantly deregulated networks correlating with ccRCC progression. These analyses uncovered several uncharacterized transcripts, including lncRNAs FGD5-AS1 and AL035661.1, as potential regulators of the tricarboxylic acid cycle associated with ccRCC progression. As ccRCC still presents treatment challenges, our results provide a new resource of potential therapeutics targets and highlight the importance of exploring alternative methodologies in transcriptome-wide studies

A Comparative Analysis of Southeastern States’ Income Tax Treatment of Exporters

Exporters are vital to the health of the U.S. economy as well as to individual state economies. As such, this study analyzes the export-related provisions of the southeastern states’ income tax laws and proposes tax policy changes that could potentially improve the tax environment for exporters while enhancing the overall economic environment in those states. In order to develop and support tax policy recommendations relating to state’s tax treatment of exporters, statistics that highlight the importance of exports to the domestic economy are reviewed. In addition, a summary of Federal tax law incentives available to exporters is provided along with several Treasury Department studies that estimate the impact the federal tax law incentives have had on the volume of exports. Also, key issues under state income tax laws regarding the treatment of export transactions are highlighted while providing a comparative analysis of the southeastern states’ treatment of export transactions using foreign sales corporations (FSC). The results of this study demonstrate not only that disparity among the southeastern states treatment of exporters exists, but also that the method used by state governments to tax FSCs could impact the extent to which corporations find it desirable to export their goods from a particular state. Based on these findings, the authors suggest the adoption of administrative pricing rules (similar to the rules in place for Federal tax purposes) for FSCs by states not currently allowing these rules, which would decrease the effective tax rate on export sales. The reduction in taxes could ultimately provide an incentive for domiciled corporations to increase exporting activities, contributing to increased domestic jobs and overall economic activity

Assessing conventional and organic citrus farming systems eco-efficiency: a metafrontier directional distance function approach using Life Cycle Analysis

[EN] In this paper, the eco‐efficiency of citrus farms operating under two different conventional and organic technological systems is analyzed. The methodology combines Life Cycle Analysis (LCA), to estimate the environmental impacts associated with the production process, and Data Envelopment Analysis(DEA) to estimate the position of each holding in relation to a frontier formed by the best farming practices. The use of the directional distance function concept allows us to calculate farms’eco‐efficiency scoring with respect to specific environmental impacts, and not only for the whole of them. The metafrontier concept is also used in order to compare the relative eco‐efficiency of each of the two cultivation technologies used. Our results show a wide superiority of the organic farming system in relation to the conventional. An eco‐efficient('green') organic technology represents, in relation to an eco‐efficient use of conventional citrus cultivation techniques, a potential reduction of environmental impacts by 80% without worsening economic performance. In contrast, when the performance of organic and conventional citrus farms is only analyzed in relation to best practices within each system, average eco-efficiency scores are similar for both types of farms.[ES] En este trabajo se analiza la eco-eficiencia de explotaciones citrícolas que operan bajo dos sistemas tecnológicos diferentes, convencional y orgánico. La metodología empleada combina el Análisis del Ciclo de Vida, para estimar los impactos ambientales vinculados al proceso de producción, y el Análisis Envolvente de Datos, para calcular la posición de cada explotación en relación a una frontera formada por las mejores prácticas observadas. Se hace uso del concepto de función distancia direccional, lo que permite estimar la eco-eficiencia con respecto a impactos ambientales concretos, y no sólo para el conjunto de todos ellos. Se emplea también el concepto de metafrontera, al objeto de comparar la eco-eficiencia relativa de cada una de las dos tecnologías empleadas. Los resultados obtenidos muestran una amplia superioridad del sistema de cultivo orgánico en relación al convencional. Un uso eco-eficiente de la tecnología orgánica ('ecológica') representa, en relación a un empleo eco-eficiente de las técnicas de la citricultura convencional, un potencial de reducción de los impactos ambientales del 80% sin empeorar los resultados económicos. En cambio, cuando el comportamiento de las explotaciones citrícolas orgánicas y convencionales se analiza solamente en relación a las mejores prácticas dentro de cada sistema los resultados medios en términos de eco-eficiencia son similares para ambos tipos de explotación.Beltrán Esteve, M.; Reig Martinez, E.; Estruch Guitart, V. (2015). Assessing conventional and organic citrus farming systems eco-efficiency: a metafrontier directional distance function approach using Life Cycle Analysis. Working Papers in Applied Economics. (1501):1-27. http://hdl.handle.net/10251/78996S127150

Progress of the development of a two-stage supersonic rocket within a student’s association

The Ares mission is part of a student-led project with the aim of developing a two-stage supersonic amateur rocket. This paper discusses the progress since its foundation in 2016 and how it is planned to continue progressing to achieve this objective. Currently, 4 rockets have been built and launched, evolving different aspects of the design and construction process in each one. From the Ares I, a two-stage rocket intended to test the electronics and the structure, the mission has evolved into designing the Phobos, a rocket whose aim is to compete in European Rocketry Challenges for universities. The final objective of the Ares Mission is to launch a two-stage supersonic rocket, the Ares II

Graphene derivative scaffolds facilitate in vitro cell survival and maturation of dopaminergic SN4741 cells

The emerging carbon nanomaterial Graphene (G), in the form of scaffold structure, has an efficient bioconjugation with common biomolecules and activates cell differentiation of neuronal stem cells, providing a promising approach for neural regeneration. We propose the use of G as a scaffold to re-address the dopaminergic (DA) neurons and the residual axons from dead or apoptotic DA neurons in Parkinson´s disease (PD). G could act as a physical support to promote the axonal sprout as a “deceleration” support for the DA cells derived from neural stem cells or DA direct cell conversion, allowing the propagation of nerve impulses. We cultured a clonal substantia nigra (SN) DA neuronal progenitor cell line (SN4741) in presence of G as scaffold. This cell line derived from mouse embryos was cultured in Dulbecco’s modified Eagle’s medium/10% FCS to about 80% confluence. Cells were incubated in three chemically different G derivatives and two different presentation matrixes as powder and films: 1) G oxide (GO); 2) partially reduced GO (PRGO) which is hydrophobic; and 3) fully reduced GO (FRGO). Cell viability was determined using the MTT assay after adding the following G concentrations: 1mg/ml; 0.1mg/ml; 0.05mg/ml; 0.02mg/ml and 0.01mg/ml, in each type of GO. To study cellular morphology and assessment of cell engraftment into GO films (GO film, PRGO film, FRGO film), we analyzed the immunostaining of the anti-rabbit neuron-specific DNA-binding protein (NeuN) antibody, the anti-rat Beta-3-tubulin antibody in combination with the mitochondrial marker mouse anti-ATP synthase antibody, and the anti-rabbit DCX as immature neuronal marker. Hoechst label was used as nuclei marker. Reactive oxidative species (ROS) were measured by flow cytometry to study the influence of G on the cell redox-state. With this purpose, cells were loaded with dihydroethidium. The mitochondrial membrane potential after JC-1 incubation was studied by flow cytometry. Our results show an increase of survival and metabolism (30-40%) at low concentrations of PRGO and FRGO (0.05-0.01 mg/ml) respect to the higher concentration (1 mg/ml), while no changes were seen in the GO group. LDH concentration was measured in the supernatant using a COBAS analyzer showing a neuroprotective action at low concentrations. Furthermore, either PRGO film or FRGO film show an increase in the effective anchorage capacity to nest into the G matrix and in the maturation of the SN 4741 cells. We conclude that the use of G scaffolds in the research of neurological diseases like PD could offer a powerful platform for neural stem cells, direct cell conversion techniques and neural tissue engineering.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Norwegian Research Council (grant nº 215086

Urinary Cytokines Reflect Renal Inflammation in Acute Tubulointerstitial Nephritis: A Multiplex Bead-Based Assay Assessment

Background: Acute tubulointerstitial nephritis (ATIN) diagnosis lays on histological assessment through a kidney biopsy, given the absence of accurate non-invasive biomarkers. The aim of this study was to evaluate the accuracy of different urinary inflammation-related cytokines for the diagnostic of ATIN and its distinction from acute tubular necrosis (ATN). Methods: We included 33 patients (ATIN (n = 21), ATN (n = 12)), and 6 healthy controls (HC). We determined the urinary levels of 10 inflammation-related cytokines using a multiplex bead-based Luminex assay at the time of biopsy and after therapy, and registered main clinical, analytical and histological data. Results: At the time of biopsy, urinary levels of I-TAC/CXCL11, CXCL10, IL-6, TNF alpha and MCP-1 were significantly higher in ATIN compared to HC. A positive correlation between the extent of the tubulointerstitial cellular infiltrates in kidney biopsies and the urinary concentration of I-TAC/CXCL11, MIG/CXCL9, CXCL10, IL17, IFN alpha, MCP1 and EGF was observed. Notably, I-TAC/CXCL11, IL-6 and MCP-1 were significantly higher in ATIN than in ATN, with I-TAC/CXCL11 as the best discriminative classifier AUC (0.77, 95% CI 0.57-0.95, p = 0.02). A combinatory model of these three urinary cytokines increased the accuracy in the distinction of ATIN/ATN compared to the individual biomarkers. The best model resulted when combining the three cytokines with blood eosinophil and urinary leukocyte counts (LR = 9.76). Follow-up samples from 11ATIN patients showed a significant decrease in I-TAC/CXCL11, MIG/CXCL9 and CXCL10 levels. Conclusions: Urinary I-TAC/CXCL11, CXCL10, IL6 and MCP-1 levels accurately distinguish patients developing ATIN from ATN and healthy individuals and may serve as novel non-invasive biomarkers in this disease

Estimating the atmospheric concentration of Criegee intermediates and their possible interference in a FAGE-LIF instrument

We analysed the extensive dataset from the HUMPPA-COPEC 2010 and the HOPE 2012 field campaigns in the boreal forest and rural environments of Finland and Germany, respectively, and estimated the abundance of stabilised Criegee intermediates (SCIs) in the lower troposphere. Based on laboratory tests, we propose that the background OH signal observed in our IPI-LIF-FAGE instrument during the aforementioned campaigns is caused at least partially by SCIs. This hypothesis is based on observed correlations with temperature and with concentrations of unsaturated volatile organic compounds and ozone. Just like SCIs, the background OH concentration can be removed through the addition of sulfur dioxide. SCIs also add to the previously underestimated production rate of sulfuric acid. An average estimate of the SCI concentration of ∼ 5.0 x 104 molecules cm−3 (with an order of magnitude uncertainty) is calculated for the two environments. This implies a very low ambient concentration of SCIs, though, over the boreal forest, significant for the conversion of SO2 into H2SO4. The large uncertainties in these calculations, owing to the many unknowns in the chemistry of Criegee intermediates, emphasise the need to better understand these processes and their potential effect on the self-cleaning capacity of the atmosphere

Spanish version of the Dundee Ready Education Environment Measure (DREEM) applied to undergraduate physical therapy students in Spain using Google Form

[Intro] The educational climate (EC) is an important factor in determining the effectiveness and success of the curriculum in a school of medical sciences. The Dundee Ready Education Environment Measure (DREEM) questionnaire was used to assess EC in a competency-based curriculum in the physical therapy program analyzing the mean total, subscale, and item scores, as well as response rates. To carry out a psychometric evaluation of the Spanish-language version of the DREEM applied to undergraduate physical therapy students, a total of 671 students enrolled on Degrees in Physiotherapy at 22 faculties across public and private universities in Spainresponded to the DREEM questionnaire using Google Form. (...