RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

Background & Objective Managing data from large-scale projects (such as The Cancer Genome Atlas (TCGA)) for further analysis is an important and time consuming step for research projects. Several efforts, such as the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data from the Firehouse, and demonstrate its use with sample case studies. Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data. The RTCGAToolbox can also be integrated with other analysis pipelines for further data processing. Availability and implementation The RTCGAToolbox is open-source and licensed under the GNU General Public License Version 2.0. All documentation and source code for RTCGAToolbox is freely available at http://mksamur.github.io/RTCGAToolbox/ for Linux and Mac OS X operating systems

Postojanost na trošenje i koroziju novih frikcijski postojanih materijala za automobilsku industriju

In this study, after a NiCr bond layer was deposited on a pearlitic, grey cast iron rotor disc of the kind used in a production passenger car (Toyota Corolla 1600 cc), Cr3C2-NiCr and Al2O3-TiO2powders were sprayed using High Velocity Oxygen Fuel(HVOF) and plasma spray processes, respectively. The discs were subjected to cosmetic corrosion test according to SAE J2334 test standard. Additionally, wear tests were carried out using a reciprocating wear tester by rubbing a 10 mm diameter Al2O3 ball on the specimens machined from rotor discs in salt solution. It was found that the Cr3C2-NiCr coating (HSCN) sprayed using HVOF method exhibited highest hardness and highest corrosion and wear resistances.Nakon nanošenja NiCr sloja na disk od sivog lijeva tipa koji se koristi u proizvodnji putničkog automobila (Toyota Corolla 1600 CC), Cr3C2-NiCr i Al2O3-TiO2 prašak je nanešen naštrcavanjem HVOF i plazma postupkom. Disk je izložen korozijskom ispitivanju sukladno standardu SAE J2334. Dodatno je provedeno ispitivanje na trošenje na testeru za uzajamno trošenje 10 mm zrna Al2O3 na uzorcima izrađenim iz rotacijskog diska u slanoj komori. Utvrđeno je da je Cr3C2-NiCr sloj (HSCN) naštrca HVOF postupkom pokazao veću tvrdoću i veću korozijsku postojanost i otpornost na koroziju

Increased DNA methylation in the parvalbumin gene promoter is associated with methamphetamine dependence

Aim: The parvalbumin (PV)-containing subgroup of GABAergic neurons is particularly affected in schizophrenia and animal models of psychosis, including after methamphetamine (METH) administration. We investigated whether METH dependence and METH-induced psychosis may involve an effect on DNA methylation of the PVALB promoter. Materials & methods: The methylation of a PVALB promoter sequence was determined in 100 METH-dependent and 102 control subjects using pyrosequencing. Results: A significant increase in PVALB methylation was observed in METH dependence and METH-induced psychosis. No significant effect on long interspersed nucleotide element-1 methylation, a measure of global DNA methylation, was observed. Conclusion: These results demonstrate a specific association between elevated PVALB methylation and METH-induced psychosis. This finding may contribute to the GABAergic deficits associated with METH dependence

An alternative synthesis method for di calcium phosphate (monetite) powders from mediterranean mussel (mytilus galloprovincialis) shells

Marine species, such as corals, sea shells and nacres, attract special interest in bioceramics field for bone graft, bone cements and drug delivery applications. Most of the marine structures are made up of pure calcium carbonate (calcite or aragonite) with a very small amount of an organic matrix. In the past the most common way to transform these structures to hydroxyapatite was hydrothermal transformation method. This current work introduces a new approach for producing fine powders of calcium phosphates from Mediterranean mussel (Mytilus galloprovincialis) shells. A comparative study was carried out to investigate the differences of these powders under only hot plate heating and hot plate heating together with ultrasonic agitation while H3PO4 was added. The temperature of the hotplate was kept constant at 80 degrees C and then, H3PO4 was added drop wise into the solution for 2 hrs. The mixture was then placed into an oven at 100 degrees C for 24 hrs. They were further calcined at 800 degrees C for 3 hrs. XRD, FTIR. and ICP-MS were used to identify the structure and composition. It was found that the final powders were predominantly monetite, with some tricalcium phosphate as a secondary phase. This relatively simple and efficient method can be easily applied to produce calcium phosphate precursor powders for a range of biomedical applications

canEvolve: A Web Portal for Integrative Oncogenomics

Background & objective: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need. Results: canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis. Conclusion: At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets

The shaping and functional consequences of the dosage effect landscape in multiple myeloma

Background: Multiple myeloma (MM) is a malignant proliferation of plasma B cells. Based on recurrent aneuploidy such as copy number alterations (CNAs), myeloma is divided into two subtypes with different CNA patterns and patient survival outcomes. How aneuploidy events arise, and whether they contribute to cancer cell evolution are actively studied. The large amount of transcriptomic changes resultant of CNAs (dosage effect) pose big challenges for identifying functional consequences of CNAs in myeloma in terms of specific driver genes and pathways. In this study, we hypothesize that gene-wise dosage effect varies as a result from complex regulatory networks that translate the impact of CNAs to gene expression, and studying this variation can provide insights into functional effects of CNAs. Results: We propose gene-wise dosage effect score and genome-wide karyotype plot as tools to measure and visualize concordant copy number and expression changes across cancer samples. We find that dosage effect in myeloma is widespread yet variable, and it is correlated with gene expression level and CNA frequencies in different chromosomes. Our analysis suggests that despite the enrichment of differentially expressed genes between hyperdiploid MM and non-hyperdiploid MM in the trisomy chromosomes, the chromosomal proportion of dosage sensitive genes is higher in the non-trisomy chromosomes. Dosage-sensitive genes are enriched by genes with protein translation and localization functions, and dosage resistant genes are enriched by apoptosis genes. These results point to future studies on differential dosage sensitivity and resistance of pro- and anti-proliferation pathways and their variation across patients as therapeutic targets and prognosis markers. Conclusions: Our findings support the hypothesis that recurrent CNAs in myeloma are selected by their functional consequences. The novel dosage effect score defined in this work will facilitate integration of copy number and expression data for identifying driver genes in cancer genomics studies. The accompanying R code is available at http://www.canevolve.org/dosageEffect/

Association of Minimal Residual Disease With Superior Survival Outcomes in Patients With Multiple Myeloma: A Meta-analysis

Importance: Numerous studies have evaluated the prognostic value of minimal residual disease (MRD) in patients with multiple myeloma (MM). Most studies were small and varied in terms of patient population, treatment, and MRD assessment methods. Objective: To evaluate the utility of MRD detection in patients with newly diagnosed MM. Data Sources: A Medline search was conducted for articles published in English between January 1990 and January 2016. Study Selection: Eligible studies reported MRD status and progression-free survival (PFS) or overall survival (OS) in 20 or more patients following treatment. Among 405 articles identified, 21 met the initial eligibility criteria and were included in the analysis. Data Extraction and Synthesis: Information on patient characteristics, treatment, MRD assessment, and outcomes were extracted using a standard form. Main Outcomes and Measures: The impact of MRD status on PFS and OS was assessed by pooling data from relevant trials. Data were adjusted to allow for different proportions of patients with MRD in different studies, and analyzed using the Peto method. Forest plots were created based on Cox model analysis. Other prespecified research questions were addressed qualitatively. Results: Fourteen studies (n = 1273) provided data on the impact of MRD on PFS, and 12 studies (n = 1100) on OS. Results were reported specifically in patients who had achieved conventional complete response (CR) in 5 studies for PFS (n = 574) and 6 studies for OS (n = 616). An MRD-negative status was associated with significantly better PFS overall (hazard ratio [HR], 0.41; 95% CI, 0.36-0.48; P < .001) and in studies specifically looking at CR patients (HR, 0.44; 95% CI, 0.34-0.56; P < .001). Overall survival was also favorable in MRD-negative patients overall (HR, 0.57; 95% CI, 0.46-0.71; P < .001) and in CR patients (HR, 0.47; 95% CI, 0.33-0.67; P < .001). Tests of heterogeneity found no significant differences among the studies for PFS and OS. Conclusions and Relevance: Minimal residual disease-negative status after treatment for newly diagnosed MM is associated with long-term survival. These findings provide quantitative evidence to support the integration of MRD assessment as an end point in clinical trials of MM

ORGANIZATIONAL TRANSFORMATION IN SPORTS CLUBS

The dynamic nature of the information age necessitates a rapid reaction of the environment and change. It is inevitable that sports clubs, which are very sensitive to the environment and are most affected by it, become the most important candidates of organizational learning in the information management process in today's competitive environment.     Today, successful organizations are steadily creating information, spreading this knowledge across the organization and transforming that knowledge into new technologies, products, services, activities or processes. In terms of Sportive Businesses, competition is becoming more and more widespread, consumer awareness is increasing, people are looking for qualified people in all their lives, not just the goods or services they buy, but they are careful to use different choice. There is a need for sports entrepreneurship to grow in today's intense competitive environment and to expand their knowledge areas, to continual improvement and development, to do organizational learning and knowledge management, and to do learning organization stage so that they can keep themselves up to date and increase their competitiveness.  Article visualizations

THE DYNAMICS OF FOOTBALL CLUB MANAGEMENT

After the 1990’s, the changes in the football world had helped to develop and to grow the economy of football rapidly. The development of digital broadcasting led to build a bigger commercial structure. With the effect of those changes, commercial incomes, sponsor revenues, stadium and facilities incomes, and betting incomes have increased over time. This rapid change also brings several problems. UEFA has published UEFA criteria in order to protect football’s sustainability and viability in a long term. Depending on license criteria that is published by UEFA, it has used a road map for football clubs, regarding of corporate structure of UEFA to work, that identified the general rules like in a company structure and management that should be all the necessary factors of production in a systematic and effective way in order to transform football clubs to a corporate organization and make them sustainable. With this out of the common guide explains readers how to run a club in today’s demanding, high competitive and high-tech environment and, establish its brand, and bring in the revenue required to ensure long-term success. Those who manage and lead clubs will find that they can improve a successful business plan of their club mission and have the instruments to develop and sustain organizations that are feasible and financially wealthy and that satisfy the needs of footballer and those who support them.   Article visualizations