XML-VM: An XML-Based Grid Computing Middleware

This paper describes a novel distributing computing middleware named XML-VM. Its architecture is inspired by the \u2018Grid Computing\u2019 paradigm. The proposed system improves many characteristics of previous Grid systems, in particular the description of the distributed computation, the distribution of the code and the execution times. XML is a markup language commonly used to interchange arbitrary data over the Internet. The idea behind this work is to use XML to describe algorithms; XML documents are distributed by means of XML-RPC, interpreted and executed using virtual machines. XML-VM is an assembly-like language, coded in XML. Parsing of XML-VM programs is performed with a fast SAX parser for JAVA. XML-VM interpreter is coded in JAVA. Several algorithms are written in XML-VM and executed in a distributed environment. Representative experimental results are reported

Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples

During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X) resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.Supported in part by the Gerencia Regional de Salud, Junta de Castilla y León, Spain (research project GRS 698/A/2011

Obesity and survival in operable breast cancer patients treated with adjuvant anthracyclines and taxanes according to pathological subtypes: a pooled analysis

IntroductionObesity is an unfavorable prognostic factor in breast cancer (BC) patients regardless of menopausal status and treatment received. However, the association between obesity and survival outcome by pathological subtype requires further clarification.MethodsWe performed a retrospective analysis including 5,683 operable BC patients enrolled in four randomized clinical trials (GEICAM/9906, GEICAM/9805, GEICAM/2003–02, and BCIRG 001) evaluating anthracyclines and taxanes as adjuvant treatments. Our primary aim was to assess the prognostic effect of body mass index (BMI) on disease recurrence, breast cancer mortality (BCM), and overall mortality (OM). A secondary aim was to detect differences of such prognostic effects by subtype.ResultsMultivariate survival analyses adjusting for age, tumor size, nodal status, menopausal status, surgery type, histological grade, hormone receptor status, human epidermal growth factor receptor 2 (HER2) status, chemotherapy regimen, and under-treatment showed that obese patients (BMI 30.0 to 34.9) had similar prognoses to that of patients with a BMI < 25 (reference group) in terms of recurrence (Hazard Ratio [HR] = 1.08, 95% Confidence Interval [CI] = 0.90 to 1.30), BCM (HR = 1.02, 0.81 to 1.29), and OM (HR = 0.97, 0.78 to 1.19). Patients with severe obesity (BMI ≥ 35) had a significantly increased risk of recurrence (HR = 1.26, 1.00 to 1.59, P = 0.048), BCM (HR = 1.32, 1.00 to 1.74, P = 0.050), and OM (HR = 1.35, 1.06 to 1.71, P = 0.016) compared to our reference group. The prognostic effect of severe obesity did not vary by subtype.ConclusionsSeverely obese patients treated with anthracyclines and taxanes present a worse prognosis regarding recurrence, BCM, and OM than patients with BMI < 25. The magnitude of the harmful effect of BMI on survival-related outcomes was similar across subtypes

RMID: a novel and efficient image descriptor for mammogram mass classification

For mammogram image analysis, feature extraction is the most crucial step when machine learning techniques are applied. In this paper, we propose RMID (Radon-based Multi-resolution Image Descriptor), a novel image descriptor for mammogram mass classification, which perform efficiently without any clinical information. For the present experimental framework, we found that, in terms of area under the ROC curve (AUC), the proposed RMID outperforms, upto some extent, previous reported experiments using histogram based hand-crafted methods, namely Histogram of Oriented Gradient (HOG) and Histogram of Gradient Divergence (HGD) and also Convolution Neural Network (CNN). We also found that the highest AUC value (0.986) is obtained when using only the carniocaudal (CC) view compared to when using only the mediolateral oblique (MLO) (0.738) or combining both views (0.838). These results thus proves the effectiveness of CC view over MLO for better mammogram mass classification

Assessing the usability of a science gateway for medical knowledge bases with TRENCADIS

Biomedical applications are often built on top of knowledge bases that contain medical images and clinical reports. Currently, these bases are being used to improve diagnosis, research and teaching, but in many cases, the infrastructure required has a prohibitive cost for many medical centres. However, resources can be attached from existing e-Science infrastructures. Therefore, many efforts have been made to establish best practices that allow the use of such infrastructures. However, e-Science relies on open, distributed, collaborative environments, built on top of very specialized technologies, such as Grid and Cloud computing, which require reasonable technical skills for their usage. Therefore, science gateways have become essential tools that assist users in interacting with e-Science applications. This paper describes TRENCADIS, a technology that supports the creation and operation of virtual knowledge bases. To this end, it provides developers with components and APIs for building secure data services that can be annotated and queried through ontology templates, based on DICOM and DICOM-SR. This technology was used in this paper to build a gateway for assisting diagnosis and research in breast cancer. We also present here the results of a study conducted to evaluate the gateway, from the point of view of the usability perceived by a group of physicians and radiologists. © 2012 Springer Science+Business Media Dordrecht.The authors wish to thank the financial support received from The Spanish Ministry of Education and Science to develop the project "Code-Cloud", with reference TIN2010-17804, and the financial support received from The Vicerectorat d'Investigacio de la Universitat Politecnica de Valencia (UPV) to develop the project "Diseno de Componentes Cloud Facilitadores del Despliegue y la Alta Disponibilidad de Servicios TRENCADIS, para compartir Imagenes Medicas DICOM e informes Asociados DICOM-SR", with reference 20111013.Maestre Urbano, CV.; Segrelles Quilis, JD.; Torres Serrano, E.; Blanquer Espert, I.; Medina, R.; Hernández García, V.; Martí, L. (2012). Assessing the usability of a science gateway for medical knowledge bases with TRENCADIS. 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The RS4939827 polymorphism in the SMAD7 GENE and its association with Mediterranean diet in colorectal carcinogenesis

BACKGROUND: The objective of our investigation is to study the relationship between the rs4939827 SNP in the SMAD7 gene, Mediterranean diet pattern and the risk of colorectal cancer. METHODS: We examined 1087 cases of colorectal cancer and 2409 population controls with available DNA samples from the MCC-Spain study, 2008-2012. Descriptive statistical analyses, and multivariate logistic mixed models were performed. The potential synergistic effect of rs4939827 and the Mediterranean diet pattern was evaluated with logistic regression in different strata of of adherence to the Mediterranean diet and the genotype. RESULTS: High adherence to Mediterrenean diet was statistically significantly associated with colorectal cancer risk. A decreased risk for CRC cancer was observed for the CC compared to the TT genotype (OR = 0.65 and 95% CI = 0.51-0.81) of the rs4939827 SNP Also, we could show an association between the Mediterranean diet pattern (protective factor) and rs4939827. Although the decreased risk for the CC genotype was slightly more pronounced in subjects with high adherence to Mediterrenean diet, there was no statistically significant synergistic effect between genotype CC and adherence to the Mediterranean dietary pattern factors. CONCLUSION: The SMAD7 gene and specifically the allele C could be protective for colorectal cancer. An independent protective association was also observed between high adherence Mediterranean diet pattern and CRC risk. Findings form this study indicate that high adherence to Mediterranean diet pattern has a protective role for CRC cancer probably involving the Tumor Growth Factor- β pathway in this cancer