Implementing and Running a Workflow Application on Cloud Resources

Scientist need to run applications that are time and resource consuming, but, not all of them, have the requires knowledge to run this applications in a parallel manner, by using grid, cluster or cloud resources. In the past few years many workflow building frameworks were developed in order to help scientist take a better advantage of computing resources, by designing workflows based on their applications and executing them on heterogeneous resources. This paper presents a case study of implementing and running a workflow for an E-bay data retrieval application. The workflow was designed using Askalon framework and executed on the cloud resources. The purpose of this paper is to demonstrate how workflows and cloud resources can be used by scientists in order to achieve speedup for their application without the need of spending large amounts of money on computational resources.Workflow, Cloud Resource

Exploring the meaning behind twitter hashtags through clustering

Abstract. Social networks are generators of large amount of data produced by users, who are not limited with respect to the content of the information they exchange. The data generated can be a good indicator of trends and topic preferences among users. In our paper we focus on analyzing and representing hashtags by the corpus in which they appear. We cluster a large set of hashtags using K-means on map reduce in order to process data in a distributed manner. Our intention is to retrieve connections that might exist between different hashtags and their textual representation, and grasp their semantics through the main topics they occur with

Strategic and Social Competences in the Foreign Language Class

Nowadays, teaching grammar and lexis to students is undoubtedly necessary but not enough. The new approaches to language teaching place a great emphasis on developing learners’ communicative competency. Besides the professional skills, essential to a successful career, individuals also need to acquire the communicative competency, which is equally important as it includes various other competencies, such as: linguistic, social, socio-cultural, or strategic competences in order to communicate and interact with each other. Our paper aims at discussing the different ways and methods teachers can use in the language classroom to build and enhance students’ social and strategic competencies

Solid Plasmonic Substrates for Breast Cancer Detection by Means of SERS Analysis of Blood Plasma

Surface enhanced Raman spectroscopy (SERS) represents a promising technique in providing specific molecular information that could have a major impact in biomedical applications, such as early cancer detection. SERS requires the presence of a suitable plasmonic substrate that can generate enhanced and reproducible diagnostic relevant spectra. In this paper, we propose a new approach for the synthesis of such a substrate, by using concentrated silver nanoparticles purified using the Tangential Flow Filtration method. The capacity of our substrates to generate reproducible and enhanced Raman signals, in a manner that can allow cancer detection by means of Multivariate Analysis (MVA) of Surface Enhanced Raman (SER) spectra, has been tested on blood plasma samples collected from 35 healthy donors and 29 breast cancer patients. All the spectra were analyzed by a combined Principal Component-Linear Discriminant Analysis. Our results facilitated the discrimination between healthy donors and breast cancer patients with 90% sensitivity, 89% specificity and 89% accuracy. This is a direct consequence of substrates’ ability to generate diagnostic relevant spectral information by performing SERS measurements on pristine blood plasma samples. Our results suggest that this type of solid substrate could be employed for the detection of other types of cancer or other diseases by means of MVA-SERS procedure

Experimental and numerical study of PMMA combustion in counterflow configuration

PMMA burning in counterflow has been studied experimentally and numerically. Thermal and chemical structure including concentrations of main species, i.e. ММА, O2, N2, CO2, CO and H2O, as well as an integral parameter (mass loss rate of a sample) were measured. The mathematical model is set in a coupled gas–solid formulation to resolve heat and mass transfer between gas-phase flame and thermally degrading solid combustible. Gas-phase combustion was modeled in the open-source Cantera software in a one-dimensional counterflow flame configuration. Governing equations of solid fuel was solved in an in-house code in two-dimensional formulation. Two chemical mechanisms of MMA oxidation (skeletal and detailed) were employed to resolve gas-phase combustion. Two sets of parameters of PMMA pyrolysis reaction were investigated. Gas phase temperature distribution was experimentally shown to be almost uniform in the direction parallel to the sample's burning surface in the area up to 4 mm from the sample's axis. The best agreement for macroscopic parameter, mass loss rate, was obtained by employing Lengelle pyrolysis kinetics, which is within 10 %. Total heat flux from gas-phase flame to the solid sample is about 23 kW/m2. Both gas-phase combustion mechanisms overpredict maximal temperature in flame by about 200 °C

Seed Germination within Genus <i>Rosa</i>: The Complexity of the Process and Influencing Factors

Seed germination is a crucial stage in the life cycle of plants, and understanding the factors influencing germination is essential for successful cultivation, plant breeding, and conservation efforts. The genus Rosa, commonly known as roses, encompasses a diverse group of flowering plants renowned for their beauty and fragrance. Rosa germination is influenced by a variety of factors, including seed dormancy, environmental conditions, and seed treatments. Many Rosa species exhibit different types of seed dormancy, such as physical dormancy caused by hard seed coats and physiological dormancy due to internal mechanisms. Overcoming seed dormancy often requires specific treatments, including cold stratification, scarification, or chemical treatments, to promote germination. Environmental factors, including temperature, moisture, light, and substrate, play vital roles in Rosa germination. Temperatures ranging from 15 to 25 °C, moisture, and exposure to light or darkness, depending on the species, constitute suitable conditions for seed germination. Many studies have been conducted to investigate the germination requirements of different Rosa species, thereby expanding our understanding of their propagation and conservation. Additionally, advancements in techniques such as in vitro germination and molecular approaches have further enhanced our understanding of Rosa germination biology

Navigating through the Lipid Metabolism Maze: Diagnosis and Prognosis Metabolites of Hepatocellular Carcinoma versus Compensated Cirrhosis

(1) Background: The pursuit of finding biomarkers for the diagnosis and prognosis of hepatocellular carcinoma (HCC) has never been so paramount in the days of personalized medicine. The main objective of our study is to identify new biomarkers for diagnosing HCC, and to identify which patients are at risk of developing tumor recurrence, decompensation, or even possesses the risk of cancer-related death. (2) Methods: We have conducted an untargeted metabolomics study from the serum of 69 European patients—32 compensated cirrhotic patients without HCC (controls), and 37 cirrhotic patients with HCC with compensated underlying liver disease (cases), that underwent curative treatment (surgery or ablation), performing ultra-high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-QTOF- (ESI+)-MS) with an emphasis on lipid metabolites. (3) Results: 1,25-dihydroxy cholesterol (m/z = 419.281), myristyl palmitate (m/z = 453.165), 25-hydroxy vitamin D2 (m/z = 413.265), 12-ketodeoxycholic acid (m/z = 391.283), lysoPC (21:4) (m/z = 558.291), and lysoPE (22:2) (m/z = 534.286) represent notable biomarkers that differentiate compensated cirrhosis from early HCC, and ceramide species are depleted in the serum of HCC patients. Regarding prognosis, no metabolite identified in our study could determine tumor relapse. To distinguish between the HCC patients that survived curative treatment and those at risk that developed tumor burden, we have identified two notable phosphocholines (PC (30:2); PC (30:1)) with AUROCs of 0.820 and 0.807, respectively, that seem to increase when patients are at risk. In a univariate analysis, arachidonic acid was the only metabolite to predict decompensation (OR = 0.1, 95% CI: 0–0.16, p < 0.005), while in the multivariate analysis, dismally, no variable was associated with decompensation. Furthermore, in the multivariate analysis, we have found out for the first time that the increased expression of 1,25-dihydroxy cholesterol, myristyl palmitate, 12-keto deoxycholic acid, lysoPC (21:4), and lysoPE (22:2) are independent markers of survival. (4) Conclusions: Our study reveals that lipids play a crucial role in discriminating compensated cirrhosis and early hepatocellular carcinoma, and might represent markers of survival and prognosis in personalized and minimally invasive medicine

Blood Genome-Wide Transcriptional Profiles of HER2 Negative Breast Cancers Patients

Tumors act systemically to sustain cancer progression, affecting the physiological processes in the host and triggering responses in the blood circulating cells. In this study, we explored blood transcriptional patterns of patients with two subtypes of HER2 negative breast cancers, with different prognosis and therapeutic outcome. Peripheral blood samples from seven healthy female donors and 29 women with breast cancer including 14 triple-negative breast cancers and 15 hormone-dependent breast cancers were evaluated by microarray. We also evaluated the stroma in primary tumors. Transcriptional analysis revealed distinct molecular signatures in the blood of HER2− breast cancer patients according to ER/PR status. Our data showed the implication of immune signaling in both breast cancer subtypes with an enrichment of these processes in the blood of TNBC patients. We observed a significant alteration of “chemokine signaling,” “IL-8 signaling,” and “communication between innate and adaptive immune cells” pathways in the blood of TNBC patients correlated with an increased inflammation and necrosis in their primary tumors. Overall, our data indicate that the presence of triple-negative breast cancer is associated with an enrichment of altered systemic immune-related pathways, suggesting that immunotherapy could possibly be synergistic to the chemotherapy, to improve the clinical outcome of these patients

Aberrant miRNAs expressed in HER-2 negative breast cancers patient

Abstract Background Breast cancer is a highly heterogeneous pathology, exhibiting a number of subtypes commonly associated with a poor outcome. Due to their high stability, microRNAs are often regarded as non-invasive cancer biomarkers, having an expression pattern specific for their ‘cell of origin’. Method Triple negative breast cancer (TNBC: ER-, PR-, Her-2-) and double positive breast cancer (DPBC: ER+, PR+, Her-2) miRNA expression patterns were obtained by analysis of the TCGA (The Cancer Genome Atlas) data, followed by PCR-array analysis on plasma samples from 20 TNBC patients, 14 DPBC patients and 11 controls. Results Three downregulated and nine upregulated miRNAs were obtained from the TNBC analysis. Five overexpressed miRNAs were identified in the DPBC group. Four of the dysregulated miRNAs (miR-10a, miR-125b, miR-210 and miR-489) were common for both groups. The cluster miR-17-92 (miR-17, miR-20a, miR-20b, and miR-93), along with miR-130, miR-22 and miR-29a/c, were found to differentiate between TNBC and DPBC. A panel of five transcripts (miR-10a, miR-125, miR-193b, miR-200b and miR-489) was validated in a new set of plasma samples. The overlapping of TCGA and plasma profiling data revealed miR-200b, miR-200c, miR-210 and miR-29c as common signature. MiR-200b was validated on additional normal and tumor tissue samples. The expression level of this transcript from the TCGA data was correlated with lung and bone metastatic genes. Conclusion The miR-200b presents a great potential for the future advancements in the diagnostic/prognostic and therapeutic approach of TNBC, along with other coding or non-coding transcripts. However, this needs to be further integrated in a regulatory network that acts in conjunction with other markers that affect the patients’ prognosis or response to therapy