Managing Workflows on top of a Cloud Computing Orchestrator for using heterogeneous environments on e-Science

[EN] Scientific workflows (SWFs) are widely used to model processes in e-Science. SWFs are executed by means of workflow management systems (WMSs), which orchestrate the workload on top of computing infrastructures. The advent of cloud computing infrastructures has opened the door of using on-demand infrastructures to complement or even replace local infrastructures. However, new issues have arisen, such as the integration of hybrid resources or the compromise between infrastructure reutilisation and elasticity. In this article, we present an ad hoc solution for managing workflows exploiting the capabilities of cloud orchestrators to deploy resources on demand according to the workload and to combine heterogeneous cloud providers (such as on-premise clouds and public clouds) and traditional infrastructures (clusters) to minimise costs and response time. The work does not propose yet another WMS but demonstrates the benefits of the integration of cloud orchestration when running complex workflows. The article shows several configuration experiments from a realistic comparative genomics workflow called Orthosearch, to migrate memory-intensive workload to public infrastructures while keeping other blocks of the experiment running locally. The article computes running time and cost suggesting best practices.This paper wants to acknowledge the support of the EUBrazilCC project, funded by the European Commission (STREP 614048) and the Brazilian MCT/CNPq N. 13/2012, for the use of its infrastructure. The authors would like also to thank the Spanish 'Ministerio de Economia y Competitividad' for the project 'Clusters Virtuales Elasticos y Migrables sobre Infraestructuras Cloud Hibridas' with reference TIN2013-44390-R.Carrión Collado, AA.; Caballer Fernández, M.; Blanquer Espert, I.; Kotowski, N.; Jardim, R.; Dávila, AMR. (2017). Managing Workflows on top of a Cloud Computing Orchestrator for using heterogeneous environments on e-Science. International Journal of Web and Grid Services. 13(4):375-402. doi:10.1504/IJWGS.2017.10003225S37540213

Cytocompatibility assessment of Ti-Zr-Pd-Si-(Nb) alloys with low Young's modulus, increased hardness and enhanced osteoblast differentiation for biomedical applications

Ti-based alloys have increased importance for biomedical applications due to their excellent properties. In particular, the two recently developed TiZrPdSi(Nb) alloys, with a predominant β-Ti phase microstructure, have good mechanical properties, such as a relatively low Young's modulus and high hardness. In the present work, the cytocompatibility of these alloys was assessed using human osteoblast-like Saos-2 cells. Cells grown on the alloys showed larger spreading areas (more than twice) and higher vinculin content (nearly 40% increment) when compared with cells grown on glass control surfaces, indicating a better cell adhesion. Moreover, cell proliferation was 18% higher for cells growing on both alloys than for cells growing on glass and polystyrene control surfaces. Osteogenic differentiation was evaluated by quantifying the expression of four osteogenic genes (osteonectin, osteocalcin, osteopontin, and bone sialoprotein), the presence of three osteogenic proteins (alkaline phosphatase, collagen I, and osteocalcin) and the activity of alkaline phosphatase at different time-points. The results demonstrated that TiZrPdSi and TiZrPdSiNb alloys enhance osteoblast differentiation, and that cells grown on TiZrPdSiNb alloy present higher levels of some late osteogenic markers during the first week in culture. These results suggest that the TiZrPdSi(Nb) alloys can be considered as excellent candidates for orthopaedical uses

How to find information on national food and nutrient consumption surveys across Europe: systematic literature review and questionnaires to selected country experts are both good strategies

The present research was conducted within the framework of the EURopean micronutrient RECommendations Aligned project. in order to identify the best practice in assessing nutrient intakes, a search strategy for collecting data from national food consumption surveys/studies in Europe was developed. Systematic literature searches were carried out on twenty-eight European and the four European Free Trade Association Countries. A questionnaire was also sent to two to five experts in each country. Systematic reviews using PubMed yielded 12 703 abstracts that were reduced to 200 studies using inclusion and exclusion criteria. Similarly, a search of ministry web sites yielded 3033 hits. and subsequently reduced to nine Surveys. Belgium, France, Germany, Ireland, Sweden, Spain and the United Kingdom were the countries with most data and Slovenia and Liechtenstein were those with the least. Seventy-eight expert questionnaires were obtained from all Countries except for Liechtenstein. Luxembourg and Slovakia. Detailed results and references are given. A systematic search and questionnaires are equally good at identifying national surveys across countries. Literature searching provides globally accessible and objective information albeit limited, whereas the questionnaire provides information that, depending upon responders, can be more complete. A combination of both strategies is recommended

Tuberculosis treatment adherence and fatality in Spain

<p>Abstract</p> <p>Background</p> <p>The adherence to long tuberculosis (TB) treatment is a key factor in TB control programs. Always some patients abandon the treatment or die. The objective of this study is to identify factors associated with defaulting from or dying during antituberculosis treatment.</p> <p>Methods</p> <p>Prospective study of a large cohort of TB cases diagnosed during 2006-2007 by 61 members of the Spanish Society of Pneumology and Thoracic Surgery (SEPAR). Predictive factors of completion outcome (cured plus completed treatment vs. defaulters plus lost to follow-up) and fatality (died <it>vs. </it>the rest of patients) were based on logistic regression, calculating odds ratios (OR) and 95% confidence intervals (CI).</p> <p>Results</p> <p>Of the 1490 patients included, 29.7% were foreign-born. The treatment outcomes were: cured 792 (53.2%), completed treatment 540 (36.2%), failure 2 (0.1%), transfer-out 33 (2.2%), default 27 (1.8%), death 27 (1.8%), lost to follow-up 65 (4.4%), other 4 (0.3%). Completion outcome reached 93.5% and poor adherence was associated with: being an immigrant (OR = 2.03; CI:1.06-3.88), living alone (OR = 2.35; CI:1.05-5.26), residents of confined institutions (OR = 4.79; CI:1.74-13.14), previous treatment (OR = 2.93; CI:1.44-5.98), being an injecting drug user (IDU) (OR = 9.51; CI:2.70-33.47) and treatment comprehension difficulties (OR = 2.93; CI:1.44-5.98). Case fatality was 1.8% and it was associated with the following variables: age 50 or over (OR = 10.88; CI:1.12-105.01), retired (OR = 12.26;CI:1.74-86.04), HIV-infected (OR = 9.93; CI:1.48-66.34), comprehension difficulties (OR = 4.07; CI:1.24-13.29), IDU (OR = 23.59; CI:2.46-225.99) and Directly Observed Therapy (DOT) (OR = 3.54; CI:1.07-11.77).</p> <p>Conclusion</p> <p>Immigrants, those living alone, residents of confined institutions, patients treated previously, those with treatment comprehension difficulties, and IDU patients have poor adherence and should be targeted for DOT. To reduce fatality rates, stricter monitoring is required for patients who are retired, HIV-infected, IDU, and those with treatment comprehension difficulties.</p

Association of sepsis-related mortality with early increase of TIMP-1/MMP-9 ratio

Objective: Higher circulating levels of tissue inhibitor of matrix metalloproteinases (TIMP)-1 at the time of severe sepsis diagnosis have been reported in nonsurviving than in surviving patients. However, the following questions remain unanswered: 1) Does TIMP-1/MMP-9 ratio differ throughout the first week of intensive care between surviving and nonsurviving patients? 2) Is there an association between TIMP-1/MMP-9 ratio and sepsis severity and mortality during such period? 3) Could TIMP-1/MMP-9 ratio during the first week be used as an early biomarker of sepsis outcome? 4) Is there an association between TIMP-1/MMP-9 ratio and coagulation state and circulating cytokine levels during the first week of intensive care in these patients? The present study sought to answer these questions. Methods: Multicenter, observational and prospective study carried out in six Spanish Intensive Care Units (ICUs) of 295 patients with severe sepsis. Were measured circulating levels of TIMP-1, MMP-9, tumour necrosis factor (TNF)-alpha, interleukin (IL)-10 and plasminogen activator inhibitor (PAI)-1 at day 1, 4 and 8. End-point was 30-day mortality. Results: We found higher TIMP-1/MMP-9 ratio during the first week in non-surviving (n = 98) than in surviving patients (n = 197) (p, 0.01). Logistic regression analyses showed that TIMP-1/MMP-9 ratio at days 1, 4 and 8 was associated with mortality. Receiver operating characteristic (ROC) curves showed that TIMP-1/MMP-9 ratio at days 1, 4 and 8 could predict mortality. There was an association between TIMP-1/MMP-9 ratio and TNF-alpha, IL-10, PAI-1 and lactic acid levels, SOFA score and platelet count at days 1, 4 and 8. Conclusions: The novel findings of our study were that non-surviving septic patients showed persistently higher TIMP-1/ MMP-9 ratio than survivors ones during the first week, which was associated with severity, coagulation state, circulating cytokine levels and mortality; thus representing a new biomarker of sepsis outcome

Higher platelet cytochrome oxidase specific activity in surviving than in non-surviving septic patients

Introduction: In a previous study with 96 septic patients, we found that circulating platelets in 6-months surviving septic patients showed higher activity and quantity of cytochrome c oxidase (COX) normalized by citrate synthase (CS) activity at moment of severe sepsis diagnosis than non-surviving septic patients. The objective of this study was to estimate whether COX specific activity during the first week predicts 1-month sepsis survival in a larger cohort of patients.Methods: Using a prospective, multicenter, observational study carried out in six Spanish intensive care units with 198 severe septic patients, we determined COX activity per proteins (COXact/Prot) in circulating platelets at day 1, 4 and 8 of the severe sepsis diagnosis. Endpoints were 1-month and 6-months mortality.Results: Survivor patients (n = 130) showed higher COXact/Prot (P 0.30 mOD/min/mg at day 1 (P = 0.002), 4 (P = 0.006) and 8 (P = 0.02) was associated independently with 1-month mortality. Area under the curve of COXact/Prot at day 1, 4 and 8 to predict 30-day survival were 0.70 (95% CI = 0.63-0.76; P < 0.001), 0.71 (95% CI = 0.64-0.77; P < 0.001) and 0.71 (95% CI = 0.64-0.78; P < 0.001), respectively.Conclusions: The new findings of our study, to our knowledge the largest series reporting data about mitochondrial function during follow-up in septic patients, were that septic patients that survive 1-month have a higher platelet cytochrome oxidase activity at moment of sepsis diagnosis and during the first week than non-survivors, and that platelet cytochrome oxidase activity at moment of sepsis diagnosis and during the first week could be used as biomarker to predict the clinical outcome in septic patients

ZnO Nanosheet-Coated TiZrPdSiNb Alloy as a Piezoelectric Hybrid Material for Self-Stimulating Orthopedic Implants

Altres ajuts: This work has been partially supported by La Caixa Foundation under the Junior Leader Retaining program ( LCF/BQ/PR19/11700010).A Ti-based alloy (Ti45Zr15Pd30Si5Nb5) with already proven excellent mechanical and biocompatibility features has been coated with piezoelectric zinc oxide (ZnO) to induce the electrical self-stimulation of cells. ZnO was grown onto the pristine alloy in two different morphologies: a flat dense film and an array of nanosheets. The effect of the combined material on osteoblasts (electrically stimulable cells) was analyzed in terms of proliferation, cell adhesion, expression of differentiation markers and induction of calcium transients. Although both ZnO structures were biocompatible and did not induce inflammatory response, only the array of ZnO nanosheets was able to induce calcium transients, which improved the proliferation of Saos-2 cells and enhanced the expression of some early differentiation expression genes. The usual motion of the cells imposes strain to the ZnO nanosheets, which, in turn, create local electric fields owing to their piezoelectric character. These electric fields cause the opening of calcium voltage gates and boost cell proliferation and early differentiation. Thus, the modification of the Ti45Zr15Pd30Si5Nb5 surface with an array of ZnO nanosheets endows the alloy with smart characteristics, making it capable of electric self-stimulation