188 research outputs found

    CCCORE: Cloud Container for Collaborative Research

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    Cloud-based research collaboration platforms render scalable, secure and inventive environments that enabled academic and scientific researchers to share research data, applications and provide access to high- performance computing resources. Dynamic allocation of resources according to the unpredictable needs of applications used by researchers is a key challenge in collaborative research environments. We propose the design of Cloud Container based Collaborative Research (CCCORE) framework to address dynamic resource provisioning according to the variable workload of compute and data-intensive applications or analysis tools used by researchers. Our proposed approach relies onā€“demand, customized containerization and comprehensive assessment of resource requirements to achieve optimal resource allocation in a dynamic collaborative research environment. We propose algorithms for dynamic resource allocation problem in a collaborative research environment, which aim to minimize finish time, improve throughput and achieve optimal resource utilization by employing the underutilized residual resources

    Thermophilin 13: In Silico Analysis Provides New Insight in Genes Involved in Bacteriocin Production

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    Bacteriocins are a large family of ribosomally synthesised proteinaceous toxins that are produced by bacteria and archaea and have antimicrobial activity against closely related species to the producer strain. Antimicrobial proteinaceous compounds are associated with a wide range of applications, including as a pathogen inhibitor in food and medical use. Among the several lactic acid bacteria (LAB) commonly used in fresh and fermented food preservation, Streptococcus thermophilus is well known for its importance as a starter culture for yoghurt and cheese. Previous studies described the bacteriocin thermophilin 13 exclusively in S. thermophilus SFi13 and the genes encoding its production as an operon consisting of two genes (thmA and thmB). However, the majority of bacteriocins possess a complex production system, which involves several genes encoding dedicated proteins with relatively specific functions. Up to now, far too little attention has been paid to the genes involved in the synthesis, regulation and expression of thermophilin 13. The aim of the present study, using in silico gene mining, was to investigate the presence of a regulation system involved in thermophilin 13 production. Results revealed the dedicated putative bacteriocin gene cluster (PBGC), which shows high similarity with the class IIb bacteriocins genes. This newly revealed PBGC, which was also found within various strains of Streptococcus thermophilus, provides a new perspective and insights into understanding the mechanisms implicated in the production of thermophilin 13

    Pandemic Data Quality Modelling: A Bayesian Approach = Modellazione della qualit`a dei dati pandemici: un approccio bayesiano

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    When dealing with pandemics like COVID-19, it is crucial for policymakers to constantly monitor the emergency. Correct data reporting is a hard task during pandemics, and errors affect the overall mortality, resulting in excess deaths in official statistics. In this work, we provide tools for evaluating the quality of pandemic mortality data. We accomplish this through a spatio-temporal Bayesian approach accounting for the bias implicitly contained in the data

    Biochemical Effects of Exercise on a Fasciocutaneous Flap in a Rat Model.

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    Importance: An overwhelming amount of data suggest that cardiovascular exercise has a positive effect on the mind and body, although the precise mechanism is not always clear. Objective: To assess the clinical and biochemical effects of voluntary cardiovascular exercise on pedicled flaps in a rodent model. Design, Setting, and Participants: Eighteen adult Sprague-Dawley male rats were randomized into a resting animal group (RAG) (n=9) and an exercise animal group (EAG) (n=9) for 14 days (July 23, 2013, through July 30, 2013). A pedicled transposition flap was performed on the ventral surface of the rat, and biopsy specimens were taken from the proximal, middle, and distal portions on postoperative days 0, 2, 5, and 9. Flap survival was analyzed planimetrically, and biopsy specimens were analyzed by hematoxylin-eosin-stained microscopy and immunoblotting. The housing, exercise, surgery, and analysis of the rats were conducted at a single basic science research laboratory at the tertiary care center campus of Thomas Jefferson University in Philadelphia, Pennsylvania. Exposures: The rats were caged for 14 days or housed in a cage connected to an exercise wheel and pedometer. Main Outcomes and Measures: Study measures were gross and micrographic necrosis and expression of proteins within cell survival and apoptosis pathways. Results: A total of 18 rats were studied, 9 in the RAG and 9 in the EAG. the mean (SEM) amount of necrosis in flaps was 41.3% (3%) in the RAG rats and 10.5% (3.5%) in the EAG rats (Pā€‰\u3cā€‰.001). Immunoblotting revealed increased Caspase-9 activity resulting in poly-(adenosine diphosphate-ribose) polymerase 1 cleavage in the RAG vs the EAG, as well as lower phosphorylated protein kinase B (also known as Akt), signal transducer and activator of transcription 3, and total B-cell leukemia/lymphoma 2 protein levels. Throughout the postoperative period, the cumulative vascular endothelial growth factor A levels of the EAG flaps were significantly higher than those of the RAG flaps (2.30 vs 1.25 fold induction [FI], Pā€‰=ā€‰.002), with differences of 2.76 vs 1.54 FI in the proximal segment, 2.40 vs 1.20 FI in the middle segment, and 1.90 vs 0.79 FI in the distal segment. A similar response was noted when comparing phosphorylated Akt, with cumulative mean (SEM) p-Akt expression levels of 0.62 (0.04) for RAG and 1.98 (0.09) for EAG (Pā€‰=ā€‰.002 between the 2 groups). Conclusions and Relevance: Voluntary preoperative exercise improves survival in pedicled fasciocutaneous flaps; the EAG rats had less necrosis, decreased apoptotic markers, and increased amounts of vascular endothelial growth factor A and prosurvival proteins. These results have implications to increase flap survival in other mammal populations, such as humans. Level of Evidence: 3

    Modeling provincial Covid-19 epidemic data in Italy using an adjusted time-dependent SIRD model

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    In this paper we develop a predictive model for the spread of COVID-19 infection at a provincial (i.e. EU NUTS-3) level in Italy by using official data from the Italian Ministry of Health integrated with data extracted from daily official press conferences of regional authorities and from local newspaper websites. This integration is mainly concerned with COVID-19 cause specific death data which are not available at NUTS-3 level from open official data data channels. An adjusted time-dependent SIRD model is used to predict the behavior of the epidemic, specifically the number of susceptible, infected, deceased and recovered people. Predictive model performance is evaluated using comparison with real data

    Heterogeneity of covid-19 outbreak in italy

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    An outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in December 2019 in China and was declared a pandemic on 11.03.2020 by WHO. Italy is one of the most afflicted Country by this epidemic with 136,110 confirmed cases and 16,654 deaths on 9.4.2020 (at the same date, the Ministry of Health was reporting 143,626 cases). During these few months the National Health Service have made a great effort to cope with the increasing request of intensive care beds and all the elective activities in hospital have been suspended. Data from the different Italian regions shows different patterns of positive and dead for this syndrome. Moreover, striking differences of the observed lethality of the infections among different areas were immediately evident from the epidemic reports. It will be of critical relevance to understand the expected evolution of the first lock-down phase, driving the exhaustion of the Covid-19 outbreak

    Reconstruction of Simplified Microbial Consortia to Modulate Sensory Quality of Kombucha Tea

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    Kombucha is a fermented tea with a long history of production and consumption. It has been gaining popularity thanks to its refreshing taste and assumed beneficial properties. The microbial community responsible for tea fermentation-acetic acid bacteria (AAB), yeasts, and lactic acid bacteria (LAB)-is mainly found embedded in an extracellular cellulosic matrix located at the liquid-air interphase. To optimize the production process and investigate the contribution of individual strains, a collection of 26 unique strains was established from an artisanal-scale kombucha production; it included 13 AAB, 12 yeasts, and one LAB. Among these, distinctive strains, namely Novacetimonas hansenii T7SS-4G1, Brettanomyces bruxellensis T7SB-5W6, and Zygosaccharomyces parabailii T7SS-4W1, were used in mono- and co-culture fermentations. The monocultures highlighted important species-specific differences in the metabolism of sugars and organic acids, while binary co-cultures demonstrated the roles played by bacteria and yeasts in the production of cellulose and typical volatile acidity. Aroma complexity and sensory perception were comparable between reconstructed (with the three strains) and native microbial consortia. This study provided a broad picture of the strains' metabolic signatures, facilitating the standardization of kombucha production in order to obtain a product with desired characteristics by modulating strains presence or abundance

    High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

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    The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant FST values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters
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